Status
±
Terminal Output
| Builder file created | |
| Configuration file | |
| ProBound run | |
| Sequence logos |
Terminal output
Pipeline Output:
> Converts the configuration file to work on run server, checks input OK > Builds configuration file OK > Runs ProBound OK > Runs Model Viewer OK
Configuration Builder File
±
ProBound builder configuration file:
[{"function": "optimizerSetting", "nThreads": 20, "lambdaL2": 1e-06}, {"function": "addTable", "leftFlank": "GGTAGTGGAGGTGGGCCTGG", "nColumns": 2, "transliterate": {"out": [], "in": []}, "modeledColumns": [0, 1], "countTableFile": "jobs/028cc79587bf/countTable.0.tsv.gz", "rightFlank": "CCAGGGAGGTGGAGTAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "GGTAGTGGAGGGCACCCTGG", "nColumns": 2, "transliterate": {"out": ["cg"], "in": ["CG"]}, "modeledColumns": [0, 1], "countTableFile": "jobs/028cc79587bf/countTable.1.tsv.gz", "rightFlank": "CCAGGGAGGTGGAGTAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "GGTAGTGGAGGTGGGCCTGG", "nColumns": 2, "transliterate": {"out": [], "in": []}, "modeledColumns": [0, 1], "countTableFile": "jobs/028cc79587bf/countTable.2.tsv.gz", "rightFlank": "CCAGGGAGGTGGAGTAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "GGTAGTGGAGGGCACCCTGG", "nColumns": 2, "transliterate": {"out": ["cg"], "in": ["CG"]}, "modeledColumns": [0, 1], "countTableFile": "jobs/028cc79587bf/countTable.3.tsv.gz", "rightFlank": "CCAGGGAGGTGGAGTAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "GGTAGTGGAGGTGGGCCTGG", "nColumns": 2, "transliterate": {"out": [], "in": []}, "modeledColumns": [0, 1], "countTableFile": "jobs/028cc79587bf/countTable.4.tsv.gz", "rightFlank": "CCAGGGAGGTGGAGTAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "GGTAGTGGAGGGCACCCTGG", "nColumns": 2, "transliterate": {"out": ["cg"], "in": ["CG"]}, "modeledColumns": [0, 1], "countTableFile": "jobs/028cc79587bf/countTable.5.tsv.gz", "rightFlank": "CCAGGGAGGTGGAGTAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addSELEX", "bindingModes": [0, 1]}, {"function": "addSELEX", "bindingModes": [0, 1]}, {"function": "addSELEX", "bindingModes": [0, 2]}, {"function": "addSELEX", "bindingModes": [0, 2]}, {"function": "addSELEX", "bindingModes": [0, 1, 2, 3]}, {"function": "addSELEX", "bindingModes": [0, 1, 2, 3]}, {"function": "setAlphabet", "letterComplement": "C-G,A-T,c-g", "letterOrder": "ACGTcg"}, {"function": "addNS"}, {"function": "addBindingMode", "flankLength": 3, "dinucleotideDistance": 1, "size": 12}, {"function": "addBindingMode", "flankLength": 3, "dinucleotideDistance": 1, "size": 12}, {"function": "addBindingMode", "flankLength": 3, "dinucleotideDistance": 1, "size": 12}, {"function": "bindingModeSeed", "index": 1, "mononucleotideIUPAC": "NNTGACGTCANN"}, {"function": "bindingModeSeed", "index": 2, "mononucleotideIUPAC": "NNTTGCGCAANN"}, {"function": "bindingModeSeed", "index": 3, "mononucleotideIUPAC": "NNTTGCATCANN"}, {"function": "symmetry", "index": 1, "symmetryString": "1:12:1"}, {"function": "symmetry", "index": 2, "symmetryString": "1:12:1"}, {"function": "bindingModeConstraints", "index": 1, "maxFlankLength": -1, "fittingStages": [{"optimizeFlankLength": true}]}, {"function": "bindingModeConstraints", "index": 2, "maxFlankLength": -1, "fittingStages": [{"optimizeFlankLength": true}]}, {"function": "bindingModeConstraints", "index": 3, "maxFlankLength": -1, "fittingStages": [{"optimizeFlankLength": true}]}, {"function": "output", "outputPath": "jobs/028cc79587bf", "baseName": "fit", "storeHessian": false, "printTrajectory": false}]Configuration File
±
ProBound configuration file:
{
"modelSeeding": {"bindingModes": [
{"seedScale": 1},
{
"mononucleotideIUPAC": "NNTGACGTCANN",
"seedScale": 1
},
{
"mononucleotideIUPAC": "NNTTGCGCAANN",
"seedScale": 1
},
{
"mononucleotideIUPAC": "NNTTGCATCANN",
"seedScale": 1
}
]},
"optimizerSetting": {
"nThreads": 20,
"likelihoodThreshold": 0,
"lambdaL2": 1.0E-6,
"patternSearchSettings": {},
"pseudocount": 0,
"minimizerType": "lbfgs",
"nRetries": 3,
"hkSettings": {},
"output": {
"storeHessian": false,
"outputPath": "jobs/028cc79587bf",
"printTrajectory": false,
"baseName": "fit",
"printPSAM": false,
"verbose": true
},
"lbfgsSettings": {},
"sgdSettings": {},
"fixedLibrarySize": false,
"expBound": 40,
"slbfgs_plsSettings": {},
"slbfgsSettings": {}
},
"modelSettings": {
"enrichmentModel": [
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [
0,
1
],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [
0,
1
],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [
0,
2
],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [
0,
2
],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [
0,
1,
2,
3
],
"modifications": []
},
{
"r0KUsed": 1,
"round": 1,
"bindingSaturation": false,
"concentration": 1,
"modelType": "SELEX",
"bindingModeInteractions": [-1],
"r0KsTested": [1],
"bindingModes": [
0,
1,
2,
3
],
"modifications": []
}
],
"letterOrder": "ACGTcg",
"countTable": [
{
"leftFlank": "GGTAGTGGAGGTGGGCCTGG",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 16,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "CCAGGGAGGTGGAGTAGG",
"countTableFile": "jobs/028cc79587bf/countTable.0.tsv.gz"
},
{
"leftFlank": "GGTAGTGGAGGGCACCCTGG",
"transliterate": {
"in": ["CG"],
"out": ["cg"]
},
"variableRegionLength": 16,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "CCAGGGAGGTGGAGTAGG",
"countTableFile": "jobs/028cc79587bf/countTable.1.tsv.gz"
},
{
"leftFlank": "GGTAGTGGAGGTGGGCCTGG",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 16,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "CCAGGGAGGTGGAGTAGG",
"countTableFile": "jobs/028cc79587bf/countTable.2.tsv.gz"
},
{
"leftFlank": "GGTAGTGGAGGGCACCCTGG",
"transliterate": {
"in": ["CG"],
"out": ["cg"]
},
"variableRegionLength": 16,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "CCAGGGAGGTGGAGTAGG",
"countTableFile": "jobs/028cc79587bf/countTable.3.tsv.gz"
},
{
"leftFlank": "GGTAGTGGAGGTGGGCCTGG",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 16,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "CCAGGGAGGTGGAGTAGG",
"countTableFile": "jobs/028cc79587bf/countTable.4.tsv.gz"
},
{
"leftFlank": "GGTAGTGGAGGGCACCCTGG",
"transliterate": {
"in": ["CG"],
"out": ["cg"]
},
"variableRegionLength": 16,
"modeledColumns": [
0,
1
],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "CCAGGGAGGTGGAGTAGG",
"countTableFile": "jobs/028cc79587bf/countTable.5.tsv.gz"
}
],
"bindingModeInteractions": [],
"bindingModes": [
{
"size": 0,
"fitLogActivity": true,
"flankLength": 0,
"dinucleotideDistance": 0,
"positionBias": false,
"singleStrand": false,
"modifications": []
},
{
"size": 12,
"fitLogActivity": true,
"flankLength": 3,
"dinucleotideDistance": 1,
"positionBias": false,
"singleStrand": false,
"modifications": []
},
{
"size": 12,
"fitLogActivity": true,
"flankLength": 3,
"dinucleotideDistance": 1,
"positionBias": false,
"singleStrand": false,
"modifications": []
},
{
"size": 12,
"fitLogActivity": true,
"flankLength": 3,
"dinucleotideDistance": 1,
"positionBias": false,
"singleStrand": false,
"modifications": []
}
],
"letterComplement": "C-G,A-T,c-g"
},
"modelFittingConstraints": {
"enrichmentModel": [
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
},
{
"fitDelta": [false],
"roundSpecificGamma": true,
"fitRho": false,
"roundSpecificDelta": true,
"fitGamma": false,
"trySaturation": false,
"roundSpecificRho": true
}
],
"nShifts": 0,
"countTable": [
{},
{},
{},
{},
{},
{}
],
"addBindingModesSequentially": true,
"flankLengths": [0],
"bindingModeInteractions": [],
"singleModeLengthSweep": false,
"bindingModes": [
{
"maxFlankLength": -1,
"positionBiasBinWidth": 1,
"optimizeSizeHeuristic": false,
"maxSize": -1,
"optimizeFlankLength": false,
"symmetryString": "null",
"roundSpecificActivity": true,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": true,
"optimizeSize": false
},
{
"maxFlankLength": -1,
"positionBiasBinWidth": 1,
"optimizeSizeHeuristic": false,
"maxSize": -1,
"symmetryString": "1:12:1",
"optimizeFlankLength": false,
"roundSpecificActivity": true,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [{"optimizeFlankLength": true}],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": true,
"optimizeSize": false
},
{
"maxFlankLength": -1,
"positionBiasBinWidth": 1,
"optimizeSizeHeuristic": false,
"maxSize": -1,
"symmetryString": "1:12:1",
"optimizeFlankLength": false,
"roundSpecificActivity": true,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [{"optimizeFlankLength": true}],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": true,
"optimizeSize": false
},
{
"maxFlankLength": -1,
"positionBiasBinWidth": 1,
"optimizeSizeHeuristic": false,
"maxSize": -1,
"optimizeFlankLength": false,
"symmetryString": "null",
"roundSpecificActivity": true,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [{"optimizeFlankLength": true}],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": true,
"optimizeSize": false
}
]
}
}Probound Text Output
±
Output from ProBound:
> Reading configuration JSON object and validating general schema.
> Validating configuration schema.
{"enrichmentModel":[{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true}],"nShifts":0,"countTable":[{},{},{},{},{},{}],"addBindingModesSequentially":true,"flankLengths":[0],"bindingModeInteractions":[],"singleModeLengthSweep":false,"bindingModes":[{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"symmetryString":"1:12:1","optimizeFlankLength":false,"roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true}],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"symmetryString":"1:12:1","optimizeFlankLength":false,"roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true}],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true}],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false}]}
Entry=bindingModes, aEntry=[{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"symmetryString":"1:12:1","optimizeFlankLength":false,"roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true}],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"symmetryString":"1:12:1","optimizeFlankLength":false,"roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true}],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true}],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false}]
Entry=bindingModeInteractions, aEntry=[]
Entry=countTable, aEntry=[{},{},{},{},{},{}]
Entry=enrichmentModel, aEntry=[{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true}]
> Builds likelihood object.
>> Creating CombinedLikelihood object.
Alphabet
========
Letter Complement: C-G,A-T,c-g
Letter Order: ACGTcg
Optimizer settings:
===================
lambdaL2 = 1.0E-6
pseudocount = 0.0
expBound = 40.0
fixedLibrarySize = false
>> Determining fitting order.
Summary of experiments
======================
Experiment 0:
-------------
Count table: Count table 0
Enrichment model: SELEX enrichment model 0
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 1:
-------------
Count table: Count table 1
Enrichment model: SELEX enrichment model 1
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode interactions:
NONE
Experiment 2:
-------------
Count table: Count table 2
Enrichment model: SELEX enrichment model 2
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 2
Binding mode interactions:
NONE
Experiment 3:
-------------
Count table: Count table 3
Enrichment model: SELEX enrichment model 3
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 2
Binding mode interactions:
NONE
Experiment 4:
-------------
Count table: Count table 4
Enrichment model: SELEX enrichment model 4
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode 2
Binding mode 3
Binding mode interactions:
NONE
Experiment 5:
-------------
Count table: Count table 5
Enrichment model: SELEX enrichment model 5
Concentration: 1.0
Binding modes:
Binding mode 0
Binding mode 1
Binding mode 2
Binding mode 3
Binding mode interactions:
NONE
> Builds optimizer.
> Using LBFGS.
> Starting optimization.
==================================
== Starts fiting Binding mode 0 ==
==================================
> Optimizing h (component0-0-h).
>> Starting new optimization: component0-0-h. (2021-05-21 17:37:11.546).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]},{"h":[6,7]},{"h":[8,9]},{"h":[10,11]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{}]}
Value and gradient before optimization:
=======================================
value = 19.57574989472101
gradient = {0.4985,-0.4985,0.4985,-0.4985,0.4985,-0.4985,0.4985,-0.4985,0.4985,-0.4985,0.4985,-0.4985}
gradient norm = 1.7269640210564523
Starting Function Value: 19.57574989472101
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 11.062902444957464 5.000000000000000 2.895254295420296 1.643023212672335
2 6 4.207045274381962 5.860638839938574 0.059883117667176 0.216813353632106
3 8 4.159665150563106 0.435816217734139 0.489165518227999 0.000047927308380
4 9 4.159665148265752 0.435816217734139 1.000000000000000 0.000000252842292
Convergence criteria met.
After: gradient norm = 2.528422923229409E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-3.2610,3.2610}
Count Table 1:
---------------
h: {-3.2610,3.2610}
Count Table 2:
---------------
h: {-3.2610,3.2610}
Count Table 3:
---------------
h: {-3.2610,3.2610}
Count Table 4:
---------------
h: {-3.2610,3.2610}
Count Table 5:
---------------
h: {-3.2610,3.2610}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-6.5221,-6.5221}
Activity(exp=1): {-6.5221,-6.5221}
Activity(exp=2): {-6.5221,-6.5221}
Activity(exp=3): {-6.5221,-6.5221}
Activity(exp=4): {-6.5221,-6.5221}
Activity(exp=5): {-6.5221,-6.5221}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
> Initial optimization (component0-1-f0).
>> Starting new optimization: component0-1-f0. (2021-05-21 17:37:13.887).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[12,13]},{"h":[14,15]},{"h":[16,17]},{"h":[18,19]},{"h":[20,21]},{"h":[22,23]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7],[8,9],[10,11]]},{},{},{}]}
Value and gradient before optimization:
=======================================
value = 4.159665148265788
gradient = {-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 5.7453394037333876E-5
Starting Function Value: 4.159665148265788
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 4.159665138563716 0.000336176802172 5.851295781645478 0.000105583564313
2 8 4.159660057040529 0.101752521958794 341.00000000000000 0.000289800026203
3 9 4.159253338985963 12.527502405381975 1.000000000000000 0.010004647851826
4 10 4.159090653272278 8.363758733097090 1.000000000000000 0.008249142305080
5 11 4.159030702080374 4.587978340639318 1.000000000000000 0.002296346396012
6 12 4.159027181014656 0.094123273676940 1.000000000000000 0.000262710274379
7 13 4.159027083794044 0.206444843159598 1.000000000000000 0.000001444698735
8 14 4.159027083360867 0.020165513549312 1.000000000000000 0.000000752986817
9 15 4.159027083359936 0.000642730906487 1.000000000000000 0.000000117556625
10 17 4.159027083359694 0.000642730906487 0.476344660332781 0.000000005145978
Convergence criteria met.
After: gradient norm = 5.1459781416649426E-9
>>> Parameters after optimization
Count Table 0:
---------------
h: {-0.0000,0.0000}
Count Table 1:
---------------
h: {-0.0000,0.0000}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {-0.0000,0.0000}
Count Table 5:
---------------
h: {-0.0000,0.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Suggested variations:
key=0;0;0, description = Initial model.
> Optimizing variation "Initial model." (component0-2-variation0).
>> Starting new optimization: component0-2-variation0. (2021-05-21 17:37:17.313).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[12,13]},{"h":[14,15]},{"h":[16,17]},{"h":[18,19]},{"h":[20,21]},{"h":[22,23]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7],[8,9],[10,11]]},{},{},{}]}
Value and gradient before optimization:
=======================================
value = 4.159027083359694
gradient = {-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 5.145978142397992E-9
Already at minimum!
After: gradient norm = 5.145978142397992E-9
>>> Parameters after optimization
Count Table 0:
---------------
h: {-0.0000,0.0000}
Count Table 1:
---------------
h: {-0.0000,0.0000}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {-0.0000,0.0000}
Count Table 5:
---------------
h: {-0.0000,0.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID NOT improve. Discarding fit component0-2-variation0.
> No varitions possible for Binding mode 0.
> Optimizing the full model (component0-4-all).
>> Starting new optimization: component0-4-all. (2021-05-21 17:37:17.416).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[12,13]},{"h":[14,15]},{"h":[16,17]},{"h":[18,19]},{"h":[20,21]},{"h":[22,23]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7],[8,9],[10,11]]},{},{},{}]}
Value and gradient before optimization:
=======================================
value = 4.159027083359693
gradient = {-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 5.14597814335047E-9
Already at minimum!
After: gradient norm = 5.14597814335047E-9
>>> Parameters after optimization
Count Table 0:
---------------
h: {-0.0000,0.0000}
Count Table 1:
---------------
h: {-0.0000,0.0000}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {-0.0000,0.0000}
Count Table 5:
---------------
h: {-0.0000,0.0000}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
==================================
== Starts fiting Binding mode 1 ==
==================================
> Optimizing h (component1-0-h).
>> Starting new optimization: component1-0-h. (2021-05-21 17:37:18.561).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]},{"h":[6,7]},{"h":[8,9]},{"h":[10,11]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{}]}
Value and gradient before optimization:
=======================================
value = 5.9587461362956375
gradient = {-0.4091,0.4091,-0.3530,0.3530,0.0000,-0.0000,0.0000,-0.0000,-0.4112,0.4112,-0.3496,0.3496}
gradient norm = 1.080130940022073
Starting Function Value: 5.9587461362956375
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 4.994256366159390 1.000000000000000 0.925813679570705 0.831076435683376
2 3 4.559180511618635 3.488627072442732 1.000000000000000 0.607301414641249
3 4 4.085110380117674 1.498268653176909 1.000000000000000 0.013803526992747
4 5 4.084905739822959 0.031764746843728 1.000000000000000 0.001051416970840
5 6 4.084904558041338 0.002276480934096 1.000000000000000 0.000029206963132
6 7 4.084904557120656 0.000065766506016 1.000000000000000 0.000001323127694
7 8 4.084904557118734 0.000065766506016 1.000000000000000 0.000000005514180
Convergence criteria met.
After: gradient norm = 5.514179561110607E-9
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.2020,-1.2020}
Count Table 1:
---------------
h: {0.9371,-0.9371}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {1.2065,-1.2065}
Count Table 5:
---------------
h: {0.9243,-0.9243}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {4.3714,4.3714}
Activity(exp=1): {4.3714,4.3714}
Activity(exp=2): {4.3714,4.3714}
Activity(exp=3): {4.3714,4.3714}
Activity(exp=4): {4.3714,4.3714}
Activity(exp=5): {4.3714,4.3714}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
> Initial optimization (component1-1-f1).
>> Starting new optimization: component1-1-f1. (2021-05-21 17:37:23.046).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 4.084904557118739
gradient = {0.0260,0.0024,-0.0041,-0.0065,0.0022,0.0138,0.0226,-0.0460,-0.0033,-0.0041,0.0303,0.0343,0.0192,0.0114,-0.0151,-0.0033,-0.0257,0.0472,0.0275,0.0079,-0.0100,-0.0151,-0.0555,0.0788,0.0310,0.0132,-0.0077,-0.0100,0.0094,-0.0022,0.0525,0.0070,-0.0272,-0.0077,-0.0369,0.0460,0.0000,0.0018,0.0000,0.0079,0.0000,0.0000,0.0000,0.0000,0.0000,0.0003,0.0000,0.0070,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 0.16835321871252276
Starting Function Value: 4.084904557118739
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 4.068616239871060 0.202771132299751 1.204438702452134 0.349277252467740
2 4 4.043571156546170 0.178034645333041 1.000000000000000 0.273822388330584
3 5 4.014924967822506 1.115684115209343 1.000000000000000 0.471187843044275
4 6 3.988463378095106 0.465081584411050 1.000000000000000 0.096016361573677
5 7 3.982249784607501 0.131954730197187 1.000000000000000 0.095080332412090
6 8 3.962583762026198 0.494766289905423 1.000000000000000 0.137083316636775
7 9 3.950741364850019 0.261366952133320 1.000000000000000 0.105930583546013
8 10 3.939378510728392 0.407184243341067 1.000000000000000 0.038051590797213
9 11 3.937614099854339 0.115987648398792 1.000000000000000 0.038029402399636
10 12 3.936630375539764 0.097099510921722 1.000000000000000 0.033762666273870
11 13 3.933429894812325 0.299312320623876 1.000000000000000 0.022919897543118
12 14 3.930466250370126 0.366592451404960 1.000000000000000 0.058856588755537
13 15 3.927350506608474 0.357739337598478 1.000000000000000 0.089271492110253
14 16 3.921877319840601 0.633145712861253 1.000000000000000 0.136342661411296
15 17 3.915460940621373 0.476460766919530 1.000000000000000 0.132915873573207
16 18 3.905118843978161 0.712585743916691 1.000000000000000 0.163037488930812
17 19 3.903086203582593 0.655917118587197 1.000000000000000 0.072644466458865
18 20 3.892031782279337 0.543549005933838 1.000000000000000 0.091267417345118
19 21 3.889171713155891 0.138667999073819 1.000000000000000 0.066738498219484
20 22 3.885452726416730 0.281276331711904 1.000000000000000 0.036828046778388
21 23 3.883012089637117 0.272127431977939 1.000000000000000 0.029420738616802
22 24 3.877828376145299 0.562745191061392 1.000000000000000 0.025608395441627
23 25 3.873448521010464 1.129771524617296 1.000000000000000 0.062245220906954
24 26 3.868606690255301 0.508215316926366 1.000000000000000 0.037137400972762
25 27 3.865753867545624 0.409613034264606 1.000000000000000 0.021446295350158
26 28 3.863259178252795 0.757087006703340 1.000000000000000 0.020576524914203
27 29 3.861450886010073 0.556648829360390 1.000000000000000 0.020400990989946
28 30 3.859188665432268 1.133218349512814 1.000000000000000 0.024787013948919
29 31 3.857546836168735 0.610395675079581 1.000000000000000 0.013475200248787
30 32 3.856562114937791 0.253174451057171 1.000000000000000 0.013455924073217
31 33 3.855623075333841 0.312660897743296 1.000000000000000 0.009994013002358
32 34 3.854697388570515 0.273599712874888 1.000000000000000 0.007709930669948
33 35 3.853838312313743 0.330954612591465 1.000000000000000 0.010845408167124
34 36 3.853231550274284 0.274068916879132 1.000000000000000 0.010819434810878
35 37 3.852654902345160 0.499477543622095 1.000000000000000 0.009948813743822
36 38 3.852342890778049 0.379773628100039 1.000000000000000 0.003482606613642
37 39 3.852256810478512 0.195637293793564 1.000000000000000 0.002336551871349
38 40 3.852176409463129 0.171070443867097 1.000000000000000 0.001994207257528
39 41 3.852080852834453 0.173743951244489 1.000000000000000 0.002055851789355
40 42 3.851978680554441 0.182642523486034 1.000000000000000 0.002930553259236
41 44 3.851951274927671 0.067271732751690 0.205725731629000 0.002871881584959
42 45 3.851910342912307 0.082358351066642 1.000000000000000 0.001298451761017
43 46 3.851891972022663 0.052837083272258 1.000000000000000 0.001180204362502
44 47 3.851874016640998 0.039371397653532 1.000000000000000 0.001116564810796
45 48 3.851851112994206 0.067459284977167 1.000000000000000 0.000986843098887
46 49 3.851834701853413 0.072704263034659 1.000000000000000 0.000846134361967
47 51 3.851832351009846 0.016887605075811 0.173159569168611 0.001480819584834
48 52 3.851822826346417 0.059054894270464 1.000000000000000 0.000884800140171
49 53 3.851815594892214 0.035958285887829 1.000000000000000 0.000716826731853
50 54 3.851801256086118 0.085747110869734 1.000000000000000 0.000678180846537
51 55 3.851789020457685 0.073850194945486 1.000000000000000 0.000637939027637
52 56 3.851773123451782 0.106656330601196 1.000000000000000 0.000557122321032
53 57 3.851756600807917 0.133333383871145 1.000000000000000 0.000780289026874
54 58 3.851739186490796 0.193106695799340 1.000000000000000 0.000624534608965
55 59 3.851729771762136 0.133110455560554 1.000000000000000 0.000488049496520
56 60 3.851723350491378 0.101718795228653 1.000000000000000 0.000385290329985
57 61 3.851720204217982 0.046852827945062 1.000000000000000 0.000210612074296
58 62 3.851718730376776 0.021794102937134 1.000000000000000 0.000201687851726
59 63 3.851717346908573 0.021476027117642 1.000000000000000 0.000208387040135
60 64 3.851715145265799 0.042419257250508 1.000000000000000 0.000247165077270
61 65 3.851712537572855 0.062648652139739 1.000000000000000 0.000211196640987
62 66 3.851710243432387 0.069856642441638 1.000000000000000 0.000164294954909
63 67 3.851708364690540 0.053359361546951 1.000000000000000 0.000262724567270
64 68 3.851706012784435 0.071155643085904 1.000000000000000 0.000403770006666
65 69 3.851703941358782 0.059316032317811 1.000000000000000 0.000461554352872
66 70 3.851700197767271 0.108009845701105 1.000000000000000 0.000436422283556
67 71 3.851695307142141 0.163580895660695 1.000000000000000 0.000307295113035
68 72 3.851691399307458 0.181349759241741 1.000000000000000 0.000235040502342
69 73 3.851689471390043 0.107832446159790 1.000000000000000 0.000221426633919
70 74 3.851688823784228 0.040453749504275 1.000000000000000 0.000148032318246
71 75 3.851688223274952 0.044976174468686 1.000000000000000 0.000096161052719
72 76 3.851687620732168 0.042801210239527 1.000000000000000 0.000077234951101
73 77 3.851686850310878 0.057478768373931 1.000000000000000 0.000100834469701
74 78 3.851685977478367 0.052025273135193 1.000000000000000 0.000149960172964
75 79 3.851684167623704 0.111156828979912 1.000000000000000 0.000167332110141
76 80 3.851681988518464 0.126129447187096 1.000000000000000 0.000278532997093
77 81 3.851678612508517 0.193012107072998 1.000000000000000 0.000270858487259
78 82 3.851674341241396 0.243320779080507 1.000000000000000 0.000284425930457
79 83 3.851668675173618 0.361851487235877 1.000000000000000 0.000297556247746
80 84 3.851664329587679 0.311366616446581 1.000000000000000 0.000256447332912
81 85 3.851660710398617 0.287631567667006 1.000000000000000 0.000250034840236
82 86 3.851656904228633 0.395831806411637 1.000000000000000 0.000281089043810
83 87 3.851653234875922 0.429586193988550 1.000000000000000 0.000240283218033
84 88 3.851649167028266 0.530392377836537 1.000000000000000 0.000207540313526
85 89 3.851644064793459 0.576342846702489 1.000000000000000 0.000209624870774
86 90 3.851635288220856 0.955454683176267 1.000000000000000 0.000253320852709
87 91 3.851622228103257 1.253048912781838 1.000000000000000 0.000430430448128
88 92 3.851597172692499 2.132438681708477 1.000000000000000 0.000467742725532
89 93 3.851565768419913 2.916684995257545 1.000000000000000 0.001192933652660
90 94 3.851528846243465 1.362421116565003 1.000000000000000 0.000570148837131
91 96 3.851506146330444 0.860135227772857 0.462833296685404 0.000344724185068
92 97 3.851496766837482 0.297870435244864 1.000000000000000 0.000288789597313
93 98 3.851494006121746 0.096469740644771 1.000000000000000 0.000418999249571
94 99 3.851492634583295 0.064939381897718 1.000000000000000 0.000287780742491
95 100 3.851491785062688 0.115058214092042 1.000000000000000 0.000106021828544
96 101 3.851491339492908 0.041805977505410 1.000000000000000 0.000075269825482
97 102 3.851490978539207 0.029442199273530 1.000000000000000 0.000081100866705
98 103 3.851490412986370 0.034026722144734 1.000000000000000 0.000115021921636
99 104 3.851489730353474 0.040955054103513 1.000000000000000 0.000154171697198
100 105 3.851488451749606 0.077968426197287 1.000000000000000 0.000192498467969
101 106 3.851486118115107 0.141846438286986 1.000000000000000 0.000222222765267
102 107 3.851481578981015 0.356730515297022 1.000000000000000 0.000412423645025
103 108 3.851474491208517 0.561800331225063 1.000000000000000 0.000293646298667
104 109 3.851464695389869 0.507066175070668 1.000000000000000 0.000436279124155
105 110 3.851447241224886 1.240636090035912 1.000000000000000 0.000923272224146
106 111 3.851438309550156 0.717087366183609 1.000000000000000 0.000893269136701
107 112 3.851428304352594 1.483951273509424 1.000000000000000 0.000903775112866
108 113 3.851425373633977 0.565542179423370 1.000000000000000 0.000592712615300
109 114 3.851420326385227 0.246016615110655 1.000000000000000 0.000150608684856
110 115 3.851420097222203 0.096088547561013 1.000000000000000 0.000078671376951
111 116 3.851419997973771 0.034912690952008 1.000000000000000 0.000082990462232
112 117 3.851419942851718 0.035108225903152 1.000000000000000 0.000048162252891
113 118 3.851419913553030 0.014671627323428 1.000000000000000 0.000024718199432
114 119 3.851419903364964 0.002968824603794 1.000000000000000 0.000012256250107
115 120 3.851419899650148 0.007499765449587 1.000000000000000 0.000005545594907
116 121 3.851419897986769 0.002332815082972 1.000000000000000 0.000009037258290
117 122 3.851419895379371 0.003986073182012 1.000000000000000 0.000006650018983
118 123 3.851419891682425 0.002289954325437 1.000000000000000 0.000007590614463
119 124 3.851419883489088 0.004753677979313 1.000000000000000 0.000023388925422
120 125 3.851419874558122 0.005755588871374 1.000000000000000 0.000017069379527
121 126 3.851419857809344 0.010559000939149 1.000000000000000 0.000025038772215
122 127 3.851419825211173 0.019613511593831 1.000000000000000 0.000030621241696
123 128 3.851419759436378 0.034142064621691 1.000000000000000 0.000036838176811
124 129 3.851419567936238 0.104214592267732 1.000000000000000 0.000119071941392
125 130 3.851419219408298 0.175111176599149 1.000000000000000 0.000103760125281
126 131 3.851418588157344 0.387090905127026 1.000000000000000 0.000219417810889
127 132 3.851418129479175 0.287356559911792 1.000000000000000 0.000119550992716
128 133 3.851417953216948 0.055151615675210 1.000000000000000 0.000067563553943
129 135 3.851417929408739 0.018478032108827 0.442286959684269 0.000048806832218
130 136 3.851417919205737 0.029490487230219 1.000000000000000 0.000014030750385
131 137 3.851417917038509 0.005390766286147 1.000000000000000 0.000022602044824
132 138 3.851417913639569 0.001551714583695 1.000000000000000 0.000012075339786
133 139 3.851417912703200 0.009205136974295 1.000000000000000 0.000003144980385
134 140 3.851417912661231 0.001820760198036 1.000000000000000 0.000001859713374
135 141 3.851417912654473 0.001820760198036 1.000000000000000 0.000000726992024
Convergence criteria met.
After: gradient norm = 7.269920242561924E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0892,-0.0892}
Count Table 1:
---------------
h: {0.0624,-0.0624}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {0.2128,-0.2128}
Count Table 5:
---------------
h: {0.2928,-0.2928}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {-1.2798,-1.7294,-0.8429,-0.9854,-1.2249,-1.3367,0.1830,-0.8795,-0.8825,-2.4404,-2.1548,-1.2249,-2.0592,-2.1706,-3.8430,2.2982,0.4829,-2.1548,-3.2818,-3.3709,0.1277,0.4392,-1.8436,0.4829,1.3103,-3.2111,0.1479,-0.8616,-2.9886,-1.8436,-2.7284,1.0336,-2.9234,-0.1367,0.2969,-2.9886,-0.1367,-2.9234,1.0336,-2.7284,-2.9886,0.2969,-0.8616,0.1479,-3.2111,1.3103,-1.8436,-2.9886,0.4392,0.1277,-3.3709,-3.2818,0.4829,-1.8436,2.2982,-3.8430,-2.1706,-2.0592,-2.1548,0.4829,-2.4404,-0.8825,-0.8795,0.1830,-1.2249,-2.1548,-0.9854,-0.8429,-1.7294,-1.2798,-1.3367,-1.2249}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0487,-2.8054}
Activity(exp=1): {0.0487,-2.9551}
Activity(exp=2): {0.0487,0.0487}
Activity(exp=3): {0.0487,0.0487}
Activity(exp=4): {0.0487,-1.2631}
Activity(exp=5): {0.0487,-0.7233}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Suggested variations:
key=12;3;0, description = Initial model.
> Optimizing variation "Initial model." (component1-2-variation0).
>> Starting new optimization: component1-2-variation0. (2021-05-21 17:39:05.752).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 3.851417912654472
gradient = {0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 7.269920242559412E-7
Already at minimum!
After: gradient norm = 7.269920242559412E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0892,-0.0892}
Count Table 1:
---------------
h: {0.0624,-0.0624}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {0.2128,-0.2128}
Count Table 5:
---------------
h: {0.2928,-0.2928}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {-1.2798,-1.7294,-0.8429,-0.9854,-1.2249,-1.3367,0.1830,-0.8795,-0.8825,-2.4404,-2.1548,-1.2249,-2.0592,-2.1706,-3.8430,2.2982,0.4829,-2.1548,-3.2818,-3.3709,0.1277,0.4392,-1.8436,0.4829,1.3103,-3.2111,0.1479,-0.8616,-2.9886,-1.8436,-2.7284,1.0336,-2.9234,-0.1367,0.2969,-2.9886,-0.1367,-2.9234,1.0336,-2.7284,-2.9886,0.2969,-0.8616,0.1479,-3.2111,1.3103,-1.8436,-2.9886,0.4392,0.1277,-3.3709,-3.2818,0.4829,-1.8436,2.2982,-3.8430,-2.1706,-2.0592,-2.1548,0.4829,-2.4404,-0.8825,-0.8795,0.1830,-1.2249,-2.1548,-0.9854,-0.8429,-1.7294,-1.2798,-1.3367,-1.2249}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0487,-2.8054}
Activity(exp=1): {0.0487,-2.9551}
Activity(exp=2): {0.0487,0.0487}
Activity(exp=3): {0.0487,0.0487}
Activity(exp=4): {0.0487,-1.2631}
Activity(exp=5): {0.0487,-0.7233}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;4;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation1).
>> Starting new optimization: component1-2-variation1. (2021-05-21 17:39:06.47).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 3.85141107007079
gradient = {-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 8.070492213321876E-5
Starting Function Value: 3.85141107007079
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.851411061310897 0.000213562740765 2.646217047483320 0.000032292018046
2 4 3.851411059553862 0.000083181749777 1.000000000000000 0.000016897571204
3 5 3.851411058330341 0.000104947632646 1.000000000000000 0.000015541405675
4 6 3.851411056557521 0.000197490136737 1.000000000000000 0.000022137304411
5 7 3.851411053674869 0.000449845515387 1.000000000000000 0.000027469356755
6 8 3.851411053134884 0.000593995071115 1.000000000000000 0.000045971443395
7 9 3.851411050769565 0.000117071369182 1.000000000000000 0.000014538827949
8 10 3.851411050072553 0.000066723431541 1.000000000000000 0.000011362510462
9 11 3.851411048974771 0.000182144426926 1.000000000000000 0.000019056898963
10 12 3.851411046928241 0.000432475780507 1.000000000000000 0.000029814378767
11 13 3.851411043348121 0.000894205372969 1.000000000000000 0.000034889463817
12 14 3.851411040805933 0.001531254869856 1.000000000000000 0.000064615663632
13 15 3.851411035535276 0.000822690314444 1.000000000000000 0.000023115021822
14 16 3.851411033078261 0.000435672634949 1.000000000000000 0.000011841777360
15 17 3.851411031409338 0.000492573605705 1.000000000000000 0.000020017469484
16 18 3.851411029493324 0.000636415225035 1.000000000000000 0.000021392098531
17 19 3.851411024340573 0.001919778247495 1.000000000000000 0.000043928889547
18 20 3.851411017486097 0.002726975434660 1.000000000000000 0.000022807199141
19 21 3.851411013341926 0.001294400760953 1.000000000000000 0.000024824496842
20 22 3.851411010315690 0.001092159801123 1.000000000000000 0.000023462021698
21 23 3.851411008307700 0.000197123985927 1.000000000000000 0.000018155643363
22 24 3.851411001966473 0.001471261316638 1.000000000000000 0.000025542417409
23 25 3.851410997825715 0.001839184272339 1.000000000000000 0.000028679892799
24 26 3.851410992707713 0.002525302095480 1.000000000000000 0.000015378343310
25 27 3.851410990442977 0.001387524073318 1.000000000000000 0.000006781225745
26 28 3.851410989465245 0.000596542839242 1.000000000000000 0.000009159323925
27 29 3.851410988725882 0.000309684503133 1.000000000000000 0.000008011949511
28 30 3.851410987766425 0.000501941925673 1.000000000000000 0.000005093493395
29 32 3.851410987620489 0.000129909880919 0.292598442945516 0.000010290746523
30 33 3.851410987301489 0.000254741009103 1.000000000000000 0.000004166616646
31 34 3.851410987182834 0.000081080779304 1.000000000000000 0.000003361466945
32 35 3.851410986916597 0.000263658080412 1.000000000000000 0.000002653459765
33 36 3.851410986797313 0.000154294346391 1.000000000000000 0.000001838606815
34 37 3.851410986659737 0.000224368239527 1.000000000000000 0.000001519404850
35 38 3.851410986545520 0.000218869476332 1.000000000000000 0.000001892441588
36 39 3.851410986389229 0.000339757931049 1.000000000000000 0.000002573568688
37 40 3.851410986268752 0.000382569241802 1.000000000000000 0.000002060386706
38 41 3.851410986210689 0.000382569241802 1.000000000000000 0.000001018130838
Convergence criteria met.
After: gradient norm = 1.0181308379700185E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0892,-0.0892}
Count Table 1:
---------------
h: {0.0624,-0.0624}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {0.2130,-0.2130}
Count Table 5:
---------------
h: {0.2930,-0.2930}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {-1.2790,-1.7282,-0.8423,-0.9849,-1.2243,-1.3363,0.1833,-0.8789,-0.8820,-2.4379,-2.1553,-1.2243,-2.0624,-2.1742,-3.8247,2.2939,0.4813,-2.1553,-3.2801,-3.3691,0.1285,0.4407,-1.8428,0.4813,1.3108,-3.2094,0.1488,-0.8605,-2.9885,-1.8428,-2.7268,1.0342,-2.9220,-0.1357,0.2973,-2.9885,-0.1357,-2.9220,1.0342,-2.7268,-2.9885,0.2973,-0.8605,0.1488,-3.2094,1.3108,-1.8428,-2.9885,0.4407,0.1285,-3.3691,-3.2801,0.4813,-1.8428,2.2939,-3.8247,-2.1742,-2.0624,-2.1553,0.4813,-2.4379,-0.8820,-0.8789,0.1833,-1.2243,-2.1553,-0.9849,-0.8423,-1.7282,-1.2790,-1.3363,-1.2243}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0482,-2.8034}
Activity(exp=1): {0.0482,-2.9533}
Activity(exp=2): {0.0482,0.0482}
Activity(exp=3): {0.0482,0.0482}
Activity(exp=4): {0.0482,-1.2620}
Activity(exp=5): {0.0482,-0.7223}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;5;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation2).
>> Starting new optimization: component1-2-variation2. (2021-05-21 17:39:38.596).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 3.867919760788682
gradient = {0.0363,0.0075,0.0009,0.0011,0.0078,0.0111,0.0393,0.0146,0.0000,0.0009,0.0021,0.0078,0.0006,0.0007,0.0024,0.0000,0.0607,0.0001,0.0008,0.0007,0.0000,0.0024,0.0158,0.0449,0.0005,0.0203,0.0000,0.0000,0.0037,0.0400,0.0318,0.0017,0.0068,0.0000,0.0227,0.0016,0.0000,0.0043,0.0000,0.0022,0.0000,0.0000,0.0000,0.0000,0.0000,0.0121,0.0000,0.0137,-0.0107,0.0107,-0.0067,0.0067,-0.0000,0.0000,-0.0000,0.0000,-0.0290,0.0290,-0.0272,0.0272}
gradient norm = 0.12963267102165552
Starting Function Value: 3.867919760788682
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.855922325568042 0.187088222883921 1.443218144079339 0.030099515767307
2 4 3.854736576388585 0.043201752034382 1.000000000000000 0.026553928185539
3 5 3.848905260965976 0.500573476290930 1.000000000000000 0.022095819921183
4 7 3.848391303266392 0.060894478845927 0.311310208148879 0.009017319237230
5 8 3.848288065587241 0.019902547660599 1.000000000000000 0.004498852763621
6 9 3.848213028343169 0.022942999012892 1.000000000000000 0.005001368362920
7 10 3.848096470379123 0.049569794882745 1.000000000000000 0.007140032741223
8 11 3.847943204586475 0.083875264902339 1.000000000000000 0.006949535066435
9 12 3.847863289141937 0.096543027950720 1.000000000000000 0.007187016956839
10 13 3.847813124602085 0.033801256552631 1.000000000000000 0.001774546221776
11 14 3.847805420145338 0.016866069905384 1.000000000000000 0.000822797881100
12 15 3.847801664320646 0.008151590031220 1.000000000000000 0.000850559729810
13 16 3.847795386480400 0.020689448109342 1.000000000000000 0.001105217826993
14 17 3.847794357540841 0.023510146593500 1.000000000000000 0.001533276417493
15 18 3.847790294002372 0.007857650256639 1.000000000000000 0.000471634435893
16 19 3.847789095994718 0.005103327935290 1.000000000000000 0.000431404332389
17 20 3.847787305136373 0.009451883504708 1.000000000000000 0.000557970343278
18 21 3.847785009299388 0.013768152981296 1.000000000000000 0.000498608156612
19 22 3.847781486464349 0.024964296024308 1.000000000000000 0.000443446998178
20 24 3.847780410492595 0.013822841856795 0.397929799716867 0.000750664459164
21 25 3.847778741252564 0.018445455671839 1.000000000000000 0.000333710892718
22 26 3.847778226529344 0.005311578469622 1.000000000000000 0.000232149894339
23 27 3.847777595168128 0.008871151808374 1.000000000000000 0.000279647562458
24 28 3.847777130388633 0.006416436017105 1.000000000000000 0.000179156943454
25 29 3.847776799317810 0.005999847638630 1.000000000000000 0.000202784462413
26 30 3.847776222512792 0.009267795071023 1.000000000000000 0.000201918198277
27 31 3.847775002665573 0.024459816849708 1.000000000000000 0.000178339833241
28 32 3.847774336204709 0.025418673781731 1.000000000000000 0.000550911470494
29 33 3.847773991935192 0.020030685657022 1.000000000000000 0.000337630879380
30 34 3.847773757644598 0.010194076123832 1.000000000000000 0.000088003691798
31 35 3.847773716866842 0.001753709944852 1.000000000000000 0.000080416019153
32 36 3.847773605452353 0.003008466143720 1.000000000000000 0.000094657509233
33 37 3.847773385392149 0.007632492496385 1.000000000000000 0.000131058094551
34 38 3.847773131841876 0.011463023988429 1.000000000000000 0.000119494600508
35 39 3.847772881627274 0.016039295217402 1.000000000000000 0.000103776375519
36 40 3.847772840988984 0.008271889927285 1.000000000000000 0.000084602409986
37 41 3.847772784144627 0.002822805062557 1.000000000000000 0.000030483987042
38 42 3.847772767712977 0.000962874089278 1.000000000000000 0.000021393397671
39 43 3.847772734809351 0.003385680224391 1.000000000000000 0.000029858003280
40 44 3.847772715111239 0.003048539551633 1.000000000000000 0.000027528948077
41 45 3.847772692973987 0.004092408805853 1.000000000000000 0.000014499875608
42 46 3.847772679617109 0.003468850831054 1.000000000000000 0.000015837228057
43 47 3.847772671995012 0.002245153939571 1.000000000000000 0.000019802892704
44 48 3.847772663522693 0.002610001312069 1.000000000000000 0.000017228043541
45 49 3.847772655278383 0.003545636195126 1.000000000000000 0.000021730390239
46 50 3.847772649156696 0.001362910050904 1.000000000000000 0.000012688104060
47 51 3.847772644248685 0.001525909267826 1.000000000000000 0.000015393281298
48 52 3.847772640016748 0.001627478633216 1.000000000000000 0.000015302005471
49 53 3.847772629875997 0.004173429154724 1.000000000000000 0.000013977830455
50 54 3.847772617794529 0.006032059700680 1.000000000000000 0.000010718742139
51 55 3.847772610061651 0.004566657634115 1.000000000000000 0.000009697980600
52 56 3.847772605823188 0.002492686927363 1.000000000000000 0.000007955035257
53 57 3.847772603732340 0.001059305558411 1.000000000000000 0.000005901423583
54 58 3.847772602063871 0.000852872836836 1.000000000000000 0.000004076507393
55 59 3.847772600768681 0.000926972866688 1.000000000000000 0.000003473800170
56 60 3.847772599780542 0.000951015864216 1.000000000000000 0.000004558945347
57 61 3.847772598413106 0.001457001248803 1.000000000000000 0.000005434220582
58 62 3.847772595658391 0.002950651914997 1.000000000000000 0.000008374646861
59 63 3.847772591185872 0.005211019362488 1.000000000000000 0.000008900755386
60 64 3.847772586836600 0.005347063028327 1.000000000000000 0.000007181578782
61 65 3.847772583422970 0.003810279976526 1.000000000000000 0.000006443451707
62 66 3.847772580995469 0.002088372600814 1.000000000000000 0.000005775690450
63 67 3.847772578774138 0.001760233197290 1.000000000000000 0.000006247107519
64 68 3.847772575865190 0.003305804619070 1.000000000000000 0.000006969452948
65 69 3.847772573856991 0.003615150501478 1.000000000000000 0.000005529390144
66 70 3.847772572892107 0.001497608248496 1.000000000000000 0.000003346302771
67 71 3.847772572193797 0.001105577754384 1.000000000000000 0.000003626670254
68 72 3.847772571382495 0.001064716810005 1.000000000000000 0.000003128937366
69 73 3.847772570331470 0.001494181633713 1.000000000000000 0.000003317030844
70 74 3.847772569680522 0.001244205694418 1.000000000000000 0.000002073203634
71 75 3.847772569196992 0.000953803443010 1.000000000000000 0.000002991565828
72 76 3.847772568446489 0.001700752060404 1.000000000000000 0.000003173637191
73 77 3.847772568096161 0.001082428657711 1.000000000000000 0.000002132691323
74 78 3.847772568022757 0.001082428657711 1.000000000000000 0.000000508346535
Convergence criteria met.
After: gradient norm = 5.083465347827953E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0963,-0.0963}
Count Table 1:
---------------
h: {0.0664,-0.0664}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {0.2451,-0.2451}
Count Table 5:
---------------
h: {0.3177,-0.3177}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {-1.2173,-2.2926,-0.6864,-0.8696,-1.1950,-1.2985,0.2639,-1.2362,-0.8274,-2.4035,-2.1613,-1.1950,-2.0820,-2.2866,-3.8250,2.2823,0.4733,-2.1613,-3.3134,-3.4405,-0.0283,0.5762,-1.8666,0.4733,1.3722,-3.2868,0.0081,-0.7975,-3.0287,-1.8666,-2.7376,0.9967,-2.9204,-0.1676,0.2582,-3.0287,-0.1676,-2.9204,0.9967,-2.7376,-3.0287,0.2582,-0.7975,0.0081,-3.2868,1.3722,-1.8666,-3.0287,0.5762,-0.0283,-3.4405,-3.3134,0.4733,-1.8666,2.2823,-3.8250,-2.2866,-2.0820,-2.1613,0.4733,-2.4035,-0.8274,-1.2362,0.2639,-1.1950,-2.1613,-0.8696,-0.6864,-2.2926,-1.2173,-1.2985,-1.1950}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0447,-2.7847}
Activity(exp=1): {0.0447,-2.9546}
Activity(exp=2): {0.0447,0.0447}
Activity(exp=3): {0.0447,0.0447}
Activity(exp=4): {0.0447,-1.2402}
Activity(exp=5): {0.0447,-0.8239}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;6;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation3).
>> Starting new optimization: component1-2-variation3. (2021-05-21 17:40:44.368).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 3.8477670061692804
gradient = {-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0001,0.0001,-0.0000,0.0000}
gradient norm = 9.772569374206116E-5
Starting Function Value: 3.8477670061692804
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.847766994760780 0.000229499074953 2.348400570666421 0.000042479978254
2 4 3.847766992323651 0.000096135683890 1.000000000000000 0.000017066832068
3 5 3.847766991547730 0.000071341788050 1.000000000000000 0.000012297174305
4 6 3.847766990750935 0.000093138052446 1.000000000000000 0.000015292955864
5 7 3.847766988606425 0.000334562616898 1.000000000000000 0.000021722531229
6 8 3.847766987696093 0.000446319679700 1.000000000000000 0.000039943357271
7 9 3.847766985796735 0.000164617971265 1.000000000000000 0.000016898379558
8 10 3.847766984666372 0.000166429006220 1.000000000000000 0.000012443999735
9 11 3.847766983362412 0.000283352274089 1.000000000000000 0.000020703988665
10 12 3.847766981213582 0.000553403922664 1.000000000000000 0.000028449298391
11 13 3.847766978099789 0.000894432647400 1.000000000000000 0.000024529091561
12 15 3.847766977026541 0.000453665329957 0.365052732160315 0.000033119051065
13 16 3.847766974825598 0.000680058683720 1.000000000000000 0.000014148229130
14 17 3.847766973774829 0.000291713727149 1.000000000000000 0.000010261515827
15 18 3.847766972970124 0.000279864259918 1.000000000000000 0.000011363034807
16 19 3.847766972896235 0.000339347313945 1.000000000000000 0.000026479406672
17 20 3.847766972194905 0.000049285027305 1.000000000000000 0.000008306010120
18 21 3.847766971945239 0.000066724392838 1.000000000000000 0.000006218787876
19 22 3.847766971547328 0.000192154546658 1.000000000000000 0.000011037346709
20 23 3.847766971041266 0.000284571478652 1.000000000000000 0.000013696485315
21 24 3.847766970096536 0.000492069072026 1.000000000000000 0.000011260645498
22 25 3.847766969131647 0.000630149031010 1.000000000000000 0.000006768173125
23 26 3.847766968690171 0.000562886238417 1.000000000000000 0.000017043293166
24 27 3.847766968212910 0.000157463943425 1.000000000000000 0.000007169673061
25 28 3.847766967981236 0.000099816385889 1.000000000000000 0.000005919362734
26 29 3.847766967676808 0.000201704542601 1.000000000000000 0.000004941375338
27 30 3.847766967354549 0.000295380957920 1.000000000000000 0.000003884353754
28 31 3.847766967025343 0.000348578028204 1.000000000000000 0.000002985533604
29 33 3.847766966981059 0.000080202914613 0.239971561172214 0.000005885098316
30 34 3.847766966860764 0.000180823170882 1.000000000000000 0.000003115060980
31 35 3.847766966779477 0.000085798303193 1.000000000000000 0.000002297067040
32 36 3.847766966618466 0.000218649566472 1.000000000000000 0.000002242926727
33 37 3.847766966531283 0.000146480792299 1.000000000000000 0.000001785986763
34 38 3.847766966420333 0.000227074913911 1.000000000000000 0.000001649035847
35 39 3.847766966335904 0.000278676872682 1.000000000000000 0.000002194335960
36 40 3.847766966251997 0.000137654618217 1.000000000000000 0.000001671011897
37 41 3.847766966137526 0.000239416397412 1.000000000000000 0.000001662213937
38 42 3.847766966042067 0.000267241886661 1.000000000000000 0.000001296950646
39 43 3.847766965955948 0.000267241886661 1.000000000000000 0.000001096457429
Convergence criteria met.
After: gradient norm = 1.0964574291573373E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0964,-0.0964}
Count Table 1:
---------------
h: {0.0664,-0.0664}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {0.2454,-0.2454}
Count Table 5:
---------------
h: {0.3178,-0.3178}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {-1.2169,-2.2915,-0.6862,-0.8692,-1.1946,-1.2980,0.2640,-1.2355,-0.8270,-2.4023,-2.1611,-1.1946,-2.0816,-2.2819,-3.8245,2.2808,0.4728,-2.1611,-3.3119,-3.4388,-0.0281,0.5766,-1.8662,0.4728,1.3720,-3.2847,0.0084,-0.7967,-3.0284,-1.8662,-2.7364,0.9962,-2.9175,-0.1675,0.2580,-3.0284,-0.1675,-2.9175,0.9962,-2.7364,-3.0284,0.2580,-0.7967,0.0084,-3.2847,1.3720,-1.8662,-3.0284,0.5766,-0.0281,-3.4388,-3.3119,0.4728,-1.8662,2.2808,-3.8245,-2.2819,-2.0816,-2.1611,0.4728,-2.4023,-0.8270,-1.2355,0.2640,-1.1946,-2.1611,-0.8692,-0.6862,-2.2915,-1.2169,-1.2980,-1.1946}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0443,-2.7836}
Activity(exp=1): {0.0443,-2.9534}
Activity(exp=2): {0.0443,0.0443}
Activity(exp=3): {0.0443,0.0443}
Activity(exp=4): {0.0443,-1.2396}
Activity(exp=5): {0.0443,-0.8232}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;7;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation4).
>> Starting new optimization: component1-2-variation4. (2021-05-21 17:41:23.514).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 3.8477666806811257
gradient = {0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 5.841832246592671E-6
Starting Function Value: 3.8477666806811257
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.847766680640341 0.000013704303338 2.345891281898323 0.000002878364846
2 4 3.847766680628487 0.000006304732957 1.000000000000000 0.000001634829182
3 5 3.847766680617626 0.000009935577705 1.000000000000000 0.000001430269005
4 6 3.847766680605398 0.000015312730860 1.000000000000000 0.000001935381427
5 7 3.847766680582952 0.000037170358728 1.000000000000000 0.000002301322096
6 9 3.847766680571793 0.000027223365792 0.488141129725572 0.000002698298642
7 10 3.847766680558531 0.000020457417696 1.000000000000000 0.000001591188646
8 11 3.847766680542025 0.000030213086485 1.000000000000000 0.000001740293838
9 12 3.847766680524199 0.000038539715532 1.000000000000000 0.000002692942884
10 13 3.847766680490089 0.000086651534896 1.000000000000000 0.000003467964510
11 15 3.847766680475631 0.000055195101014 0.394887929128995 0.000004035242514
12 16 3.847766680448802 0.000069001489549 1.000000000000000 0.000002175538872
13 17 3.847766680433419 0.000069001489549 1.000000000000000 0.000001161209990
Convergence criteria met.
After: gradient norm = 1.161209990010653E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0964,-0.0964}
Count Table 1:
---------------
h: {0.0664,-0.0664}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {0.2454,-0.2454}
Count Table 5:
---------------
h: {0.3179,-0.3179}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {-1.2169,-2.2915,-0.6862,-0.8692,-1.1946,-1.2981,0.2640,-1.2354,-0.8270,-2.4023,-2.1611,-1.1946,-2.0817,-2.2818,-3.8244,2.2808,0.4728,-2.1611,-3.3119,-3.4386,-0.0281,0.5765,-1.8661,0.4728,1.3720,-3.2848,0.0085,-0.7966,-3.0284,-1.8661,-2.7364,0.9962,-2.9173,-0.1675,0.2580,-3.0284,-0.1675,-2.9173,0.9962,-2.7364,-3.0284,0.2580,-0.7966,0.0085,-3.2848,1.3720,-1.8661,-3.0284,0.5765,-0.0281,-3.4386,-3.3119,0.4728,-1.8661,2.2808,-3.8244,-2.2818,-2.0817,-2.1611,0.4728,-2.4023,-0.8270,-1.2354,0.2640,-1.1946,-2.1611,-0.8692,-0.6862,-2.2915,-1.2169,-1.2981,-1.1946}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0443,-2.7836}
Activity(exp=1): {0.0443,-2.9534}
Activity(exp=2): {0.0443,0.0443}
Activity(exp=3): {0.0443,0.0443}
Activity(exp=4): {0.0443,-1.2395}
Activity(exp=5): {0.0443,-0.8231}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;8;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation5).
>> Starting new optimization: component1-2-variation5. (2021-05-21 17:41:40.052).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 3.8477666778072384
gradient = {-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000}
gradient norm = 1.1663017227471854E-6
Already at minimum!
After: gradient norm = 1.1663017227471854E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0964,-0.0964}
Count Table 1:
---------------
h: {0.0664,-0.0664}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {0.2454,-0.2454}
Count Table 5:
---------------
h: {0.3179,-0.3179}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {-1.2169,-2.2915,-0.6862,-0.8692,-1.1946,-1.2981,0.2640,-1.2354,-0.8270,-2.4023,-2.1611,-1.1946,-2.0817,-2.2818,-3.8244,2.2808,0.4728,-2.1611,-3.3119,-3.4386,-0.0281,0.5765,-1.8661,0.4728,1.3720,-3.2848,0.0085,-0.7966,-3.0284,-1.8661,-2.7364,0.9962,-2.9173,-0.1675,0.2580,-3.0284,-0.1675,-2.9173,0.9962,-2.7364,-3.0284,0.2580,-0.7966,0.0085,-3.2848,1.3720,-1.8661,-3.0284,0.5765,-0.0281,-3.4386,-3.3119,0.4728,-1.8661,2.2808,-3.8244,-2.2818,-2.0817,-2.1611,0.4728,-2.4023,-0.8270,-1.2354,0.2640,-1.1946,-2.1611,-0.8692,-0.6862,-2.2915,-1.2169,-1.2981,-1.1946}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0443,-2.7836}
Activity(exp=1): {0.0443,-2.9534}
Activity(exp=2): {0.0443,0.0443}
Activity(exp=3): {0.0443,0.0443}
Activity(exp=4): {0.0443,-1.2395}
Activity(exp=5): {0.0443,-0.8231}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;9;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation6).
>> Starting new optimization: component1-2-variation6. (2021-05-21 17:41:41.144).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 3.8477666769878462
gradient = {-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000}
gradient norm = 1.1664032257313063E-6
Already at minimum!
After: gradient norm = 1.1664032257313063E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0964,-0.0964}
Count Table 1:
---------------
h: {0.0664,-0.0664}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {0.2454,-0.2454}
Count Table 5:
---------------
h: {0.3179,-0.3179}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {-1.2169,-2.2915,-0.6862,-0.8692,-1.1946,-1.2981,0.2640,-1.2354,-0.8270,-2.4023,-2.1611,-1.1946,-2.0817,-2.2818,-3.8244,2.2808,0.4728,-2.1611,-3.3119,-3.4386,-0.0281,0.5765,-1.8661,0.4728,1.3720,-3.2848,0.0085,-0.7966,-3.0284,-1.8661,-2.7364,0.9962,-2.9173,-0.1675,0.2580,-3.0284,-0.1675,-2.9173,0.9962,-2.7364,-3.0284,0.2580,-0.7966,0.0085,-3.2848,1.3720,-1.8661,-3.0284,0.5765,-0.0281,-3.4386,-3.3119,0.4728,-1.8661,2.2808,-3.8244,-2.2818,-2.0817,-2.1611,0.4728,-2.4023,-0.8270,-1.2354,0.2640,-1.1946,-2.1611,-0.8692,-0.6862,-2.2915,-1.2169,-1.2981,-1.1946}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0443,-2.7836}
Activity(exp=1): {0.0443,-2.9534}
Activity(exp=2): {0.0443,0.0443}
Activity(exp=3): {0.0443,0.0443}
Activity(exp=4): {0.0443,-1.2395}
Activity(exp=5): {0.0443,-0.8231}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;10;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation7).
>> Starting new optimization: component1-2-variation7. (2021-05-21 17:41:42.356).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 3.8477666779765523
gradient = {-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 1.1721429259072175E-6
Already at minimum!
After: gradient norm = 1.1721429259072175E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0964,-0.0964}
Count Table 1:
---------------
h: {0.0664,-0.0664}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {0.2454,-0.2454}
Count Table 5:
---------------
h: {0.3179,-0.3179}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {-1.2169,-2.2915,-0.6862,-0.8692,-1.1946,-1.2981,0.2640,-1.2354,-0.8270,-2.4023,-2.1611,-1.1946,-2.0817,-2.2818,-3.8244,2.2808,0.4728,-2.1611,-3.3119,-3.4386,-0.0281,0.5765,-1.8661,0.4728,1.3720,-3.2848,0.0085,-0.7966,-3.0284,-1.8661,-2.7364,0.9962,-2.9173,-0.1675,0.2580,-3.0284,-0.1675,-2.9173,0.9962,-2.7364,-3.0284,0.2580,-0.7966,0.0085,-3.2848,1.3720,-1.8661,-3.0284,0.5765,-0.0281,-3.4386,-3.3119,0.4728,-1.8661,2.2808,-3.8244,-2.2818,-2.0817,-2.1611,0.4728,-2.4023,-0.8270,-1.2354,0.2640,-1.1946,-2.1611,-0.8692,-0.6862,-2.2915,-1.2169,-1.2981,-1.1946}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0443,-2.7836}
Activity(exp=1): {0.0443,-2.9534}
Activity(exp=2): {0.0443,0.0443}
Activity(exp=3): {0.0443,0.0443}
Activity(exp=4): {0.0443,-1.2395}
Activity(exp=5): {0.0443,-0.8231}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID NOT improve. Discarding fit component1-2-variation7.
> No varitions possible for Binding mode 1.
> Unfreezing component (component1-3-f0).
>> Starting new optimization: component1-3-f0. (2021-05-21 17:41:43.639).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[249,250]},{"h":[251,252]},{"h":[253,254]},{"h":[255,256]},{"h":[257,258]},{"h":[259,260]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[237,238],[239,240],[241,242],[243,244],[245,246],[247,248]],"dinucleotide":[[43,42,47,46,44,45,37,36,41,40,38,39,67,66,71,70,68,69,61,60,65,64,62,63,49,48,53,52,50,51,55,54,59,58,56,57,79,78,83,82,80,81,73,72,77,76,74,75,103,102,107,106,104,105,97,96,101,100,98,99,85,84,89,88,86,87,91,90,95,94,92,93,115,114,119,118,116,117,109,108,113,112,110,111,139,138,143,142,140,141,133,132,137,136,134,135,121,120,125,124,122,123,127,126,131,130,128,129,151,150,155,154,152,153,145,144,149,148,146,147,175,174,179,178,176,177,169,168,173,172,170,171,157,156,161,160,158,159,163,162,167,166,164,165,187,186,191,190,188,189,181,180,185,184,182,183,211,210,215,214,212,213,205,204,209,208,206,207,193,192,197,196,194,195,199,198,203,202,200,201,223,222,220,226,224,225,217,216,221,220,218,219,234,236,216,222,231,227,235,234,217,223,232,228,228,227,219,225,229,230,232,231,218,224,233,229,208,214,184,190,202,196,209,215,185,191,203,197,204,210,180,186,198,192,205,211,181,187,199,193,207,213,183,189,201,195,206,212,182,188,200,194,172,178,148,154,166,160,173,179,149,155,167,161,168,174,144,150,162,156,169,175,145,151,163,157,171,177,147,153,165,159,170,176,146,152,164,158,136,142,112,118,130,124,137,143,113,119,131,125,132,138,108,114,126,120,133,139,109,115,127,121,135,141,111,117,129,123,134,140,110,116,128,122,100,106,76,82,94,88,101,107,77,83,95,89,96,102,72,78,90,84,97,103,73,79,91,85,99,105,75,81,93,87,98,104,74,80,92,86,64,70,40,46,58,52,65,71,41,47,59,53,60,66,36,42,54,48,61,67,37,43,55,49,63,69,39,45,57,51,62,68,38,44,56,50]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 3.8477666769878476
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gradient norm = 0.027223577232811092
Starting Function Value: 3.8477666769878476
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
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461 495 3.811600909974330 0.001176040702820 1.000000000000000 0.000003317806047
462 496 3.811600909655253 0.001050826040728 1.000000000000000 0.000002343068954
463 497 3.811600909403994 0.000821139780814 1.000000000000000 0.000002827605602
464 498 3.811600908878964 0.001889572024933 1.000000000000000 0.000003833336801
465 500 3.811600908655096 0.001242077031268 0.356098663443814 0.000005782338829
466 501 3.811600908237561 0.001703650801742 1.000000000000000 0.000003420279652
467 502 3.811600907917352 0.001439217892130 1.000000000000000 0.000002361919981
468 503 3.811600907627522 0.001208099567168 1.000000000000000 0.000002581612102
469 504 3.811600907239446 0.001644693100196 1.000000000000000 0.000002888709767
470 505 3.811600906997347 0.002362559396329 1.000000000000000 0.000005311611679
471 506 3.811600906635298 0.001150100262857 1.000000000000000 0.000003359697347
472 507 3.811600906479806 0.000604665182896 1.000000000000000 0.000002410028836
473 508 3.811600906360911 0.000454253553583 1.000000000000000 0.000002102244492
474 509 3.811600906138081 0.001208292163182 1.000000000000000 0.000001881344976
475 510 3.811600905988698 0.001944263058581 1.000000000000000 0.000004261425369
476 511 3.811600905768046 0.001118881044961 1.000000000000000 0.000001434366794
477 512 3.811600905671949 0.000563117734703 1.000000000000000 0.000001467635900
478 513 3.811600905530037 0.000802780689465 1.000000000000000 0.000001783097596
479 514 3.811600905365767 0.001029697043366 1.000000000000000 0.000001793176885
480 516 3.811600905299172 0.000728503988459 0.358076845651612 0.000002103183393
481 517 3.811600905239353 0.000728503988459 1.000000000000000 0.000000968813667
Convergence criteria met.
After: gradient norm = 9.68813666752238E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.1027,-0.1027}
Count Table 1:
---------------
h: {0.0676,-0.0676}
Count Table 2:
---------------
h: {-0.0000,0.0000}
Count Table 3:
---------------
h: {-0.0000,0.0000}
Count Table 4:
---------------
h: {0.2720,-0.2720}
Count Table 5:
---------------
h: {0.3569,-0.3569}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0000}
Activity(exp=1): {-0.0000,-0.0000}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,-0.0000}
Activity(exp=5): {-0.0000,-0.0000}
Binding mode 1:
---------------
Mononucleotide: {-0.6773,-1.0030,-0.3017,-0.6784,-0.7444,-0.8219,-0.1330,-0.6162,-0.6867,-1.0530,-0.9934,-0.7444,-0.8463,-1.0573,-1.7345,0.4497,-0.0450,-0.9934,-0.9727,-0.7558,-1.4381,-0.7471,-0.2682,-0.0450,0.3787,-1.4740,-0.8218,-0.6682,-1.3734,-0.2682,-1.1231,0.0133,-1.4100,-0.5051,0.1714,-1.3734,-0.5051,-1.4100,0.0133,-1.1231,-1.3734,0.1714,-0.6682,-0.8218,-1.4740,0.3787,-0.2682,-1.3734,-0.7471,-1.4381,-0.7558,-0.9727,-0.0450,-0.2682,0.4497,-1.7345,-1.0573,-0.8463,-0.9934,-0.0450,-1.0530,-0.6867,-0.6162,-0.1330,-0.7444,-0.9934,-0.6784,-0.3017,-1.0030,-0.6773,-0.8219,-0.7444}
Dinucleotide(d=1): {-0.2569,-0.3750,0.0560,-0.0640,-0.0372,0.0000,-0.2856,-0.4151,-0.2106,-0.2340,0.1428,0.0000,-0.0328,0.0584,-0.3564,0.0073,0.0219,0.0000,0.2766,0.2554,0.0897,-0.6032,-0.6967,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7442,0.1657,-0.1397,-0.2652,-0.1586,-0.4239,0.0000,-0.2536,-0.4222,-0.6370,0.7109,0.4687,0.0000,-0.1427,-0.1384,-0.0268,-0.0025,-0.3056,0.0000,-0.4070,-0.2166,-0.7378,0.2961,0.3788,0.0000,0.6122,0.0360,0.2052,-1.1815,-0.7244,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9930,-0.6548,-0.3155,-0.5374,0.6262,0.1373,0.0000,0.0501,0.2037,-0.8194,-0.6404,0.3602,0.0000,-0.1041,0.2654,-0.2138,-0.5533,-0.4509,0.0000,0.1345,-0.2359,-1.4213,-0.8070,0.5960,0.0000,-0.4325,-1.1234,2.2282,1.8557,-2.0786,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0451,-0.6199,0.1352,-1.2117,-0.6021,1.3056,0.0000,-0.8281,0.2284,-0.6048,0.0315,0.2010,0.0000,-0.3760,0.1958,-0.6258,-0.3349,0.3857,0.0000,0.9073,-0.6677,-0.8137,-0.2508,-0.6132,0.0000,-0.1284,-1.5731,1.9453,0.2048,-1.1958,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2678,0.8036,0.3433,-0.7228,-0.3186,-0.1506,0.0000,-0.8331,0.7657,-0.1176,0.4601,0.1032,0.0000,0.3580,-1.0799,0.4137,-0.2974,-0.8678,0.0000,-0.6481,0.7026,-0.5123,-0.6204,0.2564,0.0000,-0.0087,0.4671,-0.4041,-0.7224,0.0001,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3728,0.0093,-0.8424,-0.7891,0.6750,0.6794,0.0000,0.0877,0.2038,-0.6067,-0.8566,0.0373,0.0000,0.9551,-0.8892,0.6479,-0.6067,-0.0788,0.0000,-0.8754,0.6433,-0.8892,0.2038,-0.5155,0.0000,0.1401,-0.8754,0.9551,0.0877,-0.8038,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1737,-0.8038,-0.5155,-0.0788,0.0373,-0.0095,0.0000,-0.7224,-0.6204,-0.2974,0.4601,0.6750,0.0000,-0.4041,-0.5123,0.4137,-0.1176,-0.7891,0.0000,0.4671,0.7026,-1.0799,0.7657,-0.8424,0.0000,-0.0087,-0.6481,0.3580,-0.8331,0.0093,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3728,0.0001,0.2564,-0.8678,0.1032,0.6794,0.0000,0.2048,-0.2508,-0.3349,0.0315,-0.3186,0.0000,1.9453,-0.8137,-0.6258,-0.6048,-0.7228,0.0000,-1.5731,-0.6677,0.1958,0.2284,0.3433,0.0000,-0.1284,0.9073,-0.3760,-0.8281,0.8036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2678,-1.1958,-0.6132,0.3857,0.2010,-0.1506,0.0000,1.8557,-0.8070,-0.5533,-0.6404,-0.6021,0.0000,2.2282,-1.4213,-0.2138,-0.8194,-1.2117,0.0000,-1.1234,-0.2359,0.2654,0.2037,0.1352,0.0000,-0.4325,0.1345,-0.1041,0.0501,-0.6199,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0451,-2.0786,0.5960,-0.4509,0.3602,1.3056,0.0000,-1.1815,0.2961,-0.0025,0.7109,0.6262,0.0000,0.2052,-0.7378,-0.0268,-0.6370,-0.5374,0.0000,0.0360,-0.2166,-0.1384,-0.4222,-0.3155,0.0000,0.6122,-0.4070,-0.1427,-0.2536,-0.6548,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9930,-0.7244,0.3788,-0.3056,0.4687,0.1373,0.0000,-0.6032,0.0073,-0.2340,-0.0640,-0.1586,0.0000,0.0897,-0.3564,-0.2106,0.0560,-0.2652,0.0000,0.2554,0.0584,-0.4151,-0.3750,-0.1397,0.0000,0.2766,-0.0328,-0.2856,-0.2569,0.1657,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7442,-0.6967,0.0219,0.1428,-0.0372,-0.4239,0.0000}
Activity(exp=0): {0.0024,-1.8380}
Activity(exp=1): {0.0024,-2.1995}
Activity(exp=2): {0.0024,0.0024}
Activity(exp=3): {0.0024,0.0024}
Activity(exp=4): {0.0024,-0.3357}
Activity(exp=5): {0.0024,0.0187}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
> Optimizing the full model (component1-4-all).
>> Starting new optimization: component1-4-all. (2021-05-21 18:02:35.622).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[261,262]},{"h":[263,264]},{"h":[265,266]},{"h":[267,268]},{"h":[269,270]},{"h":[271,272]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7],[8,9],[10,11]]},{"mononucleotide":[13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,37,36,41,40,38,39,43,42,47,46,44,45,46,47,42,43,45,44,40,41,36,37,39,38,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14],"activity":[[249,250],[251,252],[253,254],[255,256],[257,258],[259,260]],"dinucleotide":[[55,54,59,58,56,57,49,48,53,52,50,51,79,78,83,82,80,81,73,72,77,76,74,75,61,60,65,64,62,63,67,66,71,70,68,69,91,90,95,94,92,93,85,84,89,88,86,87,115,114,119,118,116,117,109,108,113,112,110,111,97,96,101,100,98,99,103,102,107,106,104,105,127,126,131,130,128,129,121,120,125,124,122,123,151,150,155,154,152,153,145,144,149,148,146,147,133,132,137,136,134,135,139,138,143,142,140,141,163,162,167,166,164,165,157,156,161,160,158,159,187,186,191,190,188,189,181,180,185,184,182,183,169,168,173,172,170,171,175,174,179,178,176,177,199,198,203,202,200,201,193,192,197,196,194,195,223,222,227,226,224,225,217,216,221,220,218,219,205,204,209,208,206,207,211,210,215,214,212,213,235,234,232,238,236,237,229,228,233,232,230,231,246,248,228,234,243,239,247,246,229,235,244,240,240,239,231,237,241,242,244,243,230,236,245,241,220,226,196,202,214,208,221,227,197,203,215,209,216,222,192,198,210,204,217,223,193,199,211,205,219,225,195,201,213,207,218,224,194,200,212,206,184,190,160,166,178,172,185,191,161,167,179,173,180,186,156,162,174,168,181,187,157,163,175,169,183,189,159,165,177,171,182,188,158,164,176,170,148,154,124,130,142,136,149,155,125,131,143,137,144,150,120,126,138,132,145,151,121,127,139,133,147,153,123,129,141,135,146,152,122,128,140,134,112,118,88,94,106,100,113,119,89,95,107,101,108,114,84,90,102,96,109,115,85,91,103,97,111,117,87,93,105,99,110,116,86,92,104,98,76,82,52,58,70,64,77,83,53,59,71,65,72,78,48,54,66,60,73,79,49,55,67,61,75,81,51,57,69,63,74,80,50,56,68,62]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 3.8116009052393527
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gradient norm = 5.534572175251069E-6
Starting Function Value: 3.8116009052393527
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.811600905163119 0.000027038910527 4.885456304557035 0.000008333830314
2 4 3.811600905057803 0.000023511251784 1.000000000000000 0.000008273174168
3 5 3.811600902226177 0.001342189958856 1.000000000000000 0.000020117956362
4 7 3.811600901696800 0.000223008402686 0.205951095099920 0.000015313145746
5 8 3.811600901368659 0.000031363162307 1.000000000000000 0.000012443697847
6 9 3.811600900341492 0.000270300193123 1.000000000000000 0.000014174687430
7 10 3.811600899396250 0.000484246992767 1.000000000000000 0.000020391116255
8 11 3.811600898053154 0.000929766591565 1.000000000000000 0.000023314001627
9 12 3.811600896131901 0.000913676363690 1.000000000000000 0.000022208429831
10 13 3.811600890483989 0.002998247029187 1.000000000000000 0.000038648599890
11 14 3.811600884258368 0.004009531019789 1.000000000000000 0.000066171491379
12 15 3.811600876478062 0.003386699226505 1.000000000000000 0.000050802890481
13 16 3.811600865166158 0.004633152677680 1.000000000000000 0.000037997447456
14 17 3.811600852393711 0.005583427965334 1.000000000000000 0.000048766861691
15 18 3.811600833457970 0.010339973743797 1.000000000000000 0.000069000840569
16 19 3.811600817976535 0.013682930979587 1.000000000000000 0.000095434372663
17 20 3.811600801394479 0.004644618749928 1.000000000000000 0.000047449063162
18 21 3.811600786896168 0.004296435693624 1.000000000000000 0.000049076273663
19 22 3.811600773186825 0.005298817942513 1.000000000000000 0.000067031287207
20 23 3.811600742416733 0.014602300391295 1.000000000000000 0.000081125378765
21 24 3.811600688840992 0.026454442810108 1.000000000000000 0.000084424314482
22 25 3.811600685380363 0.062344910817119 1.000000000000000 0.000374782470424
23 26 3.811600571732964 0.010990749787299 1.000000000000000 0.000087815366426
24 27 3.811600535245928 0.003928026878452 1.000000000000000 0.000066517813147
25 28 3.811600481091089 0.026809630932717 1.000000000000000 0.000100601188986
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27 30 3.811600305127299 0.080954647336792 1.000000000000000 0.000076673585049
28 31 3.811600213787504 0.041580638046557 1.000000000000000 0.000099823389405
29 32 3.811600120484390 0.043273713392696 1.000000000000000 0.000083122481316
30 33 3.811600021730082 0.043537801955018 1.000000000000000 0.000082661803200
31 34 3.811599787879570 0.108237225900385 1.000000000000000 0.000100012503759
32 35 3.811599605474298 0.187625062501859 1.000000000000000 0.000130975123167
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112 116 3.811597229059338 0.000541540161895 1.000000000000000 0.000009161976766
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114 118 3.811597228887098 0.000161746136232 1.000000000000000 0.000002111678178
115 119 3.811597228800746 0.000369549807054 1.000000000000000 0.000003122310584
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180 184 3.811597220655194 0.000596909923803 1.000000000000000 0.000001261116584
181 185 3.811597220609276 0.000547196377481 1.000000000000000 0.000001375581441
182 186 3.811597220544924 0.000866980330272 1.000000000000000 0.000001599164369
183 187 3.811597220530718 0.001311838905809 1.000000000000000 0.000002605455390
184 188 3.811597220470425 0.001311838905809 1.000000000000000 0.000000929882164
Convergence criteria met.
After: gradient norm = 9.298821636899628E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5862,-0.5862}
Count Table 2:
---------------
h: {0.0000,-0.0000}
Count Table 3:
---------------
h: {0.0000,-0.0000}
Count Table 4:
---------------
h: {0.3812,-0.3812}
Count Table 5:
---------------
h: {0.3792,-0.3792}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
==================================
== Starts fiting Binding mode 2 ==
==================================
> Optimizing h (component2-0-h).
>> Starting new optimization: component2-0-h. (2021-05-21 18:10:16.547).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]},{"h":[6,7]},{"h":[8,9]},{"h":[10,11]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{}]}
Value and gradient before optimization:
=======================================
value = 5.399479675337159
gradient = {-0.0000,0.0000,-0.0000,0.0000,-0.4054,0.4054,-0.3474,0.3474,-0.3676,0.3676,-0.2829,0.2829}
gradient norm = 1.0001533685018544
Starting Function Value: 5.399479675337159
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 4.528853034106944 1.000000000000000 0.999846655016436 0.723815796407443
2 3 4.063493799477711 2.721982716703495 1.000000000000000 0.415749032516962
3 4 3.852088059054915 1.002991462129803 1.000000000000000 0.011427455608216
4 5 3.851942187307744 0.026346047702348 1.000000000000000 0.000832254572215
5 6 3.851941441769771 0.001771294456709 1.000000000000000 0.000061424684438
6 7 3.851941429704246 0.000148265103352 1.000000000000000 0.000001426798267
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {5.4279e-01,-5.4279e-01,5.8622e-01,-5.8622e-01,1.1753e+00,-1.1753e+00,9.1969e-01,-9.1969e-01,1.4153e+00,-1.4153e+00,1.1390e+00,-1.1390e+00}
> Gradient: {1.5050e-12,-1.5050e-12,3.2451e-13,-3.2451e-13,-3.5965e-07,3.5965e-07,-2.9658e-07,2.9658e-07,-3.7077e-07,3.7077e-07,-8.1430e-07,8.1430e-07}
>>>> Re-trying (1/3).
Starting Function Value: 3.8519414373969028
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.851941437163399 0.000003404156505 2.385769908735938 0.000000098619206
2 4 3.851941437163385 0.000003404156505 1.000000000000000 0.000000007437353
Convergence criteria met.
After: gradient norm = 7.437352801972699E-9
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5862,-0.5862}
Count Table 2:
---------------
h: {1.1753,-1.1753}
Count Table 3:
---------------
h: {0.9197,-0.9197}
Count Table 4:
---------------
h: {1.4153,-1.4153}
Count Table 5:
---------------
h: {1.1390,-1.1390}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {4.3755,5.2520}
Activity(exp=1): {4.3755,5.4089}
Activity(exp=2): {4.3714,4.3714}
Activity(exp=3): {4.3714,4.3714}
Activity(exp=4): {4.3755,4.5917}
Activity(exp=5): {4.3755,4.4186}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
> Initial optimization (component2-1-f1).
>> Starting new optimization: component2-1-f1. (2021-05-21 18:10:41.315).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.851941454675771
gradient = {0.0313,-0.0004,-0.0040,-0.0050,0.0239,0.0433,0.0397,-0.0225,-0.0030,-0.0040,0.0337,0.0453,0.0317,0.0042,-0.0052,-0.0030,0.0176,0.0439,0.0229,0.0089,-0.0042,-0.0052,0.0468,0.0198,0.0242,-0.0292,-0.0066,-0.0042,-0.0030,0.1079,0.0889,0.0043,-0.0406,-0.0066,0.0052,0.0380,0.0000,0.0000,0.0000,0.0000,0.0000,0.0029,0.0000,0.0065,0.0000,0.0141,0.0000,0.0211,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000}
gradient norm = 0.20055144008501286
Starting Function Value: 3.851941454675771
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.843393294749353 0.086483987310875 0.431230946405646 0.180415792229807
2 4 3.835859183910921 0.057768104656573 1.000000000000000 0.169083352253582
3 5 3.776267213213167 1.353032974452009 1.000000000000000 0.386137713330108
4 6 3.758850077127265 0.340081239685386 1.000000000000000 0.052820543639721
5 7 3.755206198255042 0.150177013351281 1.000000000000000 0.052705001619696
6 8 3.741902272205190 0.530165148006062 1.000000000000000 0.086700026214698
7 9 3.734635085590825 0.270032263432228 1.000000000000000 0.050834639419080
8 10 3.730221473860071 0.234869410262726 1.000000000000000 0.032330324752062
9 11 3.725663436739529 0.348273707790729 1.000000000000000 0.040907666755264
10 12 3.717489196186500 0.891794014407943 1.000000000000000 0.127135023870197
11 13 3.711887357550834 0.158641367371459 1.000000000000000 0.072015298579986
12 14 3.705523877316904 0.499366363773466 1.000000000000000 0.069060950992947
13 15 3.699537918869445 0.423193150646637 1.000000000000000 0.048531165527557
14 16 3.695086435068617 0.562124887318264 1.000000000000000 0.057964812774494
15 17 3.692819904142192 0.216765284438057 1.000000000000000 0.028216976849774
16 18 3.690751496200017 0.363395531743493 1.000000000000000 0.035316868770690
17 19 3.688542994868414 0.383081688573427 1.000000000000000 0.036907008717216
18 20 3.686813901311083 0.321431984544651 1.000000000000000 0.030777459354567
19 21 3.685141540033090 0.342280710159890 1.000000000000000 0.018572043748195
20 22 3.684063626246504 0.294366069399087 1.000000000000000 0.011471514053004
21 23 3.682686701355091 0.479004674592480 1.000000000000000 0.009711847759737
22 24 3.681163875168919 0.751525883505304 1.000000000000000 0.013500250269565
23 25 3.679596538571964 0.846152752622730 1.000000000000000 0.009952228644822
24 26 3.678632704190389 0.786107295821397 1.000000000000000 0.013683487811567
25 27 3.677846984402888 0.523317487200332 1.000000000000000 0.012503853939511
26 29 3.677486828190319 0.329931605702450 0.365158097788392 0.015590678651532
27 30 3.676904333294393 0.347939995554951 1.000000000000000 0.008009487152882
28 31 3.676594403840436 0.202279156683992 1.000000000000000 0.005442019664239
29 32 3.676310704788266 0.165031007319481 1.000000000000000 0.005273736305726
30 33 3.676040491454830 0.304259649569113 1.000000000000000 0.013764178660580
31 34 3.675633928896540 0.232173546711666 1.000000000000000 0.005863361599898
32 35 3.675359498633863 0.267877967332035 1.000000000000000 0.005364048233854
33 36 3.675068035620114 0.484780598896177 1.000000000000000 0.003904467710936
34 37 3.674959300671261 0.291302979315208 1.000000000000000 0.003970071814868
35 38 3.674855284976904 0.314441628437138 1.000000000000000 0.003203414477844
36 39 3.674812022392088 0.137514221038602 1.000000000000000 0.002639423953808
37 40 3.674776000127365 0.061613534979303 1.000000000000000 0.001684410716145
38 41 3.674731874431234 0.100182679128132 1.000000000000000 0.001494018150242
39 42 3.674672228712191 0.140066270002742 1.000000000000000 0.001973954475038
40 43 3.674603704523156 0.163952118932503 1.000000000000000 0.001764489353360
41 44 3.674537076176670 0.235706869952409 1.000000000000000 0.001210648846916
42 45 3.674499419927362 0.227900436542623 1.000000000000000 0.001054234373540
43 46 3.674480112555206 0.163685821688725 1.000000000000000 0.000912962460364
44 47 3.674463920372859 0.121588372430756 1.000000000000000 0.000830873529373
45 48 3.674449358520424 0.087915331282918 1.000000000000000 0.001058326966093
46 49 3.674435332324820 0.081877342656320 1.000000000000000 0.001427942266771
47 50 3.674417475569300 0.128256129064646 1.000000000000000 0.001507448475198
48 51 3.674388408760099 0.206867894415199 1.000000000000000 0.001084533274259
49 52 3.674356559653198 0.273537420777017 1.000000000000000 0.000910433927978
50 53 3.674337606069690 0.119478683057779 1.000000000000000 0.001246103540218
51 54 3.674323754256346 0.060367302836120 1.000000000000000 0.001271657990280
52 55 3.674310102340062 0.077981520579947 1.000000000000000 0.000965831250180
53 56 3.674294858079349 0.133770289051129 1.000000000000000 0.000494113950775
54 57 3.674287992548305 0.082499244217215 1.000000000000000 0.000503414299705
55 58 3.674279233195110 0.110035347002720 1.000000000000000 0.000517078076269
56 59 3.674269663189385 0.154848693767949 1.000000000000000 0.000541971208026
57 60 3.674254190948490 0.187279567508667 1.000000000000000 0.000741678830671
58 61 3.674247996879652 0.085486504141551 1.000000000000000 0.000418253043497
59 63 3.674247060271597 0.008267394380482 0.219697458463750 0.000412206362878
60 64 3.674239353871815 0.085938003668602 1.000000000000000 0.000541141869332
61 65 3.674234497316368 0.069060470332304 1.000000000000000 0.000398074546488
62 66 3.674230400585588 0.073220164608117 1.000000000000000 0.000392208451187
63 67 3.674227448312342 0.047699502291995 1.000000000000000 0.000288279149419
64 68 3.674225697869716 0.033325749883445 1.000000000000000 0.000211556807703
65 69 3.674224659007440 0.020499461374744 1.000000000000000 0.000221061701286
66 70 3.674222695588563 0.042085576740705 1.000000000000000 0.000244552678016
67 72 3.674222250870501 0.008416994952738 0.152172368886258 0.000236440605909
68 73 3.674216133011070 0.110512791041402 1.000000000000000 0.000143416994144
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9717e+00,-1.5121e+00,-1.2853e+00,-1.4102e+00,-1.0097e+00,-1.4021e+00,-1.5919e+00,-1.0936e-02,-2.4001e+00,-1.2853e+00,-2.4104e+00,-8.9230e-01,-2.8674e+00,-2.8667e+00,-1.1589e+00,-2.4001e+00,1.7706e+00,-3.9022e+00,-3.9875e+00,-3.4755e+00,-2.8403e+00,-1.1589e+00,8.3903e-01,-8.0172e-01,-4.0590e+00,-1.5877e-01,-3.5150e+00,-2.8403e+00,-7.5201e-01,-9.9760e-02,-5.4780e-01,-2.4499e+00,-4.2599e-01,-3.5150e+00,-2.0222e+00,-2.4638e+00,4.2530e+00,5.1050e+00,4.2530e+00,5.2575e+00,4.2490e+00,4.4180e+00,4.2490e+00,4.6740e+00,4.2530e+00,2.2620e+00,4.2530e+00,2.4697e+00,5.4269e-01,-5.4269e-01,5.8626e-01,-5.8626e-01,9.7551e-02,-9.7551e-02,1.9006e-01,-1.9006e-01,3.8348e-01,-3.8348e-01,3.8435e-01,-3.8435e-01}
> Gradient: {2.2259e-05,1.0130e-05,2.0290e-06,-7.6886e-06,-5.2234e-06,1.1799e-05,4.0485e-05,-2.3028e-06,8.3279e-06,2.0290e-06,-1.3358e-05,-1.8777e-06,-1.6215e-05,4.7603e-06,1.4281e-05,8.3279e-06,1.3184e-05,-2.3697e-06,1.3187e-07,-9.2869e-06,-7.0375e-06,1.4281e-05,9.5124e-06,1.4367e-05,-3.2307e-06,1.4390e-05,1.9229e-06,-7.0375e-06,-3.5225e-06,1.9446e-05,1.7059e-05,1.7233e-05,6.9955e-06,1.9229e-06,-1.2053e-05,-9.1898e-06,8.5060e-06,1.0210e-05,8.5060e-06,1.0515e-05,8.4981e-06,-2.5316e-08,8.4981e-06,5.1426e-05,8.5060e-06,-1.5580e-06,8.5060e-06,1.1639e-05,-4.7061e-05,4.7061e-05,1.8430e-05,-1.8430e-05,2.6330e-05,-2.6330e-05,-3.3346e-05,3.3346e-05,-2.7258e-05,2.7258e-05,-2.6691e-05,2.6691e-05}
>>>> Re-trying (1/3).
Starting Function Value: 3.6742184422084994
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.674218318531539 0.000524824437762 3.648479029838824 0.000109084102681
2 7 3.674218305254422 0.000177855789959 0.552271710998798 0.000106522955594
3 8 3.674217732839853 0.011223105246893 1.000000000000000 0.000248055009154
4 11 3.674217726449386 0.000093034012401 0.006677549372116 0.000246377776555
5 12 3.674217120957492 0.015359239349758 1.000000000000000 0.000233475630287
6 13 3.674216970723267 0.006547637138828 1.000000000000000 0.000214289419733
7 14 3.674216883977763 0.002754369557165 1.000000000000000 0.000103091885399
8 15 3.674216519932127 0.000860759410089 1.000000000000000 0.000110849703037
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9796e+00,-1.5144e+00,-1.2856e+00,-1.4063e+00,-1.0056e+00,-1.4029e+00,-1.6061e+00,-6.4255e-03,-2.4039e+00,-1.2856e+00,-2.4039e+00,-8.8852e-01,-2.8600e+00,-2.8687e+00,-1.1652e+00,-2.4039e+00,1.7757e+00,-3.9011e+00,-3.9875e+00,-3.4711e+00,-2.8370e+00,-1.1652e+00,8.4212e-01,-8.0437e-01,-4.0574e+00,-1.6088e-01,-3.5159e+00,-2.8370e+00,-7.4907e-01,-1.0271e-01,-5.5169e-01,-2.4560e+00,-4.2469e-01,-3.5159e+00,-2.0157e+00,-2.4590e+00,4.2491e+00,5.1003e+00,4.2491e+00,5.2527e+00,4.2452e+00,4.4180e+00,4.2452e+00,4.6563e+00,4.2491e+00,2.2628e+00,4.2491e+00,2.4645e+00,5.4284e-01,-5.4284e-01,5.8617e-01,-5.8617e-01,9.7673e-02,-9.7673e-02,1.8992e-01,-1.8992e-01,3.8354e-01,-3.8354e-01,3.8442e-01,-3.8442e-01}
> Gradient: {-1.3719e-06,5.1561e-07,-2.9356e-06,-6.9677e-06,2.4816e-05,2.0744e-05,-2.6575e-05,2.4604e-05,7.8777e-06,-2.9356e-06,-3.5984e-06,3.5428e-05,-1.2809e-05,3.3021e-06,9.6301e-06,7.8777e-06,1.7504e-05,-2.0195e-06,1.0349e-06,-6.5855e-06,-6.9363e-06,9.6301e-06,2.9597e-05,-3.2548e-06,-1.4493e-06,5.2577e-06,1.8035e-06,-6.9363e-06,2.1371e-05,3.4386e-06,1.8872e-05,-2.0093e-07,-1.8087e-05,1.8035e-06,1.0261e-05,1.0837e-05,8.4982e-06,1.0201e-05,8.4982e-06,1.0505e-05,8.4903e-06,3.6806e-05,8.4903e-06,1.1842e-05,8.4982e-06,-7.5356e-07,8.4982e-06,1.4297e-05,2.1783e-05,-2.1783e-05,-2.5727e-05,2.5727e-05,2.8483e-06,-2.8483e-06,-2.7116e-06,2.7116e-06,-1.2874e-05,1.2874e-05,-1.3761e-05,1.3761e-05}
>>>> Re-trying (2/3).
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9796e+00,-1.5144e+00,-1.2856e+00,-1.4063e+00,-1.0056e+00,-1.4029e+00,-1.6061e+00,-6.4255e-03,-2.4039e+00,-1.2856e+00,-2.4039e+00,-8.8852e-01,-2.8600e+00,-2.8687e+00,-1.1652e+00,-2.4039e+00,1.7757e+00,-3.9011e+00,-3.9875e+00,-3.4711e+00,-2.8370e+00,-1.1652e+00,8.4212e-01,-8.0437e-01,-4.0574e+00,-1.6088e-01,-3.5159e+00,-2.8370e+00,-7.4907e-01,-1.0271e-01,-5.5169e-01,-2.4560e+00,-4.2469e-01,-3.5159e+00,-2.0157e+00,-2.4590e+00,4.2491e+00,5.1003e+00,4.2491e+00,5.2527e+00,4.2452e+00,4.4180e+00,4.2452e+00,4.6563e+00,4.2491e+00,2.2628e+00,4.2491e+00,2.4645e+00,5.4284e-01,-5.4284e-01,5.8617e-01,-5.8617e-01,9.7673e-02,-9.7673e-02,1.8992e-01,-1.8992e-01,3.8354e-01,-3.8354e-01,3.8442e-01,-3.8442e-01}
> Gradient: {-1.3719e-06,5.1561e-07,-2.9356e-06,-6.9677e-06,2.4816e-05,2.0744e-05,-2.6575e-05,2.4604e-05,7.8777e-06,-2.9356e-06,-3.5984e-06,3.5428e-05,-1.2809e-05,3.3021e-06,9.6301e-06,7.8777e-06,1.7504e-05,-2.0195e-06,1.0349e-06,-6.5855e-06,-6.9363e-06,9.6301e-06,2.9597e-05,-3.2548e-06,-1.4493e-06,5.2577e-06,1.8035e-06,-6.9363e-06,2.1371e-05,3.4386e-06,1.8872e-05,-2.0093e-07,-1.8087e-05,1.8035e-06,1.0261e-05,1.0837e-05,8.4982e-06,1.0201e-05,8.4982e-06,1.0505e-05,8.4903e-06,3.6806e-05,8.4903e-06,1.1842e-05,8.4982e-06,-7.5356e-07,8.4982e-06,1.4297e-05,2.1783e-05,-2.1783e-05,-2.5820e-05,2.5820e-05,2.8483e-06,-2.8483e-06,-2.7116e-06,2.7116e-06,-1.2874e-05,1.2874e-05,-1.3761e-05,1.3761e-05}
>>>> Re-trying (3/3).
After: gradient norm = 1.1089519230861222E-4
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5862,-0.5862}
Count Table 2:
---------------
h: {0.0977,-0.0977}
Count Table 3:
---------------
h: {0.1899,-0.1899}
Count Table 4:
---------------
h: {0.3835,-0.3835}
Count Table 5:
---------------
h: {0.3844,-0.3844}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-1.5144,-1.9796,-1.4029,-1.0056,-1.2856,-1.4063,-0.0064,-1.6061,-0.8885,-2.4039,-2.4039,-1.2856,-2.8687,-2.8600,-3.9011,1.7757,-1.1652,-2.4039,-3.4711,-3.9875,-0.8044,0.8421,-2.8370,-1.1652,-0.1609,-4.0574,-0.1027,-0.7491,-3.5159,-2.8370,-2.4560,-0.5517,-2.4590,-2.0157,-0.4247,-3.5159,-2.0157,-2.4590,-0.5517,-2.4560,-3.5159,-0.4247,-0.7491,-0.1027,-4.0574,-0.1609,-2.8370,-3.5159,0.8421,-0.8044,-3.9875,-3.4711,-1.1652,-2.8370,1.7757,-3.9011,-2.8600,-2.8687,-2.4039,-1.1652,-2.4039,-0.8885,-1.6061,-0.0064,-1.2856,-2.4039,-1.0056,-1.4029,-1.9796,-1.5144,-1.4063,-1.2856}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {4.2491,5.1003}
Activity(exp=1): {4.2491,5.2527}
Activity(exp=2): {4.2452,4.4180}
Activity(exp=3): {4.2452,4.6563}
Activity(exp=4): {4.2491,2.2628}
Activity(exp=5): {4.2491,2.4645}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
Suggested variations:
key=12;3;0, description = Initial model.
> Optimizing variation "Initial model." (component2-2-variation0).
>> Starting new optimization: component2-2-variation0. (2021-05-21 18:14:03.652).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.674216846081103
gradient = {-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 1.1089519230861225E-4
Starting Function Value: 3.674216846081103
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.674216807290734 0.000696836961700 6.283743660956771 0.000131439046231
2 4 3.674216766747938 0.000537721931271 1.000000000000000 0.000109178856620
3 7 3.674216632216953 0.002335952895166 0.660000000000000 0.000111107051658
4 8 3.674216443589388 0.006146448937992 1.000000000000000 0.000228127176371
5 9 3.674216260597036 0.006563228658028 1.000000000000000 0.000244678829535
6 10 3.674216020287787 0.001572732419983 1.000000000000000 0.000125235024878
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9784e+00,-1.5136e+00,-1.2848e+00,-1.4045e+00,-1.0095e+00,-1.4046e+00,-1.5993e+00,-9.3506e-03,-2.4058e+00,-1.2848e+00,-2.4027e+00,-8.9345e-01,-2.8568e+00,-2.8694e+00,-1.1674e+00,-2.4058e+00,1.7786e+00,-3.9005e+00,-3.9876e+00,-3.4695e+00,-2.8354e+00,-1.1674e+00,8.4038e-01,-8.0180e-01,-4.0570e+00,-1.5971e-01,-3.5163e+00,-2.8354e+00,-7.5246e-01,-1.0045e-01,-5.5242e-01,-2.4552e+00,-4.2014e-01,-3.5163e+00,-2.0168e+00,-2.4604e+00,4.2471e+00,5.0978e+00,4.2471e+00,5.2502e+00,4.2431e+00,4.4111e+00,4.2431e+00,4.6550e+00,4.2471e+00,2.2630e+00,4.2471e+00,2.4612e+00,5.4281e-01,-5.4281e-01,5.8617e-01,-5.8617e-01,9.7460e-02,-9.7460e-02,1.8990e-01,-1.8990e-01,3.8350e-01,-3.8350e-01,3.8436e-01,-3.8436e-01}
> Gradient: {-1.8734e-06,3.2918e-06,2.7577e-06,-3.7036e-06,-7.8713e-06,-1.6569e-05,2.6188e-06,-1.0712e-05,7.8528e-06,2.7577e-06,-8.0042e-08,-2.6405e-05,-1.4017e-05,2.0399e-06,8.7910e-06,7.8528e-06,-3.7267e-05,-2.6713e-06,3.5670e-07,-5.7043e-06,-6.8426e-06,8.7910e-06,-2.5821e-05,-6.0513e-06,-2.2814e-06,-9.2721e-06,1.7175e-06,-6.8426e-06,-9.5873e-06,-9.0053e-06,-4.3992e-05,-9.3427e-06,3.7552e-05,1.7175e-06,-1.0889e-05,-1.0317e-05,8.4941e-06,1.0196e-05,8.4941e-06,1.0500e-05,8.4862e-06,-4.1617e-06,8.4862e-06,2.3770e-05,8.4941e-06,-9.5269e-07,8.4941e-06,1.4132e-05,9.2353e-06,-9.2353e-06,-2.7299e-05,2.7299e-05,-1.1495e-05,1.1495e-05,-1.6454e-05,1.6454e-05,-2.6271e-05,2.6271e-05,-3.5950e-05,3.5950e-05}
>>>> Re-trying (1/3).
Starting Function Value: 3.674216165036283
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.674216122990435 0.000668092615220 5.333301423029973 0.000118406742848
2 4 3.674216088531880 0.000464532058956 1.000000000000000 0.000093905679408
3 5 3.674215984999164 0.002288877941288 1.000000000000000 0.000113988806811
4 6 3.674215897197922 0.002907868617099 1.000000000000000 0.000187296305217
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9785e+00,-1.5142e+00,-1.2850e+00,-1.4042e+00,-1.0093e+00,-1.4041e+00,-1.5998e+00,-9.2075e-03,-2.4064e+00,-1.2850e+00,-2.4028e+00,-8.9217e-01,-2.8556e+00,-2.8696e+00,-1.1682e+00,-2.4064e+00,1.7796e+00,-3.9003e+00,-3.9877e+00,-3.4690e+00,-2.8348e+00,-1.1682e+00,8.4105e-01,-8.0187e-01,-4.0568e+00,-1.5965e-01,-3.5165e+00,-2.8348e+00,-7.5203e-01,-1.0066e-01,-5.5000e-01,-2.4546e+00,-4.2317e-01,-3.5165e+00,-2.0163e+00,-2.4599e+00,4.2464e+00,5.0970e+00,4.2464e+00,5.2493e+00,4.2424e+00,4.4108e+00,4.2424e+00,4.6526e+00,4.2464e+00,2.2631e+00,4.2464e+00,2.4600e+00,5.4284e-01,-5.4284e-01,5.8601e-01,-5.8601e-01,9.7615e-02,-9.7615e-02,1.8999e-01,-1.8999e-01,3.8361e-01,-3.8361e-01,3.8453e-01,-3.8453e-01}
> Gradient: {1.0651e-05,1.2957e-05,2.2870e-06,-2.9575e-06,1.2879e-05,2.5887e-05,1.1635e-05,1.8741e-05,7.6918e-06,2.2870e-06,3.1647e-06,1.8183e-05,-1.3116e-05,1.1503e-06,7.6448e-06,7.6918e-06,5.0178e-05,-3.1464e-06,8.0070e-07,-5.3888e-06,-6.8418e-06,7.6448e-06,3.6450e-05,1.7737e-05,-1.7887e-06,2.0802e-05,1.7761e-06,-6.8418e-06,6.5214e-06,2.9933e-05,2.8459e-05,3.1877e-06,2.2847e-06,1.7761e-06,9.4077e-06,5.2869e-06,8.4927e-06,1.0194e-05,8.4927e-06,1.0499e-05,8.4848e-06,3.3707e-05,8.4848e-06,2.8491e-05,8.4927e-06,-5.4208e-07,8.4927e-06,1.3959e-05,2.1089e-05,-2.1089e-05,-1.0145e-04,1.0145e-04,-1.1971e-05,1.1971e-05,8.3335e-07,-8.3335e-07,1.1294e-05,-1.1294e-05,2.5362e-05,-2.5362e-05}
>>>> Re-trying (2/3).
Starting Function Value: 3.674217131048808
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 6 3.674215870308422 0.000254436703043 1.357541834122882 0.000104948270800
2 7 3.674215851959819 0.000411365747180 1.000000000000000 0.000065870751261
Gradient = {5.3046e-06,6.4731e-06,1.1282e-06,-3.9814e-06,3.2085e-06,8.3472e-06,5.3076e-06,3.3460e-06,7.6635e-06,1.1282e-06,6.8391e-07,2.3510e-06,-1.3673e-05,7.0974e-07,7.4355e-06,7.6635e-06,1.0410e-05,-3.3656e-06,4.6943e-07,-6.0288e-06,-6.8585e-06,7.4355e-06,8.1085e-06,6.0541e-06,-2.1760e-06,6.5432e-06,1.7529e-06,-6.8585e-06,-9.9514e-07,1.0914e-05,1.0876e-05,-7.9816e-07,-5.7881e-06,1.7529e-06,2.8753e-06,2.6233e-07,8.4926e-06,1.0194e-05,8.4926e-06,1.0498e-05,8.4847e-06,2.4756e-05,8.4847e-06,1.6924e-05,8.4926e-06,-5.8751e-07,8.4926e-06,1.3912e-05,-4.6085e-06,4.6085e-06,2.1585e-05,-2.1585e-05,8.0484e-06,-8.0484e-06,8.3814e-06,-8.3814e-06,-1.8948e-06,1.8948e-06,-3.6541e-06,3.6541e-06}
pCurr = {-3.7075e-05,-4.5189e-05,-7.9133e-06,2.1699e-05,-3.0251e-05,-6.9455e-05,-3.8287e-05,-3.8019e-05,-4.4198e-05,-7.9133e-06,-6.9494e-06,-3.2817e-05,7.8132e-05,-4.6104e-06,-4.3101e-05,-4.4198e-05,-1.0842e-04,1.9140e-05,-3.1001e-06,3.3979e-05,3.9506e-05,-4.3101e-05,-8.1248e-05,-4.9097e-05,1.2077e-05,-5.5055e-05,-1.0130e-05,3.9506e-05,-3.3839e-06,-8.6076e-05,-8.4105e-05,-2.3444e-07,2.3533e-05,-1.0130e-05,-2.4513e-05,-7.6122e-06,-4.8943e-05,-5.8747e-05,-4.8943e-05,-6.0502e-05,-4.8897e-05,-1.5354e-04,-4.8897e-05,-1.1159e-04,-4.8943e-05,3.3257e-06,-4.8943e-05,-8.0249e-05,-2.0802e-06,2.0802e-06,1.1411e-05,-1.1411e-05,-2.5133e-05,2.5133e-05,-4.1170e-05,4.1170e-05,-4.3310e-06,4.3310e-06,-1.2991e-05,1.2991e-05}
grad*pCur = -2.0457153661297655E-8
parameters = {-1.9786e+00,-1.5142e+00,-1.2850e+00,-1.4042e+00,-1.0094e+00,-1.4042e+00,-1.5998e+00,-9.2879e-03,-2.4064e+00,-1.2850e+00,-2.4028e+00,-8.9225e-01,-2.8555e+00,-2.8696e+00,-1.1682e+00,-2.4064e+00,1.7794e+00,-3.9003e+00,-3.9877e+00,-3.4690e+00,-2.8348e+00,-1.1682e+00,8.4090e-01,-8.0195e-01,-4.0568e+00,-1.5975e-01,-3.5165e+00,-2.8348e+00,-7.5206e-01,-1.0080e-01,-5.5013e-01,-2.4547e+00,-4.2317e-01,-3.5165e+00,-2.0163e+00,-2.4599e+00,4.2463e+00,5.0969e+00,4.2463e+00,5.2492e+00,4.2424e+00,4.4107e+00,4.2424e+00,4.6525e+00,4.2463e+00,2.2631e+00,4.2463e+00,2.4599e+00,5.4278e-01,-5.4278e-01,5.8627e-01,-5.8627e-01,9.7624e-02,-9.7624e-02,1.8995e-01,-1.8995e-01,3.8357e-01,-3.8357e-01,3.8445e-01,-3.8445e-01}
|grad|/|x| = 3.323851959053614E-6
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9786e+00,-1.5142e+00,-1.2850e+00,-1.4042e+00,-1.0094e+00,-1.4042e+00,-1.5998e+00,-9.2878e-03,-2.4064e+00,-1.2850e+00,-2.4028e+00,-8.9225e-01,-2.8555e+00,-2.8696e+00,-1.1682e+00,-2.4064e+00,1.7794e+00,-3.9003e+00,-3.9877e+00,-3.4690e+00,-2.8348e+00,-1.1682e+00,8.4090e-01,-8.0195e-01,-4.0568e+00,-1.5975e-01,-3.5165e+00,-2.8348e+00,-7.5206e-01,-1.0080e-01,-5.5013e-01,-2.4547e+00,-4.2317e-01,-3.5165e+00,-2.0163e+00,-2.4599e+00,4.2463e+00,5.0969e+00,4.2463e+00,5.2492e+00,4.2424e+00,4.4107e+00,4.2424e+00,4.6525e+00,4.2463e+00,2.2631e+00,4.2463e+00,2.4599e+00,5.4278e-01,-5.4278e-01,5.8627e-01,-5.8627e-01,9.7625e-02,-9.7625e-02,1.8995e-01,-1.8995e-01,3.8357e-01,-3.8357e-01,3.8445e-01,-3.8445e-01}
> Gradient: {5.3046e-06,6.4731e-06,1.1282e-06,-3.9814e-06,3.2085e-06,8.3472e-06,5.3076e-06,3.3460e-06,7.6635e-06,1.1282e-06,6.8391e-07,2.3510e-06,-1.3673e-05,7.0974e-07,7.4355e-06,7.6635e-06,1.0410e-05,-3.3656e-06,4.6943e-07,-6.0288e-06,-6.8585e-06,7.4355e-06,8.1085e-06,6.0541e-06,-2.1760e-06,6.5432e-06,1.7529e-06,-6.8585e-06,-9.9514e-07,1.0914e-05,1.0876e-05,-7.9816e-07,-5.7881e-06,1.7529e-06,2.8753e-06,2.6233e-07,8.4926e-06,1.0194e-05,8.4926e-06,1.0498e-05,8.4847e-06,2.4756e-05,8.4847e-06,1.6924e-05,8.4926e-06,-5.8751e-07,8.4926e-06,1.3912e-05,-4.6085e-06,4.6085e-06,2.1585e-05,-2.1585e-05,8.0484e-06,-8.0484e-06,8.3814e-06,-8.3814e-06,-1.8948e-06,1.8948e-06,-3.6541e-06,3.6541e-06}
>>>> Re-trying (3/3).
After: gradient norm = 6.583704399205123E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5863,-0.5863}
Count Table 2:
---------------
h: {0.0976,-0.0976}
Count Table 3:
---------------
h: {0.1900,-0.1900}
Count Table 4:
---------------
h: {0.3836,-0.3836}
Count Table 5:
---------------
h: {0.3844,-0.3844}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-1.5142,-1.9786,-1.4042,-1.0094,-1.2850,-1.4042,-0.0093,-1.5998,-0.8922,-2.4028,-2.4064,-1.2850,-2.8696,-2.8555,-3.9003,1.7794,-1.1682,-2.4064,-3.4690,-3.9877,-0.8019,0.8409,-2.8348,-1.1682,-0.1597,-4.0568,-0.1008,-0.7521,-3.5165,-2.8348,-2.4547,-0.5501,-2.4599,-2.0163,-0.4232,-3.5165,-2.0163,-2.4599,-0.5501,-2.4547,-3.5165,-0.4232,-0.7521,-0.1008,-4.0568,-0.1597,-2.8348,-3.5165,0.8409,-0.8019,-3.9877,-3.4690,-1.1682,-2.8348,1.7794,-3.9003,-2.8555,-2.8696,-2.4064,-1.1682,-2.4028,-0.8922,-1.5998,-0.0093,-1.2850,-2.4064,-1.0094,-1.4042,-1.9786,-1.5142,-1.4042,-1.2850}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {4.2463,5.0969}
Activity(exp=1): {4.2463,5.2492}
Activity(exp=2): {4.2424,4.4107}
Activity(exp=3): {4.2424,4.6525}
Activity(exp=4): {4.2463,2.2631}
Activity(exp=5): {4.2463,2.4599}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;4;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component2-2-variation1).
>> Starting new optimization: component2-2-variation1. (2021-05-21 18:15:21.937).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.6742123961115865
gradient = {0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 6.409487664000965E-5
Starting Function Value: 3.6742123961115865
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 6 3.674212383264353 0.000169001912530 2.636746045693795 0.000049632705996
2 7 3.674212368046645 0.000406843608828 1.000000000000000 0.000072904289578
3 8 3.674212322414391 0.001493646718351 1.000000000000000 0.000145358407549
4 9 3.674212232382373 0.003295165098166 1.000000000000000 0.000228441791064
5 10 3.674212013646268 0.008578112039728 1.000000000000000 0.000337992074581
6 11 3.674211592346059 0.017923860817281 1.000000000000000 0.000429931984960
7 12 3.674210956529429 0.031709123879467 1.000000000000000 0.000483773557060
8 13 3.674210099576291 0.058681665967310 1.000000000000000 0.000384065254041
9 14 3.674209201007574 0.020444473270603 1.000000000000000 0.000253569713264
10 15 3.674208128928137 0.031269387970991 1.000000000000000 0.000509467003117
11 16 3.674207485235665 0.024896504245078 1.000000000000000 0.000621483690275
12 17 3.674206455456199 0.045825172322999 1.000000000000000 0.000514333197055
13 18 3.674206158907713 0.069603882747092 1.000000000000000 0.000857375569580
14 19 3.674205274891067 0.003645758656619 1.000000000000000 0.000244420625400
15 20 3.674205076718566 0.001730517530246 1.000000000000000 0.000244933144857
16 21 3.674204466192347 0.017042413431650 1.000000000000000 0.000405244105536
17 22 3.674203460488525 0.040157961518116 1.000000000000000 0.000563335058005
18 23 3.674203003497718 0.089129121103565 1.000000000000000 0.000992488229941
19 24 3.674201633259614 0.022896931041351 1.000000000000000 0.000368816765529
20 25 3.674201330917643 0.005188785069639 1.000000000000000 0.000172022835998
21 26 3.674201216637008 0.008293980930387 1.000000000000000 0.000132572595252
22 27 3.674201111128956 0.006349064168759 1.000000000000000 0.000178547473539
23 28 3.674200792869703 0.018758249597544 1.000000000000000 0.000331449597487
24 29 3.674200130505514 0.035936487290230 1.000000000000000 0.000518559806647
25 30 3.674199085424048 0.058410820789656 1.000000000000000 0.000577065968705
26 32 3.674198523278290 0.040297082038236 0.477130821773989 0.000732725102708
27 33 3.674197653186909 0.031440364966780 1.000000000000000 0.000367329046474
28 34 3.674197056892928 0.013970070132422 1.000000000000000 0.000234134990291
29 35 3.674196658134758 0.007874819519971 1.000000000000000 0.000380595206559
30 36 3.674195723680447 0.027304271522007 1.000000000000000 0.000628327110737
31 37 3.674194303573062 0.069105383713618 1.000000000000000 0.000790802886768
32 38 3.674191865789224 0.128582015322736 1.000000000000000 0.000653930209454
33 39 3.674188740660717 0.161976542760203 1.000000000000000 0.000354024846300
34 40 3.674185510637667 0.198569774391485 1.000000000000000 0.000433528069226
35 41 3.674183286638322 0.114993579815063 1.000000000000000 0.000725641588216
36 42 3.674180662446046 0.111089204579806 1.000000000000000 0.000792705364829
37 43 3.674176852642946 0.231263666708222 1.000000000000000 0.000812745897708
38 44 3.674173784839547 0.092532916360249 1.000000000000000 0.000482174667743
39 46 3.674173126089075 0.021284875165665 0.260100461651495 0.000417858998798
40 47 3.674171146462737 0.082245227692484 1.000000000000000 0.000413645843115
41 48 3.674170392266306 0.042322281539576 1.000000000000000 0.000382500192937
42 49 3.674167717077284 0.145032886333406 1.000000000000000 0.000348789017102
43 50 3.674165689049699 0.126184233215555 1.000000000000000 0.000526852560592
44 51 3.674163321906042 0.127221140096000 1.000000000000000 0.000689055791686
45 53 3.674162833014363 0.018895042218506 0.167656477153609 0.000660193597677
46 54 3.674158877006644 0.180203026930281 1.000000000000000 0.000253770788639
47 55 3.674158165362187 0.049331256795405 1.000000000000000 0.000268672477776
48 56 3.674156579805403 0.077598583155095 1.000000000000000 0.000585891588575
49 57 3.674154864184421 0.088173046830926 1.000000000000000 0.000802664613943
50 58 3.674152268487422 0.150410957775992 1.000000000000000 0.000774698205014
51 59 3.674148198601622 0.230049552969571 1.000000000000000 0.000471086973913
52 60 3.674143003685050 0.359234651867660 1.000000000000000 0.000364423061000
53 61 3.674140479719026 0.165020537413098 1.000000000000000 0.000681171940711
54 62 3.674137500099288 0.173561627161661 1.000000000000000 0.000793125410626
55 63 3.674132127232114 0.299956786532576 1.000000000000000 0.000600011760619
56 64 3.674123690028403 0.534167702583246 1.000000000000000 0.000247702205155
57 65 3.674119698192627 0.300584307559565 1.000000000000000 0.000509589123969
58 66 3.674115380109640 0.251513815352653 1.000000000000000 0.000732781013273
59 67 3.674108197387890 0.431582269697708 1.000000000000000 0.000801824195272
60 68 3.674088984426830 1.257314502692329 1.000000000000000 0.001319362180023
61 69 3.674069155206268 1.299260184120131 1.000000000000000 0.000627032246743
62 70 3.674054600595934 0.951656517023677 1.000000000000000 0.000416303252345
63 71 3.674046293384731 0.452713146329776 1.000000000000000 0.000497764792125
64 72 3.674038915702010 0.668135302025027 1.000000000000000 0.000527267808760
65 73 3.674026211749762 0.872898126772549 1.000000000000000 0.001010896739031
66 74 3.674021806193902 0.226509029345721 1.000000000000000 0.000246012928509
67 75 3.674019341766160 0.099485462035625 1.000000000000000 0.000170096106297
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.1918e+00,-1.7359e+00,-1.3743e+00,-1.6449e+00,-1.2309e+00,-1.6190e+00,-1.5752e+00,3.1054e-02,-3.6528e+00,-1.3743e+00,-2.3678e+00,-8.5779e-01,-2.0461e+00,-2.1167e+00,-7.0783e-01,-3.6528e+00,2.5797e+00,-3.2376e+00,-3.7775e+00,-3.3005e+00,-2.0075e+00,-7.0783e-01,1.1318e+00,-5.1973e-01,-3.6177e+00,2.1291e-01,-3.6688e+00,-2.0075e+00,-3.7548e-01,2.7521e-01,-7.0621e-02,-1.9896e+00,7.0174e-02,-3.6688e+00,-1.5424e+00,-1.9801e+00,1.5894e+00,1.9077e+00,1.5894e+00,1.9647e+00,1.5879e+00,9.0573e-01,1.5879e+00,1.1311e+00,1.5894e+00,-1.6531e+00,1.5894e+00,-1.2113e+00,5.4283e-01,-5.4283e-01,5.8622e-01,-5.8622e-01,9.7435e-02,-9.7435e-02,1.8902e-01,-1.8902e-01,3.8286e-01,-3.8286e-01,3.8371e-01,-3.8371e-01}
> Gradient: {3.5209e-05,5.1986e-06,-5.3152e-07,-3.2636e-05,-5.7277e-05,7.6790e-06,-2.2682e-05,1.4497e-05,-1.4814e-05,-5.3152e-07,1.6688e-05,-3.5516e-05,7.6393e-06,4.5419e-06,-1.9646e-05,-1.4814e-05,2.9774e-06,-2.0594e-05,-1.0430e-05,-4.6451e-05,4.2883e-05,-1.9646e-05,7.7585e-06,-1.4009e-05,2.7379e-05,-5.3066e-05,-1.0562e-05,4.2883e-05,-6.4171e-07,-4.5888e-05,-2.1248e-05,-2.2399e-05,1.3715e-05,-1.0562e-05,3.4612e-06,-2.8626e-06,3.1787e-06,3.8155e-06,3.1787e-06,3.9295e-06,3.1757e-06,5.1169e-05,3.1757e-06,-1.2344e-05,3.1787e-06,-2.4913e-05,3.1787e-06,-1.7152e-05,2.0841e-05,-2.0841e-05,-7.3765e-07,7.3765e-07,-1.9709e-05,1.9709e-05,3.6472e-06,-3.6472e-06,1.5132e-05,-1.5132e-05,-6.3321e-06,6.3321e-06}
>>>> Re-trying (1/3).
Starting Function Value: 3.6740206547140857
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.674020301821916 0.004112455568270 24.196012602703470 0.000483665116969
2 4 3.674019721105887 0.003960130809306 1.000000000000000 0.000423192977771
3 5 3.674016609899626 0.037771466774084 1.000000000000000 0.000463316193338
4 7 3.674016097201097 0.008204730733364 0.266199165765256 0.000370046284840
5 8 3.674015737157168 0.007162462349166 1.000000000000000 0.000243538538626
6 9 3.674015312761342 0.007351820308777 1.000000000000000 0.000230709513420
7 10 3.674014718455892 0.011009476056671 1.000000000000000 0.000409014828638
8 11 3.674013662229451 0.016228289684813 1.000000000000000 0.000560569427602
9 12 3.674010428344072 0.055813167729234 1.000000000000000 0.000840948295345
10 14 3.674009321584946 0.027918274749226 0.285129350868312 0.001012821019838
11 15 3.674006868344484 0.041032567883725 1.000000000000000 0.000582783677912
12 16 3.674005658273461 0.018845925308767 1.000000000000000 0.000292467239930
13 17 3.674005290787755 0.006158231739641 1.000000000000000 0.000366194977538
14 18 3.674004581468679 0.003993916945439 1.000000000000000 0.000406066612791
15 19 3.674002563240400 0.022611840374444 1.000000000000000 0.000584453537535
16 20 3.674000388998962 0.045732188345239 1.000000000000000 0.000661774771441
17 22 3.673999979106681 0.007944304496597 0.087527198044793 0.000539767349496
18 24 3.673999797935661 0.004300559351490 0.092711336040300 0.000503269922663
19 25 3.673998238608521 0.056123811898139 1.000000000000000 0.000211247898847
20 26 3.673997873202462 0.011150157397140 1.000000000000000 0.000249919561251
21 27 3.673996162057740 0.047775396271205 1.000000000000000 0.000432347699943
22 28 3.673994792456788 0.031682636259877 1.000000000000000 0.000379206252044
23 29 3.673992907913702 0.043478492469874 1.000000000000000 0.000241135772568
24 30 3.673991622774882 0.030033610289567 1.000000000000000 0.000167171093590
25 31 3.673990802237752 0.022344430400761 1.000000000000000 0.000246821237006
26 32 3.673990075453377 0.020265939603720 1.000000000000000 0.000295156524302
27 33 3.673988471812492 0.041942583524328 1.000000000000000 0.000325790448567
28 34 3.673987824161572 0.041994828885606 1.000000000000000 0.000157326521100
29 36 3.673987774342863 0.001612298034664 0.048121480237838 0.000155903224813
30 37 3.673986104527560 0.067116337578719 1.000000000000000 0.000285951936174
31 38 3.673985229088740 0.031997690334132 1.000000000000000 0.000297886157315
32 39 3.673982712335255 0.092026468056428 1.000000000000000 0.000247813406873
33 40 3.673981304369826 0.060818249414699 1.000000000000000 0.000243786871324
34 41 3.673980574310482 0.025398426963275 1.000000000000000 0.000194645089565
35 42 3.673980040355599 0.016480396099697 1.000000000000000 0.000200635442360
36 43 3.673979157982387 0.032296581182960 1.000000000000000 0.000147001482760
37 44 3.673977984711249 0.063517465809193 1.000000000000000 0.000127670586393
38 45 3.673977076447013 0.047140007731631 1.000000000000000 0.000192161846105
39 47 3.673976937470577 0.014791335144441 0.215157039614234 0.000193212729889
40 48 3.673974647402722 0.118895464327745 1.000000000000000 0.000187186005850
41 49 3.673973500274302 0.074435135020082 1.000000000000000 0.000341546253937
42 50 3.673972663438093 0.045746050889527 1.000000000000000 0.000197596636129
43 51 3.673972302327912 0.013848279361447 1.000000000000000 0.000079863116970
44 52 3.673972118043592 0.009394202654277 1.000000000000000 0.000091973241817
45 54 3.673972073862528 0.000326259967456 0.029129738148288 0.000093473930531
46 55 3.673971322720803 0.039678386997453 1.000000000000000 0.000234717829167
47 56 3.673970827078153 0.034594990345683 1.000000000000000 0.000248243981226
48 57 3.673969293470005 0.103369586710547 1.000000000000000 0.000197547197283
49 58 3.673967534011505 0.146631313603446 1.000000000000000 0.000172767120230
50 59 3.673966341565410 0.115970752206866 1.000000000000000 0.000185035949191
51 60 3.673965668205502 0.038286982255307 1.000000000000000 0.000148654487411
52 61 3.673964993955925 0.034640022936971 1.000000000000000 0.000143921290281
53 62 3.673963701847578 0.062847706920324 1.000000000000000 0.000162755441689
54 63 3.673960636228239 0.210249201618678 1.000000000000000 0.000177504738330
55 64 3.673957655121555 0.234808950389627 1.000000000000000 0.000287702995342
56 65 3.673954153997042 0.292923522778363 1.000000000000000 0.000201073688719
57 66 3.673951532041472 0.132887407489219 1.000000000000000 0.000183983885521
58 67 3.673948624834301 0.122523798465891 1.000000000000000 0.000158638256307
59 69 3.673948593127416 0.005454204337912 0.085874751538938 0.000153698931353
60 70 3.673946071510354 0.115950103772531 1.000000000000000 0.000090429280051
61 71 3.673945374051311 0.024943049109320 1.000000000000000 0.000078275678976
62 72 3.673943407906943 0.106971364110550 1.000000000000000 0.000222086507113
63 73 3.673942167257746 0.068617567310547 1.000000000000000 0.000213915399024
64 74 3.673940689803333 0.109742156281451 1.000000000000000 0.000139939251357
65 75 3.673939598987275 0.054987748191522 1.000000000000000 0.000074737917764
66 76 3.673939229557438 0.025451911987107 1.000000000000000 0.000098989205834
67 77 3.673938949135958 0.019281528327748 1.000000000000000 0.000112752777033
68 78 3.673938421591652 0.041947639372159 1.000000000000000 0.000098713249656
69 79 3.673938141048263 0.030015043837483 1.000000000000000 0.000049690005893
70 80 3.673938026761893 0.013048634579534 1.000000000000000 0.000044172241366
71 81 3.673937923549558 0.009990796291387 1.000000000000000 0.000068328292038
72 82 3.673937714252330 0.020044663963973 1.000000000000000 0.000102746757241
73 83 3.673937262007029 0.043107705896152 1.000000000000000 0.000139912098384
74 84 3.673936680560966 0.073356395693127 1.000000000000000 0.000129923127241
75 85 3.673936131293609 0.085889213523200 1.000000000000000 0.000154982087162
76 86 3.673935839826374 0.064675162633870 1.000000000000000 0.000057547894774
77 87 3.673935656782385 0.021922045793090 1.000000000000000 0.000080735149705
78 88 3.673935515032480 0.013017246293690 1.000000000000000 0.000087607619909
79 89 3.673935163176676 0.043561371582607 1.000000000000000 0.000144397093877
80 90 3.673934647195735 0.075344986622103 1.000000000000000 0.000177411099576
81 91 3.673934075828298 0.101789281269588 1.000000000000000 0.000126705205005
82 92 3.673933702044373 0.074208872406851 1.000000000000000 0.000053356856360
83 93 3.673933367410177 0.023118992403289 1.000000000000000 0.000040060939566
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9796e+00,-1.5150e+00,-1.3093e+00,-1.3980e+00,-1.0098e+00,-1.4045e+00,-1.6455e+00,-5.7643e-02,-2.2199e+00,-1.3093e+00,-2.4440e+00,-9.3972e-01,-2.2162e+00,-2.2839e+00,-6.6402e-01,-2.2199e+00,2.3687e+00,-3.2877e+00,-3.4715e+00,-2.9824e+00,-2.1730e+00,-6.6402e-01,1.3139e+00,-3.2614e-01,-3.5453e+00,3.5386e-01,-3.1121e+00,-2.1730e+00,-2.3880e-01,4.1230e-01,-9.6516e-03,-1.9111e+00,1.1853e-01,-3.1121e+00,-1.4720e+00,-1.9167e+00,1.1631e+00,1.3961e+00,1.1631e+00,1.4378e+00,1.1620e+00,2.6392e-01,1.1620e+00,5.0735e-01,1.1631e+00,-1.6750e+00,1.1631e+00,-1.6756e+00,5.4280e-01,-5.4280e-01,5.8620e-01,-5.8620e-01,9.7696e-02,-9.7696e-02,1.9009e-01,-1.9009e-01,3.8410e-01,-3.8410e-01,3.8450e-01,-3.8450e-01}
> Gradient: {-2.9772e-06,3.4723e-06,-3.6601e-07,1.9813e-07,3.7524e-06,3.1173e-06,1.9607e-06,6.4435e-07,3.9657e-06,-3.6601e-07,-8.1958e-07,1.8117e-06,9.8072e-06,-3.9189e-06,-3.3363e-06,3.9657e-06,4.2149e-06,-2.2832e-06,1.0747e-05,-1.9830e-06,4.7476e-06,-3.3363e-06,-2.0279e-06,3.0177e-07,-2.6981e-06,1.8586e-06,-6.7394e-07,4.7476e-06,-2.0722e-06,7.2875e-06,6.2951e-06,-3.5563e-06,1.6586e-06,-6.7394e-07,2.3563e-06,2.3698e-06,2.3262e-06,2.7922e-06,2.3262e-06,2.8756e-06,2.3240e-06,2.7082e-06,2.3240e-06,-3.1601e-06,2.3262e-06,9.6967e-06,2.3262e-06,6.4270e-06,6.6626e-06,-6.6626e-06,-1.2143e-05,1.2143e-05,-7.7440e-06,7.7440e-06,1.1325e-05,-1.1325e-05,3.9023e-06,-3.9023e-06,-5.7328e-06,5.7328e-06}
>>>> Re-trying (2/3).
Starting Function Value: 3.6739335945078397
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673933563650904 0.000163055928178 4.072147059511531 0.000035757957593
2 4 3.673933560774734 0.000111050722021 1.000000000000000 0.000034615301195
3 5 3.673933434374991 0.004110889662040 1.000000000000000 0.000092355757160
4 6 3.673933432867243 0.005963921626921 1.000000000000000 0.000196983255091
5 7 3.673933358191955 0.004189417904829 1.000000000000000 0.000139622891920
6 8 3.673932398842344 0.008995965367256 1.000000000000000 0.000084760251786
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9765e+00,-1.5174e+00,-1.3090e+00,-1.3981e+00,-1.0121e+00,-1.4056e+00,-1.6466e+00,-5.6927e-02,-2.2236e+00,-1.3090e+00,-2.4430e+00,-9.3961e-01,-2.2251e+00,-2.2803e+00,-6.6098e-01,-2.2236e+00,2.3688e+00,-3.2856e+00,-3.4813e+00,-2.9805e+00,-2.1773e+00,-6.6098e-01,1.3183e+00,-3.2499e-01,-3.5428e+00,3.5332e-01,-3.1115e+00,-2.1773e+00,-2.3663e-01,4.0817e-01,-1.2862e-02,-1.9077e+00,1.1720e-01,-3.1115e+00,-1.4735e+00,-1.9184e+00,1.1610e+00,1.3935e+00,1.1610e+00,1.4351e+00,1.1599e+00,2.6314e-01,1.1599e+00,5.1042e-01,1.1610e+00,-1.6840e+00,1.1610e+00,-1.6815e+00,5.4276e-01,-5.4276e-01,5.8622e-01,-5.8622e-01,9.7637e-02,-9.7637e-02,1.9013e-01,-1.9013e-01,3.8409e-01,-3.8409e-01,3.8438e-01,-3.8438e-01}
> Gradient: {8.9483e-06,-5.1466e-06,3.0911e-06,2.5756e-06,-8.6087e-06,-1.8737e-06,-5.7364e-06,5.4481e-06,3.7846e-06,3.0911e-06,-1.4735e-07,-7.4540e-06,5.0120e-06,-2.5594e-06,-2.2592e-06,3.7846e-06,-1.8069e-06,-1.9371e-06,7.0561e-06,-3.0225e-06,4.4164e-06,-2.2592e-06,9.0717e-06,-1.5029e-05,-1.4239e-06,6.9998e-06,-6.1863e-07,4.4164e-06,1.6517e-05,-2.5657e-05,-2.2915e-05,8.5623e-06,1.6413e-05,-6.1863e-07,-2.1434e-06,9.3582e-07,2.3219e-06,2.7870e-06,2.3219e-06,2.8703e-06,2.3197e-06,-1.7572e-05,2.3197e-06,1.4861e-05,2.3219e-06,8.6224e-06,2.3219e-06,5.6361e-06,-1.2473e-05,1.2473e-05,-3.9609e-06,3.9609e-06,2.9790e-06,-2.9790e-06,-1.0768e-05,1.0768e-05,1.5074e-05,-1.5074e-05,-3.7371e-05,3.7371e-05}
>>>> Re-trying (3/3).
After: gradient norm = 8.480347632413151E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5862,-0.5862}
Count Table 2:
---------------
h: {0.0976,-0.0976}
Count Table 3:
---------------
h: {0.1901,-0.1901}
Count Table 4:
---------------
h: {0.3841,-0.3841}
Count Table 5:
---------------
h: {0.3844,-0.3844}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-1.5174,-1.9765,-1.4056,-1.0121,-1.3090,-1.3981,-0.0569,-1.6466,-0.9396,-2.4430,-2.2236,-1.3090,-2.2803,-2.2251,-3.2856,2.3688,-0.6610,-2.2236,-2.9805,-3.4813,-0.3250,1.3183,-2.1773,-0.6610,0.3533,-3.5428,0.4082,-0.2366,-3.1115,-2.1773,-1.9077,-0.0129,-1.9184,-1.4735,0.1172,-3.1115,-1.4735,-1.9184,-0.0129,-1.9077,-3.1115,0.1172,-0.2366,0.4082,-3.5428,0.3533,-2.1773,-3.1115,1.3183,-0.3250,-3.4813,-2.9805,-0.6610,-2.1773,2.3688,-3.2856,-2.2251,-2.2803,-2.2236,-0.6610,-2.4430,-0.9396,-1.6466,-0.0569,-1.3090,-2.2236,-1.0121,-1.4056,-1.9765,-1.5174,-1.3981,-1.3090}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {1.1610,1.3935}
Activity(exp=1): {1.1610,1.4351}
Activity(exp=2): {1.1599,0.2631}
Activity(exp=3): {1.1599,0.5104}
Activity(exp=4): {1.1610,-1.6840}
Activity(exp=5): {1.1610,-1.6815}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;5;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component2-2-variation2).
>> Starting new optimization: component2-2-variation2. (2021-05-21 18:21:34.339).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.676549485697434
gradient = {0.0080,0.0016,0.0004,0.0004,0.0020,0.0020,0.0078,0.0038,0.0000,0.0004,0.0003,0.0020,0.0001,0.0001,0.0000,0.0000,0.0141,0.0000,0.0001,0.0001,0.0000,0.0000,0.0058,0.0083,0.0001,0.0031,0.0000,0.0000,0.0013,0.0098,0.0069,0.0008,0.0040,0.0000,0.0019,0.0008,0.0000,0.0000,0.0000,0.0000,0.0000,0.0035,0.0000,0.0037,0.0000,-0.0001,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0107,0.0107,-0.0112,0.0112,-0.0010,0.0010,-0.0012,0.0012}
gradient norm = 0.03382658326054013
Starting Function Value: 3.676549485697434
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.675254379335506 0.079262551324533 2.343202998483004 0.011802367318186
2 4 3.675015277228927 0.024190760933255 1.000000000000000 0.009030526482864
3 5 3.674340652322634 0.122280447114569 1.000000000000000 0.007704057595854
4 6 3.673937281499769 0.118452978274811 1.000000000000000 0.009753273236859
5 7 3.673618597503239 0.202524338254828 1.000000000000000 0.007901762428919
6 8 3.673527749446486 0.025161321555918 1.000000000000000 0.001811478495787
7 9 3.673519846659879 0.011279205716781 1.000000000000000 0.001192666880196
8 10 3.673511280681717 0.012672403779402 1.000000000000000 0.001189691524973
9 11 3.673495240519102 0.024763078403902 1.000000000000000 0.001686672035279
10 12 3.673472747192025 0.052267230293482 1.000000000000000 0.002049513245340
11 14 3.673463507778556 0.028562294955590 0.477575774801446 0.001833771566683
12 15 3.673456124392323 0.018085880311997 1.000000000000000 0.000756896215219
13 16 3.673454035134138 0.007427189147076 1.000000000000000 0.000407538936055
14 17 3.673453129955080 0.003830826096878 1.000000000000000 0.000460418774497
15 18 3.673450075271571 0.017881914380784 1.000000000000000 0.000799740828221
16 19 3.673448350824101 0.024119030517444 1.000000000000000 0.001351066427896
17 20 3.673446141414225 0.003704644845818 1.000000000000000 0.000528478739511
18 22 3.673445913203402 0.000570820963008 0.089033698786624 0.000488667717206
19 23 3.673444656668883 0.009788195483095 1.000000000000000 0.000318762056421
20 24 3.673444153310252 0.004121677373950 1.000000000000000 0.000371838259798
21 25 3.673441969753766 0.025252957149016 1.000000000000000 0.000665680891778
22 27 3.673441285754554 0.008619309680197 0.306973176179398 0.000554677087558
23 28 3.673440620897887 0.005082342916883 1.000000000000000 0.000301367230897
24 29 3.673440210644216 0.004401127122507 1.000000000000000 0.000181291413514
25 30 3.673439968584400 0.002806171859246 1.000000000000000 0.000231918510280
26 31 3.673438944755951 0.013793176613236 1.000000000000000 0.000433290407024
27 32 3.673437689256993 0.020198714038141 1.000000000000000 0.000500622377864
28 33 3.673435576088279 0.033367978324981 1.000000000000000 0.000396811832511
29 34 3.673432680088935 0.055537123216963 1.000000000000000 0.000185277118055
30 35 3.673430956484354 0.041275570763324 1.000000000000000 0.000265172149644
31 36 3.673429742588757 0.030404995595038 1.000000000000000 0.000368020682540
32 37 3.673428743485757 0.022152024779713 1.000000000000000 0.000316997778454
33 38 3.673427673349068 0.020478856775710 1.000000000000000 0.000191940621652
34 39 3.673426375518919 0.026673224750455 1.000000000000000 0.000320864784409
35 40 3.673424994903856 0.032593709480754 1.000000000000000 0.000505230516053
36 41 3.673423517089969 0.039339974860125 1.000000000000000 0.000487557232699
37 42 3.673421351976470 0.055711745253480 1.000000000000000 0.000188153952535
38 43 3.673420661191485 0.017501025785815 1.000000000000000 0.000106964180167
39 44 3.673420442012672 0.006010655908959 1.000000000000000 0.000147570304796
40 45 3.673420007652763 0.011844542831376 1.000000000000000 0.000157151123232
41 46 3.673418765564497 0.040038762679475 1.000000000000000 0.000202294966685
42 47 3.673417842030343 0.043937492332577 1.000000000000000 0.000154283647767
43 48 3.673417538389945 0.018007294146592 1.000000000000000 0.000057044966408
44 49 3.673417442746968 0.004713699248080 1.000000000000000 0.000076264201422
45 50 3.673417312786754 0.005529942242874 1.000000000000000 0.000076614982870
46 51 3.673416916647960 0.020435334326235 1.000000000000000 0.000056473806881
47 52 3.673416583119749 0.025532954320824 1.000000000000000 0.000057764647841
48 53 3.673416430395848 0.016110027704716 1.000000000000000 0.000043795193195
49 54 3.673416344676715 0.009404354018975 1.000000000000000 0.000040259022290
50 55 3.673416238595774 0.009647338870566 1.000000000000000 0.000041112033471
51 56 3.673416077221472 0.018950385685195 1.000000000000000 0.000073429021889
52 57 3.673416030782267 0.006562459893740 1.000000000000000 0.000016228984028
53 58 3.673416011789809 0.001920009439101 1.000000000000000 0.000015139786026
54 59 3.673415992367512 0.001918734115561 1.000000000000000 0.000015830712155
55 62 3.673415898279707 0.011108912946585 0.660000000000000 0.000023578567704
56 63 3.673415575404059 0.035642276052041 1.000000000000000 0.000048500543395
57 64 3.673415547211173 0.037665082652747 1.000000000000000 0.000059127740921
58 65 3.673415404660775 0.030310702009744 1.000000000000000 0.000041100256126
59 66 3.673415250234740 0.029166640292811 1.000000000000000 0.000026506623148
60 67 3.673415094891789 0.029346277956943 1.000000000000000 0.000033511827148
61 68 3.673414820663036 0.054332191401473 1.000000000000000 0.000056871445204
62 69 3.673414302429950 0.109203821891463 1.000000000000000 0.000078722883797
63 70 3.673413496448102 0.209526447079102 1.000000000000000 0.000117773048162
64 71 3.673412918869432 0.224753833428220 1.000000000000000 0.000077183943992
65 72 3.673412327856800 0.040916499668446 1.000000000000000 0.000040818027723
66 73 3.673411973423879 0.025966628190147 1.000000000000000 0.000050732613290
67 74 3.673411631264545 0.044206118059365 1.000000000000000 0.000070133969550
68 75 3.673410510457428 0.209363374190207 1.000000000000000 0.000109179781718
69 76 3.673409069998739 0.347567604506800 1.000000000000000 0.000122741721868
70 78 3.673408845003267 0.049801843543549 0.107421137126793 0.000112822383526
71 79 3.673407021901080 0.639023663592976 1.000000000000000 0.000045450888061
72 80 3.673406649048344 0.087590779244066 1.000000000000000 0.000048614596268
73 81 3.673405910434875 0.174547191747765 1.000000000000000 0.000065086635418
74 82 3.673405477457071 0.100045422010359 1.000000000000000 0.000069803641981
75 83 3.673404939689759 0.080950350504666 1.000000000000000 0.000054616268508
76 84 3.673404285617476 0.133182295419565 1.000000000000000 0.000098870160834
77 85 3.673403938130402 0.096519165088218 1.000000000000000 0.000087664173496
78 86 3.673403335058173 0.175019789521765 1.000000000000000 0.000048191037510
79 87 3.673402925582526 0.130629120169042 1.000000000000000 0.000040477488484
80 88 3.673402606818388 0.071106330339645 1.000000000000000 0.000075650100584
81 89 3.673401973217180 0.126956680746528 1.000000000000000 0.000118941026183
82 91 3.673401909832223 0.010254614864273 0.052655300047036 0.000119762915973
83 92 3.673399584541214 0.543360652280746 1.000000000000000 0.000095861520305
84 93 3.673398968435874 0.286778415047398 1.000000000000000 0.000119793261685
85 94 3.673398519575671 0.039155289929267 1.000000000000000 0.000044493322921
86 96 3.673398446010179 0.004587465448130 0.129102826532900 0.000041462941921
87 97 3.673397441417727 0.059162374888344 1.000000000000000 0.000051034152441
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.1109e+00,-1.2857e+00,-1.1300e+00,-1.2406e+00,-7.4863e-01,-1.1247e+00,-1.6890e+00,2.1660e-01,-2.2608e+00,-1.1300e+00,-2.1107e+00,-6.6668e-01,-2.1727e+00,-2.1504e+00,-5.7006e-01,-2.2608e+00,2.4098e+00,-3.1087e+00,-3.4022e+00,-2.8087e+00,-2.1250e+00,-5.7006e-01,1.4561e+00,-4.0308e-01,-3.4391e+00,4.4758e-01,-3.0504e+00,-2.1250e+00,-1.1378e-01,4.2770e-01,6.3394e-03,-1.7857e+00,1.2869e-01,-3.0504e+00,-1.3494e+00,-1.8024e+00,8.0771e-02,9.6951e-02,8.0771e-02,9.9848e-02,8.0696e-02,-1.2003e+00,8.0696e-02,-9.4219e-01,8.0771e-02,-2.5444e+00,8.0771e-02,-2.9581e+00,5.4278e-01,-5.4278e-01,5.8620e-01,-5.8620e-01,1.0738e-01,-1.0738e-01,2.0303e-01,-2.0303e-01,3.8790e-01,-3.8790e-01,3.8702e-01,-3.8702e-01}
> Gradient: {3.9308e-06,-3.3801e-06,-9.4478e-07,3.3922e-06,-7.5080e-06,2.7146e-06,-9.5670e-06,1.2433e-05,-3.1727e-06,-9.4478e-07,1.0266e-06,-1.5710e-06,6.3919e-06,9.4715e-07,-4.4770e-06,-3.1727e-06,-5.4979e-07,-1.7844e-06,-1.1165e-06,5.8881e-07,2.8799e-06,-4.4770e-06,-3.2980e-06,2.7780e-06,-4.2980e-06,2.2389e-06,-6.4127e-07,2.8799e-06,-5.2718e-08,-2.7715e-06,1.2886e-05,-6.7876e-06,-1.6818e-06,-6.4127e-07,-1.3961e-05,7.5410e-06,1.6154e-07,1.9390e-07,1.6154e-07,1.9970e-07,1.6139e-07,2.0712e-06,1.6139e-07,-3.9390e-06,1.6154e-07,1.8498e-06,1.6154e-07,-8.8852e-07,-5.7624e-06,5.7624e-06,-9.6159e-06,9.6159e-06,1.1426e-05,-1.1426e-05,-8.0598e-07,8.0598e-07,4.4820e-06,-4.4820e-06,2.2349e-05,-2.2349e-05}
>>>> Re-trying (1/3).
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.1109e+00,-1.2857e+00,-1.1300e+00,-1.2406e+00,-7.4863e-01,-1.1247e+00,-1.6890e+00,2.1660e-01,-2.2608e+00,-1.1300e+00,-2.1107e+00,-6.6668e-01,-2.1727e+00,-2.1504e+00,-5.7006e-01,-2.2608e+00,2.4098e+00,-3.1087e+00,-3.4022e+00,-2.8087e+00,-2.1250e+00,-5.7006e-01,1.4561e+00,-4.0308e-01,-3.4391e+00,4.4758e-01,-3.0504e+00,-2.1250e+00,-1.1378e-01,4.2770e-01,6.3394e-03,-1.7857e+00,1.2869e-01,-3.0504e+00,-1.3494e+00,-1.8024e+00,8.0771e-02,9.6951e-02,8.0771e-02,9.9848e-02,8.0696e-02,-1.2003e+00,8.0696e-02,-9.4219e-01,8.0771e-02,-2.5444e+00,8.0771e-02,-2.9581e+00,5.4278e-01,-5.4278e-01,5.8620e-01,-5.8620e-01,1.0738e-01,-1.0738e-01,2.0303e-01,-2.0303e-01,3.8790e-01,-3.8790e-01,3.8702e-01,-3.8702e-01}
> Gradient: {3.9308e-06,-3.3801e-06,-9.4478e-07,3.3922e-06,-7.5080e-06,2.7146e-06,-9.5670e-06,1.2433e-05,-3.1727e-06,-9.4478e-07,1.0266e-06,-1.5710e-06,6.3919e-06,9.4715e-07,-4.4770e-06,-3.1727e-06,-5.4979e-07,-1.7844e-06,-1.1165e-06,5.8881e-07,2.8799e-06,-4.4770e-06,-3.2980e-06,2.7780e-06,-4.2980e-06,2.2389e-06,-6.4127e-07,2.8799e-06,-5.2718e-08,-2.7715e-06,1.2886e-05,-6.7876e-06,-1.6818e-06,-6.4127e-07,-1.3961e-05,7.5410e-06,1.6154e-07,1.9390e-07,1.6154e-07,1.9970e-07,1.6139e-07,2.0712e-06,1.6139e-07,-3.9390e-06,1.6154e-07,1.8498e-06,1.6154e-07,-8.8852e-07,-5.7624e-06,5.7624e-06,-9.5984e-06,9.5984e-06,1.1426e-05,-1.1426e-05,-8.0598e-07,8.0598e-07,4.4820e-06,-4.4820e-06,2.2349e-05,-2.2349e-05}
>>>> Re-trying (2/3).
Starting Function Value: 3.6733980306563376
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673398025416280 0.000202706535717 3.997286062788233 0.000040505748580
2 4 3.673398021386835 0.000133138814637 1.000000000000000 0.000039170059904
3 5 3.673397963619780 0.003334561349360 1.000000000000000 0.000051494314722
4 7 3.673397958584957 0.000249505332913 0.079035661398834 0.000044513792050
5 8 3.673397945508707 0.001563575870703 1.000000000000000 0.000041392922249
6 9 3.673397941090874 0.000738968849923 1.000000000000000 0.000062442151978
7 10 3.673397935743065 0.000148175569002 1.000000000000000 0.000042935013524
8 11 3.673397917565332 0.001201692876845 1.000000000000000 0.000033624073784
9 12 3.673397901795080 0.001202137873895 1.000000000000000 0.000032523258056
10 14 3.673397896620316 0.000477218644045 0.272430830114311 0.000033091961162
Gradient = {-6.0814e-07,-3.6305e-07,1.4287e-07,1.7021e-06,2.9557e-06,-1.8517e-06,3.7236e-06,-1.6616e-06,-3.1399e-06,1.4287e-07,2.5088e-07,2.6619e-06,4.3852e-06,-2.2315e-07,-4.0750e-06,-3.1399e-06,6.2700e-06,-2.0874e-06,-1.4086e-06,-6.1107e-07,2.7753e-06,-4.0750e-06,3.1453e-06,1.3039e-06,-4.2677e-06,6.8289e-07,-6.5314e-07,2.7753e-06,-1.1505e-06,3.7430e-06,4.9553e-06,-4.1175e-07,-8.3381e-06,-6.5314e-07,5.3751e-06,2.0240e-07,1.6142e-07,1.9375e-07,1.6142e-07,1.9954e-07,1.6127e-07,7.7562e-07,1.6127e-07,1.2968e-07,1.6142e-07,1.1054e-06,1.6142e-07,-1.0314e-06,-1.0905e-05,1.0905e-05,-5.8086e-06,5.8086e-06,-4.3279e-06,4.3279e-06,-1.2353e-05,1.2353e-05,-7.0516e-06,7.0516e-06,-9.9346e-07,9.9346e-07}
pCurr = {2.0735e-05,6.2497e-04,-5.3647e-05,-8.5347e-04,3.0050e-04,6.7690e-04,4.7037e-04,2.2442e-04,1.0293e-03,-5.3647e-05,-2.3676e-04,-7.1765e-04,-1.7145e-03,-9.7136e-05,1.3970e-03,1.0293e-03,-2.3432e-04,6.1308e-04,4.4915e-04,5.4485e-05,-9.2146e-04,1.3970e-03,-3.0005e-04,3.1425e-04,1.4109e-03,2.7353e-04,2.1301e-04,-9.2146e-04,5.1845e-04,-5.0101e-04,-5.6714e-04,1.2261e-03,-1.3116e-04,2.1301e-04,1.0642e-03,-8.1166e-04,-5.2784e-05,-6.3357e-05,-5.2784e-05,-6.5250e-05,-5.2734e-05,6.3602e-04,-5.2734e-05,-9.8670e-05,-5.2784e-05,-4.2654e-04,-5.2784e-05,2.5019e-04,3.8103e-05,-3.8103e-05,1.7897e-05,-1.7897e-05,1.3210e-05,-1.3210e-05,3.2406e-05,-3.2406e-05,1.9051e-06,-1.9051e-06,4.7691e-06,-4.7691e-06}
grad*pCur = -4.463872220813601E-8
parameters = {-2.1116e+00,-1.2847e+00,-1.1299e+00,-1.2419e+00,-7.4695e-01,-1.1247e+00,-1.6867e+00,2.1469e-01,-2.2596e+00,-1.1299e+00,-2.1111e+00,-6.6705e-01,-2.1750e+00,-2.1507e+00,-5.6836e-01,-2.2596e+00,2.4099e+00,-3.1081e+00,-3.4017e+00,-2.8089e+00,-2.1261e+00,-5.6836e-01,1.4564e+00,-4.0315e-01,-3.4374e+00,4.4750e-01,-3.0502e+00,-2.1261e+00,-1.1344e-01,4.2781e-01,4.3654e-03,-1.7835e+00,1.2762e-01,-3.0502e+00,-1.3457e+00,-1.8044e+00,8.0709e-02,9.6876e-02,8.0709e-02,9.9770e-02,8.0633e-02,-1.1998e+00,8.0633e-02,-9.4182e-01,8.0709e-02,-2.5451e+00,8.0709e-02,-2.9578e+00,5.4277e-01,-5.4277e-01,5.8621e-01,-5.8621e-01,1.0736e-01,-1.0736e-01,2.0306e-01,-2.0306e-01,3.8787e-01,-3.8787e-01,3.8696e-01,-3.8696e-01}
|grad|/|x| = 2.7486212980150634E-6
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.1116e+00,-1.2847e+00,-1.1299e+00,-1.2419e+00,-7.4695e-01,-1.1247e+00,-1.6867e+00,2.1469e-01,-2.2596e+00,-1.1299e+00,-2.1111e+00,-6.6705e-01,-2.1750e+00,-2.1507e+00,-5.6836e-01,-2.2596e+00,2.4099e+00,-3.1081e+00,-3.4017e+00,-2.8089e+00,-2.1261e+00,-5.6836e-01,1.4564e+00,-4.0315e-01,-3.4374e+00,4.4750e-01,-3.0502e+00,-2.1261e+00,-1.1344e-01,4.2781e-01,4.3654e-03,-1.7835e+00,1.2762e-01,-3.0502e+00,-1.3457e+00,-1.8044e+00,8.0709e-02,9.6876e-02,8.0709e-02,9.9770e-02,8.0633e-02,-1.1998e+00,8.0633e-02,-9.4182e-01,8.0709e-02,-2.5451e+00,8.0709e-02,-2.9578e+00,5.4277e-01,-5.4277e-01,5.8621e-01,-5.8621e-01,1.0736e-01,-1.0736e-01,2.0306e-01,-2.0306e-01,3.8787e-01,-3.8787e-01,3.8696e-01,-3.8696e-01}
> Gradient: {-6.0814e-07,-3.6305e-07,1.4287e-07,1.7021e-06,2.9557e-06,-1.8517e-06,3.7236e-06,-1.6616e-06,-3.1399e-06,1.4287e-07,2.5088e-07,2.6619e-06,4.3852e-06,-2.2315e-07,-4.0750e-06,-3.1399e-06,6.2700e-06,-2.0874e-06,-1.4086e-06,-6.1107e-07,2.7753e-06,-4.0750e-06,3.1453e-06,1.3039e-06,-4.2677e-06,6.8289e-07,-6.5314e-07,2.7753e-06,-1.1505e-06,3.7430e-06,4.9553e-06,-4.1175e-07,-8.3381e-06,-6.5314e-07,5.3751e-06,2.0240e-07,1.6142e-07,1.9375e-07,1.6142e-07,1.9954e-07,1.6127e-07,7.7562e-07,1.6127e-07,1.2968e-07,1.6142e-07,1.1054e-06,1.6142e-07,-1.0314e-06,-1.0905e-05,1.0905e-05,-5.8086e-06,5.8086e-06,-4.3279e-06,4.3279e-06,-1.2353e-05,1.2353e-05,-7.0516e-06,7.0516e-06,-9.9346e-07,9.9346e-07}
>>>> Re-trying (3/3).
After: gradient norm = 3.309364427175176E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5862,-0.5862}
Count Table 2:
---------------
h: {0.1074,-0.1074}
Count Table 3:
---------------
h: {0.2031,-0.2031}
Count Table 4:
---------------
h: {0.3879,-0.3879}
Count Table 5:
---------------
h: {0.3870,-0.3870}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-1.2847,-2.1116,-1.1247,-0.7470,-1.1299,-1.2419,0.2147,-1.6867,-0.6671,-2.1111,-2.2596,-1.1299,-2.1507,-2.1750,-3.1081,2.4099,-0.5684,-2.2596,-2.8089,-3.4017,-0.4032,1.4564,-2.1261,-0.5684,0.4475,-3.4374,0.4278,-0.1134,-3.0502,-2.1261,-1.7835,0.0044,-1.8044,-1.3457,0.1276,-3.0502,-1.3457,-1.8044,0.0044,-1.7835,-3.0502,0.1276,-0.1134,0.4278,-3.4374,0.4475,-2.1261,-3.0502,1.4564,-0.4032,-3.4017,-2.8089,-0.5684,-2.1261,2.4099,-3.1081,-2.1750,-2.1507,-2.2596,-0.5684,-2.1111,-0.6671,-1.6867,0.2147,-1.1299,-2.2596,-0.7470,-1.1247,-2.1116,-1.2847,-1.2419,-1.1299}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0807,0.0969}
Activity(exp=1): {0.0807,0.0998}
Activity(exp=2): {0.0806,-1.1998}
Activity(exp=3): {0.0806,-0.9418}
Activity(exp=4): {0.0807,-2.5451}
Activity(exp=5): {0.0807,-2.9578}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;6;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component2-2-variation3).
>> Starting new optimization: component2-2-variation3. (2021-05-21 18:25:56.583).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.6733488074757448
gradient = {-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0001,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0002,0.0002,-0.0002,0.0002,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 4.50043034102875E-4
Starting Function Value: 3.6733488074757448
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673348552606020 0.001106434711218 2.458508692225979 0.000177860928570
2 4 3.673348492261068 0.000435373435093 1.000000000000000 0.000127926589252
3 5 3.673348386636551 0.001372337934033 1.000000000000000 0.000096275918644
4 6 3.673348292833670 0.001505830159231 1.000000000000000 0.000137983799912
5 7 3.673348094301907 0.005048638025869 1.000000000000000 0.000218213421699
6 8 3.673347120069368 0.007322735880012 1.000000000000000 0.000331827285811
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.1084e+00,-1.2847e+00,-1.1307e+00,-1.2424e+00,-7.4560e-01,-1.1236e+00,-1.6814e+00,2.1611e-01,-2.2590e+00,-1.1307e+00,-2.1107e+00,-6.6970e-01,-2.1680e+00,-2.1508e+00,-5.6764e-01,-2.2590e+00,2.4059e+00,-3.1077e+00,-3.4014e+00,-2.8089e+00,-2.1266e+00,-5.6764e-01,1.4627e+00,-4.0528e-01,-3.4365e+00,4.4646e-01,-3.0500e+00,-2.1266e+00,-1.1060e-01,4.3011e-01,2.5911e-03,-1.7834e+00,1.2656e-01,-3.0500e+00,-1.3455e+00,-1.7974e+00,8.0678e-02,9.6839e-02,8.0678e-02,9.9732e-02,8.0602e-02,-1.1981e+00,8.0602e-02,-9.4160e-01,8.0678e-02,-2.5453e+00,8.0678e-02,-2.9573e+00,5.4296e-01,-5.4296e-01,5.8629e-01,-5.8629e-01,1.0791e-01,-1.0791e-01,2.0413e-01,-2.0413e-01,3.8827e-01,-3.8827e-01,3.8710e-01,-3.8710e-01}
> Gradient: {1.4327e-05,8.8658e-06,3.2108e-06,2.8975e-06,1.7161e-05,2.1944e-05,1.4585e-05,3.9770e-05,-3.0832e-06,3.2108e-06,1.4644e-06,1.2459e-05,-3.1250e-05,2.1445e-06,-3.5891e-06,-3.0832e-06,1.0446e-04,-1.1214e-06,-2.6682e-06,-2.0699e-06,2.5560e-06,-3.5891e-06,7.6978e-05,-3.6483e-06,-4.1686e-06,7.3479e-06,-6.3678e-07,2.5560e-06,2.2631e-06,6.0197e-05,4.6250e-05,6.6608e-06,9.8420e-06,-6.3678e-07,6.4259e-06,-9.8283e-07,1.6136e-07,1.9368e-07,1.6136e-07,1.9946e-07,1.6120e-07,2.2737e-05,1.6120e-07,1.2235e-05,1.6136e-07,9.2743e-07,1.6136e-07,-1.7102e-06,8.0367e-05,-8.0367e-05,3.0845e-05,-3.0845e-05,-1.1442e-04,1.1442e-04,1.0543e-04,-1.0543e-04,9.7283e-05,-9.7283e-05,9.7711e-06,-9.7711e-06}
>>>> Re-trying (1/3).
Starting Function Value: 3.6733479107261355
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673347758460241 0.000907712715424 2.737137552516730 0.000129471731605
2 4 3.673347724880280 0.000341357879152 1.000000000000000 0.000088390276662
3 5 3.673347677611634 0.000951897479381 1.000000000000000 0.000081984356955
4 6 3.673347640601692 0.000988842863156 1.000000000000000 0.000116212828697
5 7 3.673347571429859 0.001792781623705 1.000000000000000 0.000147493468667
6 8 3.673347423910859 0.007073293250167 1.000000000000000 0.000257190247555
7 10 3.673347318954981 0.002064555746684 0.375309271587491 0.000140149817653
8 11 3.673347290500422 0.001214066414920 1.000000000000000 0.000076980318141
9 12 3.673347255906215 0.001040387602563 1.000000000000000 0.000092378602990
10 13 3.673347196195670 0.002109396932437 1.000000000000000 0.000146537683969
11 14 3.673347051298890 0.005982414536037 1.000000000000000 0.000243972800073
12 15 3.673346915328458 0.012613406098375 1.000000000000000 0.000350219480402
13 16 3.673346554653773 0.017847838209239 1.000000000000000 0.000344428152630
14 17 3.673346365835930 0.004740410613063 1.000000000000000 0.000162640715893
15 18 3.673346298874930 0.001548664163351 1.000000000000000 0.000078096256586
16 19 3.673346281065741 0.000421920015360 1.000000000000000 0.000079366172158
17 20 3.673346241666020 0.001372853898395 1.000000000000000 0.000107616760858
18 21 3.673346165420973 0.004258323518746 1.000000000000000 0.000109377104510
19 22 3.673346095791294 0.004457285128687 1.000000000000000 0.000056736761407
20 23 3.673346032713721 0.006225159437680 1.000000000000000 0.000070965166751
21 24 3.673346002983323 0.003435019410621 1.000000000000000 0.000111351602576
22 25 3.673345985022286 0.003357390667716 1.000000000000000 0.000097213860806
23 27 3.673345961255586 0.000182555910315 0.062304630090812 0.000093333228200
24 28 3.673345898683459 0.004578244573863 1.000000000000000 0.000051629863297
25 29 3.673345884366220 0.001202308290327 1.000000000000000 0.000064814343864
26 30 3.673345837222951 0.004865022761147 1.000000000000000 0.000073671491444
27 31 3.673345788324812 0.004759659095654 1.000000000000000 0.000048555245064
28 32 3.673345707024483 0.010316519307046 1.000000000000000 0.000041329159024
29 33 3.673345619166434 0.004953739363870 1.000000000000000 0.000058178421401
30 34 3.673345612389941 0.007757892051093 1.000000000000000 0.000049290671639
31 35 3.673345555091897 0.009455754303908 1.000000000000000 0.000092770194105
32 36 3.673345533438659 0.003068602200297 1.000000000000000 0.000023982608619
33 37 3.673345528482278 0.000938434600905 1.000000000000000 0.000018156914622
34 38 3.673345460196672 0.000724274388873 1.000000000000000 0.000020220165228
35 40 3.673345350621919 0.000132387671438 0.060168452750721 0.000020520165929
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0935e+00,-1.2745e+00,-1.1256e+00,-1.2379e+00,-7.3995e-01,-1.1160e+00,-1.6718e+00,2.1332e-01,-2.2439e+00,-1.1256e+00,-2.0932e+00,-6.6635e-01,-2.1003e+00,-2.1595e+00,-5.6441e-01,-2.2439e+00,2.3795e+00,-3.1063e+00,-3.3766e+00,-2.7770e+00,-2.1367e+00,-5.6441e-01,1.4574e+00,-3.9768e-01,-3.4018e+00,4.5434e-01,-3.0455e+00,-2.1367e+00,-9.9106e-02,4.3391e-01,2.5136e-03,-1.7672e+00,1.2892e-01,-3.0455e+00,-1.3325e+00,-1.7811e+00,7.9820e-02,9.5809e-02,7.9820e-02,9.8672e-02,7.9745e-02,-1.1969e+00,7.9745e-02,-9.4202e-01,7.9820e-02,-2.5432e+00,7.9820e-02,-2.9362e+00,5.4280e-01,-5.4280e-01,5.8621e-01,-5.8621e-01,1.0860e-01,-1.0860e-01,2.0448e-01,-2.0448e-01,3.8813e-01,-3.8813e-01,3.8729e-01,-3.8729e-01}
> Gradient: {4.1298e-06,1.6775e-07,4.9133e-07,1.0248e-06,-2.2788e-06,-4.7807e-06,2.9113e-06,2.9039e-06,-2.5172e-06,4.9133e-07,2.2714e-06,-7.3065e-06,2.8243e-06,-4.3251e-06,3.0923e-07,-2.5172e-06,3.8678e-06,-2.2342e-06,-2.1101e-06,2.0547e-06,1.1844e-06,3.0923e-07,-4.6558e-06,1.1423e-06,-2.9373e-06,2.2531e-06,-9.9703e-07,1.1844e-06,-5.5471e-07,-1.0236e-06,-2.8160e-06,-1.1187e-06,3.2104e-06,-9.9703e-07,-2.6584e-06,2.3045e-06,1.5964e-07,1.9162e-07,1.5964e-07,1.9734e-07,1.5949e-07,2.5007e-06,1.5949e-07,-1.1032e-06,1.5964e-07,-6.0744e-07,1.5964e-07,-1.4745e-06,6.2621e-06,-6.2621e-06,-4.3180e-06,4.3180e-06,-9.9238e-07,9.9238e-07,-3.7276e-06,3.7276e-06,-2.6604e-07,2.6604e-07,3.9823e-07,-3.9823e-07}
>>>> Re-trying (2/3).
Starting Function Value: 3.673345521134756
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673345519843951 0.000124626856472 6.072722725395646 0.000026732522181
2 4 3.673345518264728 0.000101077935132 1.000000000000000 0.000025219014426
3 5 3.673345510289849 0.002358526731263 1.000000000000000 0.000078348358753
4 7 3.673345503937950 0.000265977085092 0.479863162792597 0.000024901787408
5 11 3.673345502575676 0.000255626158197 0.504112275041316 0.000020358320101
6 12 3.673345495478379 0.000332394209795 1.000000000000000 0.000022515781081
7 13 3.673345494299776 0.000601915817242 1.000000000000000 0.000038512502999
Gradient = {-7.7547e-07,3.8122e-07,3.3783e-07,7.8158e-07,2.1660e-06,5.2269e-06,-8.3535e-08,1.6067e-06,-2.4857e-06,3.3783e-07,1.6382e-06,7.1045e-06,3.1375e-06,-3.5385e-06,3.2455e-07,-2.4857e-06,1.1650e-05,-1.7988e-06,-2.0671e-06,1.6539e-06,1.1536e-06,3.2455e-07,6.8012e-06,-5.7672e-07,-2.5489e-06,2.0579e-06,-9.7080e-07,1.1536e-06,1.9884e-06,5.6091e-06,3.6321e-06,5.8714e-07,1.1624e-06,-9.7080e-07,1.2568e-06,1.6219e-06,1.5956e-07,1.9152e-07,1.5956e-07,1.9725e-07,1.5941e-07,3.6313e-06,1.5941e-07,1.8869e-06,1.5956e-07,-3.6814e-07,1.5956e-07,-1.1528e-06,4.5463e-06,-4.5463e-06,-1.0959e-05,1.0959e-05,6.4507e-06,-6.4507e-06,1.6933e-05,-1.6933e-05,1.1465e-06,-1.1465e-06,-8.4532e-06,8.4532e-06}
pCurr = {6.5489e-05,5.7884e-05,-2.1167e-05,-6.6994e-05,1.1460e-04,9.6541e-06,7.4169e-05,9.8533e-05,2.3271e-04,-2.1167e-05,-1.7574e-04,-4.9035e-05,-2.8211e-04,3.6964e-04,-2.7771e-05,2.3271e-04,-2.4274e-04,1.8684e-04,1.9486e-04,-1.7348e-04,-1.0870e-04,-2.7771e-05,8.7547e-05,2.6413e-04,2.5624e-04,-7.0822e-05,9.1385e-05,-1.0870e-04,-1.6482e-05,8.4951e-05,1.1433e-04,2.6607e-05,1.0410e-04,9.1385e-05,9.1809e-05,-1.9166e-04,-1.4844e-05,-1.7818e-05,-1.4844e-05,-1.8350e-05,-1.4830e-05,-2.1971e-04,-1.4830e-05,1.3243e-04,-1.4844e-05,4.3135e-05,-1.4844e-05,1.2960e-04,4.4706e-07,-4.4706e-07,1.0555e-05,-1.0555e-05,-2.5582e-06,2.5582e-06,5.2818e-06,-5.2818e-06,9.5834e-07,-9.5834e-07,-1.4306e-06,1.4306e-06}
grad*pCur = -8.275994895249845E-9
parameters = {-2.0939e+00,-1.2745e+00,-1.1257e+00,-1.2381e+00,-7.3951e-01,-1.1154e+00,-1.6721e+00,2.1310e-01,-2.2433e+00,-1.1257e+00,-2.0937e+00,-6.6554e-01,-2.1010e+00,-2.1585e+00,-5.6448e-01,-2.2433e+00,2.3787e+00,-3.1057e+00,-3.3761e+00,-2.7774e+00,-2.1369e+00,-5.6448e-01,1.4581e+00,-3.9744e-01,-3.4011e+00,4.5395e-01,-3.0453e+00,-2.1369e+00,-9.9058e-02,4.3416e-01,2.9931e-03,-1.7670e+00,1.2869e-01,-3.0453e+00,-1.3320e+00,-1.7817e+00,7.9780e-02,9.5761e-02,7.9780e-02,9.8623e-02,7.9706e-02,-1.1975e+00,7.9706e-02,-9.4167e-01,7.9780e-02,-2.5430e+00,7.9780e-02,-2.9358e+00,5.4280e-01,-5.4280e-01,5.8620e-01,-5.8620e-01,1.0862e-01,-1.0862e-01,2.0456e-01,-2.0456e-01,3.8814e-01,-3.8814e-01,3.8727e-01,-3.8727e-01}
|grad|/|x| = 3.2244402432708447E-6
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0939e+00,-1.2745e+00,-1.1257e+00,-1.2381e+00,-7.3951e-01,-1.1154e+00,-1.6721e+00,2.1310e-01,-2.2433e+00,-1.1257e+00,-2.0937e+00,-6.6553e-01,-2.1010e+00,-2.1585e+00,-5.6448e-01,-2.2433e+00,2.3787e+00,-3.1057e+00,-3.3761e+00,-2.7774e+00,-2.1369e+00,-5.6448e-01,1.4581e+00,-3.9745e-01,-3.4011e+00,4.5396e-01,-3.0453e+00,-2.1369e+00,-9.9058e-02,4.3416e-01,2.9907e-03,-1.7670e+00,1.2869e-01,-3.0453e+00,-1.3320e+00,-1.7817e+00,7.9780e-02,9.5762e-02,7.9780e-02,9.8623e-02,7.9706e-02,-1.1975e+00,7.9706e-02,-9.4168e-01,7.9780e-02,-2.5430e+00,7.9780e-02,-2.9358e+00,5.4280e-01,-5.4280e-01,5.8620e-01,-5.8620e-01,1.0862e-01,-1.0862e-01,2.0456e-01,-2.0456e-01,3.8814e-01,-3.8814e-01,3.8727e-01,-3.8727e-01}
> Gradient: {-7.7547e-07,3.8122e-07,3.3783e-07,7.8158e-07,2.1660e-06,5.2269e-06,-8.3535e-08,1.6067e-06,-2.4857e-06,3.3783e-07,1.6382e-06,7.1045e-06,3.1375e-06,-3.5385e-06,3.2455e-07,-2.4857e-06,1.1650e-05,-1.7988e-06,-2.0671e-06,1.6539e-06,1.1536e-06,3.2455e-07,6.8012e-06,-5.7672e-07,-2.5489e-06,2.0579e-06,-9.7080e-07,1.1536e-06,1.9884e-06,5.6091e-06,3.6321e-06,5.8714e-07,1.1624e-06,-9.7080e-07,1.2568e-06,1.6219e-06,1.5956e-07,1.9152e-07,1.5956e-07,1.9725e-07,1.5941e-07,3.6313e-06,1.5941e-07,1.8869e-06,1.5956e-07,-3.6814e-07,1.5956e-07,-1.1528e-06,4.5463e-06,-4.5463e-06,-1.0959e-05,1.0959e-05,6.4507e-06,-6.4507e-06,1.6933e-05,-1.6933e-05,1.1465e-06,-1.1465e-06,-8.4532e-06,8.4532e-06}
>>>> Re-trying (3/3).
After: gradient norm = 3.858553718882495E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5862,-0.5862}
Count Table 2:
---------------
h: {0.1086,-0.1086}
Count Table 3:
---------------
h: {0.2046,-0.2046}
Count Table 4:
---------------
h: {0.3881,-0.3881}
Count Table 5:
---------------
h: {0.3873,-0.3873}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-1.2745,-2.0939,-1.1154,-0.7395,-1.1257,-1.2381,0.2131,-1.6721,-0.6655,-2.0937,-2.2433,-1.1257,-2.1585,-2.1010,-3.1057,2.3787,-0.5645,-2.2433,-2.7774,-3.3761,-0.3974,1.4581,-2.1369,-0.5645,0.4540,-3.4011,0.4342,-0.0991,-3.0453,-2.1369,-1.7670,0.0030,-1.7817,-1.3320,0.1287,-3.0453,-1.3320,-1.7817,0.0030,-1.7670,-3.0453,0.1287,-0.0991,0.4342,-3.4011,0.4540,-2.1369,-3.0453,1.4581,-0.3974,-3.3761,-2.7774,-0.5645,-2.1369,2.3787,-3.1057,-2.1010,-2.1585,-2.2433,-0.5645,-2.0937,-0.6655,-1.6721,0.2131,-1.1257,-2.2433,-0.7395,-1.1154,-2.0939,-1.2745,-1.2381,-1.1257}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0798,0.0958}
Activity(exp=1): {0.0798,0.0986}
Activity(exp=2): {0.0797,-1.1975}
Activity(exp=3): {0.0797,-0.9417}
Activity(exp=4): {0.0798,-2.5430}
Activity(exp=5): {0.0798,-2.9358}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;7;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component2-2-variation4).
>> Starting new optimization: component2-2-variation4. (2021-05-21 18:28:40.552).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.6733440619564623
gradient = {-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 3.117539414082324E-5
Starting Function Value: 3.6733440619564623
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673344060286883 0.000106093812043 3.403126567183701 0.000018078786433
2 4 3.673343847240586 0.000054643399119 1.000000000000000 0.000013194512583
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0939e+00,-1.2745e+00,-1.1257e+00,-1.2381e+00,-7.3951e-01,-1.1155e+00,-1.6721e+00,2.1310e-01,-2.2432e+00,-1.1257e+00,-2.0937e+00,-6.6558e-01,-2.1010e+00,-2.1585e+00,-5.6448e-01,-2.2432e+00,2.3786e+00,-3.1057e+00,-3.3761e+00,-2.7775e+00,-2.1370e+00,-5.6448e-01,1.4581e+00,-3.9744e-01,-3.4011e+00,4.5395e-01,-3.0453e+00,-2.1370e+00,-9.9057e-02,4.3412e-01,2.9789e-03,-1.7670e+00,1.2868e-01,-3.0453e+00,-1.3321e+00,-1.7817e+00,7.9779e-02,9.5760e-02,7.9779e-02,9.8622e-02,7.9705e-02,-1.1976e+00,7.9705e-02,-9.4168e-01,7.9779e-02,-2.5430e+00,7.9779e-02,-2.9358e+00,5.4279e-01,-5.4279e-01,5.8623e-01,-5.8623e-01,1.0861e-01,-1.0861e-01,2.0452e-01,-2.0452e-01,3.8814e-01,-3.8814e-01,3.8730e-01,-3.8730e-01}
> Gradient: {-1.8152e-06,-9.5974e-07,2.2928e-07,6.8699e-07,-1.2861e-06,1.8322e-06,-2.6089e-06,-1.6401e-06,-2.4818e-06,2.2928e-07,1.1432e-06,4.0458e-06,1.7224e-06,-3.4667e-06,3.5671e-07,-2.4818e-06,3.4940e-06,-1.7656e-06,-3.4799e-06,1.6719e-06,1.1605e-06,3.5671e-07,4.0787e-07,-2.2582e-06,-2.5746e-06,-7.7636e-07,-9.7098e-07,1.1605e-06,-1.0359e-06,2.0563e-06,-1.0801e-06,1.5306e-07,-4.1974e-07,-9.7098e-07,5.2803e-07,-3.5132e-07,1.5956e-07,1.9152e-07,1.5956e-07,1.9724e-07,1.5941e-07,1.5921e-06,1.5941e-07,-2.7203e-07,1.5956e-07,-5.3432e-07,1.5956e-07,-1.5038e-06,-1.3592e-06,1.3592e-06,3.0676e-06,-3.0676e-06,1.3516e-06,-1.3516e-06,-1.0084e-06,1.0084e-06,2.5166e-07,-2.5166e-07,3.3217e-06,-3.3217e-06}
>>>> Re-trying (1/3).
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0939e+00,-1.2745e+00,-1.1257e+00,-1.2381e+00,-7.3951e-01,-1.1155e+00,-1.6721e+00,2.1310e-01,-2.2432e+00,-1.1257e+00,-2.0937e+00,-6.6558e-01,-2.1010e+00,-2.1585e+00,-5.6448e-01,-2.2432e+00,2.3786e+00,-3.1057e+00,-3.3761e+00,-2.7775e+00,-2.1370e+00,-5.6448e-01,1.4581e+00,-3.9744e-01,-3.4011e+00,4.5395e-01,-3.0453e+00,-2.1370e+00,-9.9057e-02,4.3412e-01,2.9789e-03,-1.7670e+00,1.2868e-01,-3.0453e+00,-1.3321e+00,-1.7817e+00,7.9779e-02,9.5760e-02,7.9779e-02,9.8622e-02,7.9705e-02,-1.1976e+00,7.9705e-02,-9.4168e-01,7.9779e-02,-2.5430e+00,7.9779e-02,-2.9358e+00,5.4279e-01,-5.4279e-01,5.8623e-01,-5.8623e-01,1.0861e-01,-1.0861e-01,2.0452e-01,-2.0452e-01,3.8814e-01,-3.8814e-01,3.8730e-01,-3.8730e-01}
> Gradient: {-1.8152e-06,-9.5974e-07,2.2928e-07,6.8699e-07,-1.2861e-06,1.8322e-06,-2.6089e-06,-1.6401e-06,-2.4818e-06,2.2928e-07,1.1432e-06,4.0458e-06,1.7224e-06,-3.4667e-06,3.5671e-07,-2.4818e-06,3.4940e-06,-1.7656e-06,-3.4799e-06,1.6719e-06,1.1605e-06,3.5671e-07,4.0787e-07,-2.2582e-06,-2.5746e-06,-7.7636e-07,-9.7098e-07,1.1605e-06,-1.0359e-06,2.0563e-06,-1.0801e-06,1.5306e-07,-4.1974e-07,-9.7098e-07,5.2803e-07,-3.5132e-07,1.5956e-07,1.9152e-07,1.5956e-07,1.9724e-07,1.5941e-07,1.5921e-06,1.5941e-07,-2.7203e-07,1.5956e-07,-5.3432e-07,1.5956e-07,-1.5038e-06,-1.3592e-06,1.3592e-06,3.0676e-06,-3.0676e-06,1.3516e-06,-1.3516e-06,-1.0084e-06,1.0084e-06,2.5166e-07,-2.5166e-07,3.3217e-06,-3.3217e-06}
>>>> Re-trying (2/3).
Starting Function Value: 3.6733440594901703
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673344058911777 0.000100567697133 7.608931556443455 0.000019318116127
2 4 3.673344058028440 0.000084512796033 1.000000000000000 0.000018303414291
3 5 3.673344047754327 0.002052075555566 1.000000000000000 0.000032142354492
4 7 3.673344045072101 0.000518514879363 0.336855290438400 0.000024206710597
5 8 3.673344043697238 0.000118777595203 1.000000000000000 0.000018824076990
6 9 3.673344039618886 0.000668372969379 1.000000000000000 0.000026992930160
7 10 3.673344034678201 0.000979845728670 1.000000000000000 0.000042036819188
8 11 3.673344020286866 0.003244157221617 1.000000000000000 0.000065204968437
9 12 3.673344007684894 0.004792128132133 1.000000000000000 0.000099865512507
10 15 3.673344003516753 0.000596691603601 0.177964938136397 0.000086756011429
11 16 3.673343988553167 0.002746598219393 1.000000000000000 0.000022062268316
Gradient = {-3.5804e-06,3.5687e-07,-1.0619e-06,-1.3426e-06,3.1439e-06,2.3567e-06,4.7205e-06,-7.6892e-07,-2.2937e-06,-1.0619e-06,-2.4365e-06,1.7129e-06,1.7743e-06,-1.7100e-07,3.0237e-07,-2.2937e-06,-2.1408e-07,-3.4809e-07,-2.8080e-06,-1.8488e-06,9.4959e-07,3.0237e-07,8.2446e-06,-5.7899e-06,-1.3626e-06,4.7273e-06,-9.1855e-07,9.4959e-07,4.7981e-06,-9.1441e-06,5.9776e-06,-1.2501e-06,-3.4116e-06,-9.1855e-07,-2.8877e-06,1.5402e-06,1.5899e-07,1.9083e-07,1.5899e-07,1.9654e-07,1.5884e-07,-1.2620e-06,1.5884e-07,2.2371e-06,1.5899e-07,-2.1807e-07,1.5899e-07,-8.8630e-07,2.9275e-06,-2.9275e-06,-3.2693e-06,3.2693e-06,4.5134e-06,-4.5134e-06,-6.8642e-07,6.8642e-07,1.7849e-06,-1.7849e-06,1.9370e-06,-1.9370e-06}
pCurr = {2.3386e-05,1.6890e-05,2.5143e-06,-1.0456e-05,-5.6959e-06,1.1728e-05,-1.0648e-05,-2.8787e-05,8.8210e-05,2.5143e-06,-7.1032e-06,-5.8196e-06,-6.0711e-05,1.0003e-04,-1.3020e-05,8.8210e-05,-1.0016e-04,5.3868e-05,1.2030e-04,-3.2226e-05,-4.0342e-05,-1.3020e-05,-1.6800e-05,5.0303e-05,8.4058e-05,-3.1051e-05,3.4738e-05,-4.0342e-05,-1.3769e-05,3.4584e-05,-2.1731e-05,1.6415e-05,8.3846e-06,3.4738e-05,2.1518e-05,8.8942e-06,-5.7531e-06,-6.9056e-06,-5.7531e-06,-7.1119e-06,-5.7478e-06,-3.3089e-05,-5.7478e-06,-1.4048e-05,-5.7531e-06,1.8400e-05,-5.7531e-06,5.0178e-05,-2.8258e-06,2.8258e-06,1.2238e-05,-1.2238e-05,-7.7089e-06,7.7089e-06,-3.9202e-06,3.9202e-06,-4.4789e-06,4.4789e-06,-1.0428e-05,1.0428e-05}
grad*pCur = -2.597738123975208E-9
parameters = {-2.0929e+00,-1.2730e+00,-1.1259e+00,-1.2391e+00,-7.3810e-01,-1.1142e+00,-1.6701e+00,2.1269e-01,-2.2388e+00,-1.1259e+00,-2.0950e+00,-6.6612e-01,-2.1040e+00,-2.1526e+00,-5.6514e-01,-2.2388e+00,2.3743e+00,-3.1026e+00,-3.3699e+00,-2.7800e+00,-2.1390e+00,-5.6514e-01,1.4606e+00,-3.9540e-01,-3.3966e+00,4.5463e-01,-3.0435e+00,-2.1390e+00,-9.7760e-02,4.3336e-01,4.7062e-03,-1.7664e+00,1.2862e-01,-3.0435e+00,-1.3317e+00,-1.7805e+00,7.9493e-02,9.5417e-02,7.9493e-02,9.8268e-02,7.9419e-02,-1.1996e+00,7.9419e-02,-9.4123e-01,7.9493e-02,-2.5420e+00,7.9493e-02,-2.9331e+00,5.4280e-01,-5.4280e-01,5.8622e-01,-5.8622e-01,1.0863e-01,-1.0863e-01,2.0460e-01,-2.0460e-01,3.8816e-01,-3.8816e-01,3.8733e-01,-3.8733e-01}
|grad|/|x| = 1.8448300774464436E-6
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0929e+00,-1.2730e+00,-1.1259e+00,-1.2391e+00,-7.3810e-01,-1.1142e+00,-1.6701e+00,2.1269e-01,-2.2388e+00,-1.1259e+00,-2.0950e+00,-6.6612e-01,-2.1040e+00,-2.1526e+00,-5.6514e-01,-2.2388e+00,2.3743e+00,-3.1026e+00,-3.3699e+00,-2.7800e+00,-2.1390e+00,-5.6514e-01,1.4606e+00,-3.9540e-01,-3.3966e+00,4.5463e-01,-3.0435e+00,-2.1390e+00,-9.7760e-02,4.3336e-01,4.7062e-03,-1.7664e+00,1.2862e-01,-3.0435e+00,-1.3317e+00,-1.7805e+00,7.9493e-02,9.5417e-02,7.9493e-02,9.8268e-02,7.9419e-02,-1.1996e+00,7.9419e-02,-9.4123e-01,7.9493e-02,-2.5420e+00,7.9493e-02,-2.9331e+00,5.4280e-01,-5.4280e-01,5.8622e-01,-5.8622e-01,1.0863e-01,-1.0863e-01,2.0460e-01,-2.0460e-01,3.8816e-01,-3.8816e-01,3.8733e-01,-3.8733e-01}
> Gradient: {-3.5804e-06,3.5687e-07,-1.0619e-06,-1.3426e-06,3.1439e-06,2.3567e-06,4.7205e-06,-7.6892e-07,-2.2937e-06,-1.0619e-06,-2.4365e-06,1.7129e-06,1.7743e-06,-1.7100e-07,3.0237e-07,-2.2937e-06,-2.1408e-07,-3.4809e-07,-2.8080e-06,-1.8488e-06,9.4959e-07,3.0237e-07,8.2446e-06,-5.7899e-06,-1.3626e-06,4.7273e-06,-9.1855e-07,9.4959e-07,4.7981e-06,-9.1441e-06,5.9776e-06,-1.2501e-06,-3.4116e-06,-9.1855e-07,-2.8877e-06,1.5402e-06,1.5899e-07,1.9083e-07,1.5899e-07,1.9654e-07,1.5884e-07,-1.2620e-06,1.5884e-07,2.2371e-06,1.5899e-07,-2.1807e-07,1.5899e-07,-8.8630e-07,2.9275e-06,-2.9275e-06,-3.2693e-06,3.2693e-06,4.5134e-06,-4.5134e-06,-6.8642e-07,6.8642e-07,1.7849e-06,-1.7849e-06,1.9370e-06,-1.9370e-06}
>>>> Re-trying (3/3).
After: gradient norm = 2.2062268315702704E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5862,-0.5862}
Count Table 2:
---------------
h: {0.1086,-0.1086}
Count Table 3:
---------------
h: {0.2046,-0.2046}
Count Table 4:
---------------
h: {0.3882,-0.3882}
Count Table 5:
---------------
h: {0.3873,-0.3873}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-1.2730,-2.0929,-1.1142,-0.7381,-1.1259,-1.2391,0.2127,-1.6701,-0.6661,-2.0950,-2.2388,-1.1259,-2.1526,-2.1040,-3.1026,2.3743,-0.5651,-2.2388,-2.7800,-3.3699,-0.3954,1.4606,-2.1390,-0.5651,0.4546,-3.3966,0.4334,-0.0978,-3.0435,-2.1390,-1.7664,0.0047,-1.7805,-1.3317,0.1286,-3.0435,-1.3317,-1.7805,0.0047,-1.7664,-3.0435,0.1286,-0.0978,0.4334,-3.3966,0.4546,-2.1390,-3.0435,1.4606,-0.3954,-3.3699,-2.7800,-0.5651,-2.1390,2.3743,-3.1026,-2.1040,-2.1526,-2.2388,-0.5651,-2.0950,-0.6661,-1.6701,0.2127,-1.1259,-2.2388,-0.7381,-1.1142,-2.0929,-1.2730,-1.2391,-1.1259}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0795,0.0954}
Activity(exp=1): {0.0795,0.0983}
Activity(exp=2): {0.0794,-1.1996}
Activity(exp=3): {0.0794,-0.9412}
Activity(exp=4): {0.0795,-2.5420}
Activity(exp=5): {0.0795,-2.9331}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;8;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component2-2-variation5).
>> Starting new optimization: component2-2-variation5. (2021-05-21 18:30:04.147).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.673343986636629
gradient = {-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000}
gradient norm = 2.2060084022325913E-5
Starting Function Value: 3.673343986636629
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673343984077602 0.000230719961669 10.458707293932259 0.000039592674066
2 4 3.673343980465591 0.000204073292458 1.000000000000000 0.000034133960628
3 5 3.673343968931976 0.001777343975785 1.000000000000000 0.000049381062335
4 7 3.673343966120285 0.000223888567868 0.358568837373492 0.000016221425932
5 8 3.673343965344712 0.000228565300545 1.000000000000000 0.000012821221123
6 9 3.673343963713388 0.000178007917234 1.000000000000000 0.000014268583168
7 10 3.673343958942023 0.001013412427536 1.000000000000000 0.000036048885013
8 11 3.673343955201764 0.000721111846384 1.000000000000000 0.000022348440881
9 12 3.673343953221697 0.000620779449554 1.000000000000000 0.000014027647208
10 13 3.673343952389772 0.000422265101081 1.000000000000000 0.000012774006080
Gradient = {-1.2412e-06,4.9910e-08,-2.5869e-07,-9.1857e-07,-1.2278e-06,3.1551e-06,-3.0027e-06,1.7917e-06,-2.2711e-06,-2.5869e-07,-7.7320e-07,4.0726e-06,8.9174e-07,-5.1156e-07,1.6377e-07,-2.2711e-06,1.0941e-06,-6.2951e-07,-2.5210e-06,-1.3561e-06,9.1954e-07,1.6377e-07,-3.9121e-07,1.9224e-06,-1.5917e-06,-1.9428e-09,-9.2888e-07,9.1954e-07,-2.3548e-06,2.6953e-06,3.7925e-07,1.0260e-07,-2.6276e-06,-9.2888e-07,1.7328e-06,7.9246e-08,1.5885e-07,1.9067e-07,1.5885e-07,1.9637e-07,1.5870e-07,7.5492e-07,1.5870e-07,1.7148e-07,1.5885e-07,-4.2469e-07,1.5885e-07,-7.8851e-07,9.2853e-07,-9.2853e-07,4.1883e-06,-4.1883e-06,3.1826e-06,-3.1826e-06,-1.6188e-06,1.6188e-06,-3.7600e-07,3.7600e-07,9.0335e-07,-9.0335e-07}
pCurr = {3.6529e-05,4.5774e-06,2.3071e-05,3.9407e-05,-4.1256e-06,-2.5548e-05,-6.1313e-05,-9.7346e-06,7.9203e-05,2.3071e-05,6.4860e-05,-2.2175e-05,-4.3180e-05,1.2703e-05,-8.1394e-06,7.9203e-05,4.4043e-05,1.7792e-05,9.3826e-05,5.6595e-05,-3.2399e-05,-8.1394e-06,-1.0918e-05,3.4558e-06,5.3792e-05,1.8261e-05,3.2188e-05,-3.2399e-05,-1.7640e-06,3.2342e-05,-4.5432e-05,3.7812e-05,4.1400e-05,3.2188e-05,3.3975e-05,2.4768e-06,-5.5125e-06,-6.6168e-06,-5.5125e-06,-6.8145e-06,-5.5074e-06,3.2152e-05,-5.5074e-06,-3.9669e-05,-5.5125e-06,1.4886e-05,-5.5125e-06,3.1869e-05,-1.3159e-06,1.3159e-06,-1.0295e-05,1.0295e-05,-5.5245e-06,5.5245e-06,1.9329e-06,-1.9329e-06,4.8239e-06,-4.8239e-06,-1.8170e-06,1.8170e-06}
grad*pCur = -1.1510116367172184E-9
parameters = {-2.0925e+00,-1.2730e+00,-1.1256e+00,-1.2386e+00,-7.3867e-01,-1.1142e+00,-1.6720e+00,2.1276e-01,-2.2378e+00,-1.1256e+00,-2.0940e+00,-6.6589e-01,-2.1046e+00,-2.1525e+00,-5.6526e-01,-2.2378e+00,2.3748e+00,-3.1025e+00,-3.3687e+00,-2.7793e+00,-2.1394e+00,-5.6526e-01,1.4596e+00,-3.9480e-01,-3.3960e+00,4.5456e-01,-3.0431e+00,-2.1394e+00,-9.8567e-02,4.3468e-01,3.6045e-03,-1.7658e+00,1.2879e-01,-3.0431e+00,-1.3307e+00,-1.7806e+00,7.9426e-02,9.5336e-02,7.9426e-02,9.8185e-02,7.9352e-02,-1.1989e+00,7.9352e-02,-9.4210e-01,7.9426e-02,-2.5418e+00,7.9426e-02,-2.9327e+00,5.4279e-01,-5.4279e-01,5.8623e-01,-5.8623e-01,1.0864e-01,-1.0864e-01,2.0458e-01,-2.0458e-01,3.8816e-01,-3.8816e-01,3.8733e-01,-3.8733e-01}
|grad|/|x| = 1.068139566616958E-6
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0925e+00,-1.2730e+00,-1.1256e+00,-1.2386e+00,-7.3867e-01,-1.1142e+00,-1.6720e+00,2.1276e-01,-2.2378e+00,-1.1256e+00,-2.0940e+00,-6.6589e-01,-2.1046e+00,-2.1525e+00,-5.6526e-01,-2.2378e+00,2.3748e+00,-3.1025e+00,-3.3687e+00,-2.7793e+00,-2.1394e+00,-5.6526e-01,1.4596e+00,-3.9480e-01,-3.3960e+00,4.5456e-01,-3.0431e+00,-2.1394e+00,-9.8567e-02,4.3468e-01,3.6045e-03,-1.7658e+00,1.2879e-01,-3.0431e+00,-1.3307e+00,-1.7806e+00,7.9426e-02,9.5336e-02,7.9426e-02,9.8185e-02,7.9352e-02,-1.1989e+00,7.9352e-02,-9.4210e-01,7.9426e-02,-2.5418e+00,7.9426e-02,-2.9327e+00,5.4279e-01,-5.4279e-01,5.8623e-01,-5.8623e-01,1.0864e-01,-1.0864e-01,2.0458e-01,-2.0458e-01,3.8816e-01,-3.8816e-01,3.8733e-01,-3.8733e-01}
> Gradient: {-1.2412e-06,4.9910e-08,-2.5869e-07,-9.1857e-07,-1.2278e-06,3.1551e-06,-3.0027e-06,1.7917e-06,-2.2711e-06,-2.5869e-07,-7.7320e-07,4.0726e-06,8.9174e-07,-5.1156e-07,1.6377e-07,-2.2711e-06,1.0941e-06,-6.2951e-07,-2.5210e-06,-1.3561e-06,9.1954e-07,1.6377e-07,-3.9121e-07,1.9224e-06,-1.5917e-06,-1.9428e-09,-9.2888e-07,9.1954e-07,-2.3548e-06,2.6953e-06,3.7925e-07,1.0260e-07,-2.6276e-06,-9.2888e-07,1.7328e-06,7.9246e-08,1.5885e-07,1.9067e-07,1.5885e-07,1.9637e-07,1.5870e-07,7.5492e-07,1.5870e-07,1.7148e-07,1.5885e-07,-4.2469e-07,1.5885e-07,-7.8851e-07,9.2853e-07,-9.2853e-07,4.1883e-06,-4.1883e-06,3.1826e-06,-3.1826e-06,-1.6188e-06,1.6188e-06,-3.7600e-07,3.7600e-07,9.0335e-07,-9.0335e-07}
>>>> Re-trying (1/3).
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0925e+00,-1.2730e+00,-1.1256e+00,-1.2386e+00,-7.3867e-01,-1.1142e+00,-1.6720e+00,2.1276e-01,-2.2378e+00,-1.1256e+00,-2.0940e+00,-6.6589e-01,-2.1046e+00,-2.1525e+00,-5.6526e-01,-2.2378e+00,2.3748e+00,-3.1025e+00,-3.3687e+00,-2.7793e+00,-2.1394e+00,-5.6526e-01,1.4596e+00,-3.9480e-01,-3.3960e+00,4.5456e-01,-3.0431e+00,-2.1394e+00,-9.8567e-02,4.3468e-01,3.6045e-03,-1.7658e+00,1.2879e-01,-3.0431e+00,-1.3307e+00,-1.7806e+00,7.9426e-02,9.5336e-02,7.9426e-02,9.8185e-02,7.9352e-02,-1.1989e+00,7.9352e-02,-9.4210e-01,7.9426e-02,-2.5418e+00,7.9426e-02,-2.9327e+00,5.4279e-01,-5.4279e-01,5.8623e-01,-5.8623e-01,1.0864e-01,-1.0864e-01,2.0458e-01,-2.0458e-01,3.8816e-01,-3.8816e-01,3.8733e-01,-3.8733e-01}
> Gradient: {-1.2413e-06,4.9899e-08,-2.5869e-07,-9.1857e-07,-1.2278e-06,3.1551e-06,-3.0027e-06,1.7917e-06,-2.2711e-06,-2.5869e-07,-7.7321e-07,4.0725e-06,8.9174e-07,-5.1156e-07,1.6377e-07,-2.2711e-06,1.0940e-06,-6.2951e-07,-2.5210e-06,-1.3561e-06,9.1954e-07,1.6377e-07,-3.9125e-07,1.9224e-06,-1.5917e-06,-1.9641e-09,-9.2888e-07,9.1954e-07,-2.3548e-06,2.6953e-06,3.7923e-07,1.0260e-07,-2.6276e-06,-9.2888e-07,1.7328e-06,7.9240e-08,1.5885e-07,1.9067e-07,1.5885e-07,1.9637e-07,1.5870e-07,7.5491e-07,1.5870e-07,1.7146e-07,1.5885e-07,-4.2469e-07,1.5885e-07,-7.8851e-07,9.2854e-07,-9.2854e-07,4.1908e-06,-4.1908e-06,3.1827e-06,-3.1827e-06,-1.6188e-06,1.6188e-06,-3.7604e-07,3.7604e-07,9.0338e-07,-9.0338e-07}
>>>> Re-trying (2/3).
Starting Function Value: 3.67334395819661
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673343951959647 0.000066522837069 5.207897717918600 0.000014585100406
2 4 3.673343951485013 0.000051571558125 1.000000000000000 0.000013819179503
3 5 3.673343946609267 0.001252136211504 1.000000000000000 0.000029585628820
4 7 3.673343945499458 0.000212372315138 0.267292046557517 0.000010327609185
5 8 3.673343945191365 0.000103989870482 1.000000000000000 0.000008999237002
6 9 3.673343944189529 0.000171339616352 1.000000000000000 0.000010985836154
7 10 3.673343942482925 0.000784249011807 1.000000000000000 0.000035165692624
8 11 3.673343939996429 0.000450470248449 1.000000000000000 0.000015973057553
9 12 3.673343938198009 0.000766967392696 1.000000000000000 0.000013522356753
10 13 3.673343936840709 0.000682845799924 1.000000000000000 0.000014953177894
11 14 3.673343936200560 0.002590866766290 1.000000000000000 0.000072845191029
12 15 3.673343910482161 0.000480781648231 1.000000000000000 0.000029877677823
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0921e+00,-1.2729e+00,-1.1255e+00,-1.2377e+00,-7.3807e-01,-1.1143e+00,-1.6710e+00,2.1163e-01,-2.2352e+00,-1.1255e+00,-2.0934e+00,-6.6713e-01,-2.1055e+00,-2.1519e+00,-5.6542e-01,-2.2352e+00,2.3748e+00,-3.1018e+00,-3.3658e+00,-2.7777e+00,-2.1405e+00,-5.6542e-01,1.4599e+00,-3.9546e-01,-3.3942e+00,4.5477e-01,-3.0420e+00,-2.1405e+00,-9.7114e-02,4.3405e-01,4.4413e-03,-1.7653e+00,1.2894e-01,-3.0420e+00,-1.3309e+00,-1.7801e+00,7.9239e-02,9.5112e-02,7.9239e-02,9.7954e-02,7.9165e-02,-1.1990e+00,7.9165e-02,-9.4233e-01,7.9239e-02,-2.5413e+00,7.9239e-02,-2.9319e+00,5.4278e-01,-5.4278e-01,5.8623e-01,-5.8623e-01,1.0862e-01,-1.0862e-01,2.0458e-01,-2.0458e-01,3.8815e-01,-3.8815e-01,3.8737e-01,-3.8737e-01}
> Gradient: {-9.6524e-08,-1.4883e-06,1.1644e-07,-4.6850e-07,1.1599e-06,-2.4919e-06,4.5450e-06,-3.7135e-06,-2.1877e-06,1.1644e-07,1.0479e-06,-3.0770e-06,7.4916e-09,-7.4802e-07,-9.3152e-08,-2.1877e-06,-4.4021e-07,-6.2467e-07,-1.9502e-06,-1.0236e-06,8.1690e-07,-9.3152e-08,2.0790e-06,-3.9153e-06,-1.1660e-06,-4.3485e-07,-9.0793e-07,8.1690e-07,4.0153e-06,-6.4096e-06,5.0140e-06,-5.5303e-07,-4.8042e-06,-9.0793e-07,-2.7919e-06,-4.3164e-08,1.5848e-07,1.9022e-07,1.5848e-07,1.9591e-07,1.5833e-07,2.2210e-06,1.5833e-07,-3.0774e-06,1.5848e-07,-1.4557e-07,1.5848e-07,-7.0039e-07,-2.9079e-06,2.9079e-06,9.5972e-07,-9.5972e-07,-1.1749e-05,1.1749e-05,-3.6039e-06,3.6039e-06,-7.2838e-06,7.2838e-06,1.0992e-05,-1.0992e-05}
>>>> Re-trying (3/3).
After: gradient norm = 2.9867280380561986E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5862,-0.5862}
Count Table 2:
---------------
h: {0.1086,-0.1086}
Count Table 3:
---------------
h: {0.2046,-0.2046}
Count Table 4:
---------------
h: {0.3881,-0.3881}
Count Table 5:
---------------
h: {0.3874,-0.3874}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-1.2729,-2.0921,-1.1143,-0.7381,-1.1255,-1.2377,0.2116,-1.6710,-0.6671,-2.0934,-2.2352,-1.1255,-2.1519,-2.1055,-3.1018,2.3748,-0.5654,-2.2352,-2.7777,-3.3658,-0.3955,1.4599,-2.1405,-0.5654,0.4548,-3.3942,0.4340,-0.0971,-3.0420,-2.1405,-1.7653,0.0044,-1.7801,-1.3309,0.1289,-3.0420,-1.3309,-1.7801,0.0044,-1.7653,-3.0420,0.1289,-0.0971,0.4340,-3.3942,0.4548,-2.1405,-3.0420,1.4599,-0.3955,-3.3658,-2.7777,-0.5654,-2.1405,2.3748,-3.1018,-2.1055,-2.1519,-2.2352,-0.5654,-2.0934,-0.6671,-1.6710,0.2116,-1.1255,-2.2352,-0.7381,-1.1143,-2.0921,-1.2729,-1.2377,-1.1255}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0792,0.0951}
Activity(exp=1): {0.0792,0.0980}
Activity(exp=2): {0.0792,-1.1990}
Activity(exp=3): {0.0792,-0.9423}
Activity(exp=4): {0.0792,-2.5413}
Activity(exp=5): {0.0792,-2.9319}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;9;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component2-2-variation6).
>> Starting new optimization: component2-2-variation6. (2021-05-21 18:32:15.296).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.6733439289128174
gradient = {-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000}
gradient norm = 2.987347292629233E-5
Starting Function Value: 3.6733439289128174
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673343883713894 0.000094247688633 3.154895611417800 0.000017333302700
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0921e+00,-1.2729e+00,-1.1255e+00,-1.2377e+00,-7.3807e-01,-1.1143e+00,-1.6711e+00,2.1164e-01,-2.2352e+00,-1.1255e+00,-2.0934e+00,-6.6712e-01,-2.1055e+00,-2.1518e+00,-5.6542e-01,-2.2352e+00,2.3748e+00,-3.1017e+00,-3.3658e+00,-2.7777e+00,-2.1405e+00,-5.6542e-01,1.4599e+00,-3.9545e-01,-3.3942e+00,4.5477e-01,-3.0420e+00,-2.1405e+00,-9.7127e-02,4.3407e-01,4.4255e-03,-1.7653e+00,1.2896e-01,-3.0420e+00,-1.3309e+00,-1.7801e+00,7.9239e-02,9.5112e-02,7.9239e-02,9.7953e-02,7.9165e-02,-1.1991e+00,7.9165e-02,-9.4232e-01,7.9239e-02,-2.5413e+00,7.9239e-02,-2.9319e+00,5.4279e-01,-5.4279e-01,5.8622e-01,-5.8622e-01,1.0866e-01,-1.0866e-01,2.0460e-01,-2.0460e-01,3.8817e-01,-3.8817e-01,3.8733e-01,-3.8733e-01}
> Gradient: {-6.9541e-07,-1.7422e-06,1.3842e-07,-4.4106e-07,7.4016e-07,-3.0693e-06,3.8831e-06,-4.1995e-06,-2.1876e-06,1.3842e-07,9.0060e-07,-3.6043e-06,-8.8104e-08,-8.0827e-07,-9.2679e-08,-2.1876e-06,-2.0346e-06,-6.7548e-07,-2.0000e-06,-1.0804e-06,8.1637e-07,-9.2679e-08,1.0377e-06,-4.5678e-06,-1.2122e-06,-9.8778e-07,-9.0812e-07,8.1637e-07,3.6231e-06,-7.2182e-06,3.6811e-06,-8.1082e-07,-4.3228e-06,-9.0812e-07,-3.1368e-06,-3.8937e-07,1.5848e-07,1.9022e-07,1.5848e-07,1.9591e-07,1.5833e-07,1.1678e-06,1.5833e-07,-3.0131e-06,1.5848e-07,-2.5812e-07,1.5848e-07,-4.9919e-07,1.3251e-06,-1.3251e-06,-4.7856e-07,4.7856e-07,5.2121e-06,-5.2121e-06,2.6955e-07,-2.6955e-07,1.8292e-06,-1.8292e-06,-2.0999e-06,2.0999e-06}
>>>> Re-trying (1/3).
Starting Function Value: 3.673343927483195
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673343926537167 0.000106669446990 6.151538554004698 0.000022669853528
2 4 3.673343925386297 0.000089457492574 1.000000000000000 0.000021031043475
3 5 3.673343832741562 0.001401556943905 1.000000000000000 0.000036873378685
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0921e+00,-1.2728e+00,-1.1255e+00,-1.2376e+00,-7.3824e-01,-1.1141e+00,-1.6716e+00,2.1199e-01,-2.2349e+00,-1.1255e+00,-2.0935e+00,-6.6682e-01,-2.1055e+00,-2.1518e+00,-5.6541e-01,-2.2349e+00,2.3747e+00,-3.1017e+00,-3.3656e+00,-2.7776e+00,-2.1406e+00,-5.6541e-01,1.4595e+00,-3.9504e-01,-3.3940e+00,4.5479e-01,-3.0419e+00,-2.1406e+00,-9.7601e-02,4.3471e-01,3.8775e-03,-1.7652e+00,1.2934e-01,-3.0419e+00,-1.3306e+00,-1.7801e+00,7.9220e-02,9.5089e-02,7.9220e-02,9.7930e-02,7.9146e-02,-1.1993e+00,7.9146e-02,-9.4207e-01,7.9220e-02,-2.5413e+00,7.9220e-02,-2.9318e+00,5.4280e-01,-5.4280e-01,5.8622e-01,-5.8622e-01,1.0864e-01,-1.0864e-01,2.0461e-01,-2.0461e-01,3.8819e-01,-3.8819e-01,3.8730e-01,-3.8730e-01}
> Gradient: {1.4672e-06,8.5722e-07,7.6421e-07,3.9562e-07,2.5404e-06,3.9788e-06,3.8801e-06,3.6983e-06,-2.1633e-06,7.6421e-07,1.1972e-06,2.6270e-06,2.6937e-07,-3.6902e-07,1.9367e-07,-2.1633e-06,1.1705e-05,-4.4947e-07,-1.8148e-06,-5.7208e-07,8.3588e-07,1.9367e-07,6.7737e-06,3.7702e-06,-1.1293e-06,2.2831e-06,-9.0262e-07,8.3588e-07,3.0157e-06,5.0839e-06,9.0124e-07,2.3419e-07,8.3114e-06,-9.0262e-07,1.1668e-07,5.2575e-07,1.5844e-07,1.9018e-07,1.5844e-07,1.9586e-07,1.5829e-07,-9.6840e-08,1.5829e-07,5.6963e-06,1.5844e-07,-4.7868e-07,1.5844e-07,-1.8714e-07,3.3859e-06,-3.3859e-06,-3.0337e-07,3.0337e-07,-4.0692e-06,4.0692e-06,-9.3938e-06,9.3938e-06,1.1186e-05,-1.1186e-05,-1.5071e-05,1.5071e-05}
>>>> Re-trying (2/3).
Starting Function Value: 3.6733439181448304
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673343916331865 0.000098599604853 2.674629426038703 0.000012424093742
2 4 3.673343916020071 0.000031266723663 1.000000000000000 0.000009658732796
3 5 3.673343915200717 0.000137565395651 1.000000000000000 0.000010227798119
4 6 3.673343914386301 0.000164933940267 1.000000000000000 0.000012813318197
5 7 3.673343913794319 0.000461494065891 1.000000000000000 0.000024721026205
6 8 3.673343912935068 0.000084247580078 1.000000000000000 0.000008800022202
7 9 3.673343882692145 0.000045287690321 1.000000000000000 0.000007132246451
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0920e+00,-1.2727e+00,-1.1256e+00,-1.2376e+00,-7.3824e-01,-1.1141e+00,-1.6717e+00,2.1200e-01,-2.2347e+00,-1.1256e+00,-2.0936e+00,-6.6674e-01,-2.1056e+00,-2.1517e+00,-5.6542e-01,-2.2347e+00,2.3745e+00,-3.1016e+00,-3.3653e+00,-2.7775e+00,-2.1407e+00,-5.6542e-01,1.4595e+00,-3.9508e-01,-3.3939e+00,4.5489e-01,-3.0418e+00,-2.1407e+00,-9.7702e-02,4.3473e-01,4.0923e-03,-1.7651e+00,1.2894e-01,-3.0418e+00,-1.3305e+00,-1.7801e+00,7.9202e-02,9.5067e-02,7.9202e-02,9.7908e-02,7.9128e-02,-1.1991e+00,7.9128e-02,-9.4226e-01,7.9202e-02,-2.5413e+00,7.9202e-02,-2.9318e+00,5.4279e-01,-5.4279e-01,5.8622e-01,-5.8622e-01,1.0865e-01,-1.0865e-01,2.0461e-01,-2.0461e-01,3.8816e-01,-3.8816e-01,3.8734e-01,-3.8734e-01}
> Gradient: {-6.0715e-07,-5.1956e-07,-9.3829e-08,-2.7482e-07,-6.5185e-08,3.3435e-07,3.4107e-07,2.0402e-07,-2.1673e-06,-9.3829e-08,2.5252e-07,2.3737e-07,1.2518e-07,-5.8615e-07,3.3618e-08,-2.1673e-06,1.1515e-06,-5.9953e-07,-1.8424e-06,-8.2045e-07,8.1234e-07,3.3618e-08,9.9464e-08,-3.2538e-07,-1.2380e-06,-2.8121e-07,-9.0402e-07,8.1234e-07,-1.7099e-07,-2.6088e-07,2.5125e-06,-9.4041e-08,-3.5680e-06,-9.0402e-07,-6.1125e-08,7.1963e-08,1.5840e-07,1.9013e-07,1.5840e-07,1.9582e-07,1.5826e-07,1.2913e-06,1.5826e-07,-1.0877e-06,1.5840e-07,-3.1478e-07,1.5840e-07,-5.7011e-07,-6.4630e-07,6.4630e-07,3.9144e-08,-3.9144e-08,-7.0092e-07,7.0092e-07,1.2618e-06,-1.2618e-06,-2.5092e-07,2.5092e-07,-9.5010e-07,9.5010e-07}
>>>> Re-trying (3/3).
After: gradient norm = 7.135197349314042E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5862,-0.5862}
Count Table 2:
---------------
h: {0.1087,-0.1087}
Count Table 3:
---------------
h: {0.2046,-0.2046}
Count Table 4:
---------------
h: {0.3882,-0.3882}
Count Table 5:
---------------
h: {0.3873,-0.3873}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-1.2727,-2.0920,-1.1141,-0.7382,-1.1256,-1.2376,0.2120,-1.6717,-0.6667,-2.0936,-2.2347,-1.1256,-2.1517,-2.1056,-3.1016,2.3745,-0.5654,-2.2347,-2.7775,-3.3653,-0.3951,1.4595,-2.1407,-0.5654,0.4549,-3.3939,0.4347,-0.0977,-3.0418,-2.1407,-1.7651,0.0041,-1.7801,-1.3305,0.1289,-3.0418,-1.3305,-1.7801,0.0041,-1.7651,-3.0418,0.1289,-0.0977,0.4347,-3.3939,0.4549,-2.1407,-3.0418,1.4595,-0.3951,-3.3653,-2.7775,-0.5654,-2.1407,2.3745,-3.1016,-2.1056,-2.1517,-2.2347,-0.5654,-2.0936,-0.6667,-1.6717,0.2120,-1.1256,-2.2347,-0.7382,-1.1141,-2.0920,-1.2727,-1.2376,-1.1256}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0792,0.0951}
Activity(exp=1): {0.0792,0.0979}
Activity(exp=2): {0.0791,-1.1991}
Activity(exp=3): {0.0791,-0.9423}
Activity(exp=4): {0.0792,-2.5413}
Activity(exp=5): {0.0792,-2.9318}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;10;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component2-2-variation7).
>> Starting new optimization: component2-2-variation7. (2021-05-21 18:33:31.551).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.6733439137221797
gradient = {-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 7.143759264994898E-6
Starting Function Value: 3.6733439137221797
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 4 3.673343913645062 0.000011504686149 1.610452665336073 0.000006498256080
2 5 3.673343912907333 0.000160383256847 1.000000000000000 0.000011703264753
3 6 3.673343912136638 0.000228557659726 1.000000000000000 0.000013437977414
4 8 3.673343911977610 0.000037792688764 0.075910070170561 0.000012905535374
5 12 3.673343855896155 0.000375044007676 0.501655461537639 0.000009254240198
6 13 3.673343681534870 0.000812944104895 1.000000000000000 0.000025373335944
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0918e+00,-1.2726e+00,-1.1256e+00,-1.2376e+00,-7.3820e-01,-1.1141e+00,-1.6718e+00,2.1198e-01,-2.2340e+00,-1.1256e+00,-2.0937e+00,-6.6675e-01,-2.1056e+00,-2.1515e+00,-5.6544e-01,-2.2340e+00,2.3743e+00,-3.1014e+00,-3.3648e+00,-2.7772e+00,-2.1409e+00,-5.6544e-01,1.4596e+00,-3.9495e-01,-3.3935e+00,4.5501e-01,-3.0415e+00,-2.1409e+00,-9.7648e-02,4.3488e-01,3.7901e-03,-1.7650e+00,1.2947e-01,-3.0415e+00,-1.3304e+00,-1.7800e+00,7.9152e-02,9.5007e-02,7.9152e-02,9.7846e-02,7.9078e-02,-1.1993e+00,7.9078e-02,-9.4214e-01,7.9152e-02,-2.5411e+00,7.9152e-02,-2.9316e+00,5.4277e-01,-5.4277e-01,5.8623e-01,-5.8623e-01,1.0862e-01,-1.0862e-01,2.0462e-01,-2.0462e-01,3.8817e-01,-3.8817e-01,3.8734e-01,-3.8734e-01}
> Gradient: {1.0502e-06,9.2204e-07,4.7626e-07,2.2395e-07,1.3193e-06,1.5121e-06,1.7735e-06,2.6580e-06,-2.1309e-06,4.7626e-07,5.8044e-07,2.1467e-06,3.6595e-07,-2.1002e-07,1.9745e-07,-2.1309e-06,6.7937e-06,-3.2782e-07,-1.6793e-06,-5.5475e-07,8.0374e-07,1.9745e-07,3.9000e-06,2.0212e-06,-1.0760e-06,1.7997e-06,-9.0040e-07,8.0374e-07,9.1527e-07,3.1461e-06,-2.0076e-06,-2.9192e-07,8.2173e-06,-9.0040e-07,-1.8824e-07,-1.4071e-07,1.5830e-07,1.9001e-07,1.5830e-07,1.9569e-07,1.5816e-07,-6.7686e-07,1.5816e-07,4.1293e-06,1.5830e-07,-3.9474e-07,1.5830e-07,-3.7434e-07,-6.9039e-06,6.9039e-06,1.0356e-06,-1.0356e-06,-1.2752e-05,1.2752e-05,-2.4575e-06,2.4575e-06,-8.9097e-08,8.9097e-08,-8.7813e-07,8.7813e-07}
>>>> Re-trying (1/3).
Starting Function Value: 3.673344097121335
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 5 3.673343845596039 0.000031464971517 1.242388141241230 0.000014067236281
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0918e+00,-1.2726e+00,-1.1256e+00,-1.2376e+00,-7.3820e-01,-1.1141e+00,-1.6718e+00,2.1198e-01,-2.2340e+00,-1.1256e+00,-2.0937e+00,-6.6675e-01,-2.1056e+00,-2.1515e+00,-5.6544e-01,-2.2340e+00,2.3742e+00,-3.1014e+00,-3.3648e+00,-2.7772e+00,-2.1409e+00,-5.6544e-01,1.4596e+00,-3.9495e-01,-3.3935e+00,4.5501e-01,-3.0415e+00,-2.1409e+00,-9.7649e-02,4.3488e-01,3.7926e-03,-1.7650e+00,1.2946e-01,-3.0415e+00,-1.3304e+00,-1.7800e+00,7.9152e-02,9.5007e-02,7.9152e-02,9.7846e-02,7.9078e-02,-1.1993e+00,7.9078e-02,-9.4215e-01,7.9152e-02,-2.5411e+00,7.9152e-02,-2.9316e+00,5.4278e-01,-5.4278e-01,5.8622e-01,-5.8622e-01,1.0863e-01,-1.0863e-01,2.0463e-01,-2.0463e-01,3.8817e-01,-3.8817e-01,3.8734e-01,-3.8734e-01}
> Gradient: {4.0506e-07,4.8538e-07,4.0635e-07,1.6020e-07,6.6577e-07,4.6180e-07,1.0839e-06,1.6396e-06,-2.1321e-06,4.0635e-07,4.0331e-07,1.1835e-06,2.9408e-07,-2.6553e-07,1.8133e-07,-2.1321e-06,4.0583e-06,-3.6711e-07,-1.7141e-06,-6.1762e-07,8.0158e-07,1.8133e-07,2.0751e-06,1.0428e-06,-1.1131e-06,8.9772e-07,-9.0128e-07,8.0158e-07,4.0623e-07,1.6779e-06,-3.1753e-06,-5.7287e-07,7.5379e-06,-9.0128e-07,-6.2587e-07,-4.9349e-07,1.5830e-07,1.9001e-07,1.5830e-07,1.9569e-07,1.5816e-07,-1.4116e-06,1.5816e-07,3.4375e-06,1.5830e-07,-4.0485e-07,1.5830e-07,-3.9734e-07,-2.9981e-06,2.9981e-06,4.2183e-07,-4.2183e-07,-4.9153e-06,4.9153e-06,-1.6691e-07,1.6691e-07,3.9684e-08,-3.9684e-08,-3.5777e-07,3.5777e-07}
>>>> Re-trying (2/3).
Starting Function Value: 3.6733439086491315
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673343908195151 0.000063977404482 4.539869215030778 0.000014355860549
2 4 3.673343907759764 0.000046467866242 1.000000000000000 0.000012716048636
3 5 3.673343905722506 0.000512772106622 1.000000000000000 0.000016312482156
4 7 3.673343905403521 0.000070723995876 0.252882770334198 0.000005927423004
5 8 3.673343905310511 0.000036494610842 1.000000000000000 0.000005607415080
6 14 3.673343905069783 0.000050629261389 0.336803034211890 0.000005889489122
7 15 3.673343902723221 0.000935148427951 1.000000000000000 0.000024322837976
8 16 3.673343899380938 0.001072165191810 1.000000000000000 0.000024738185960
9 17 3.673343892051554 0.002317908304587 1.000000000000000 0.000038377980382
10 18 3.673343861063066 0.012920169913535 1.000000000000000 0.000083154581032
11 19 3.673343808616679 0.012416006495813 1.000000000000000 0.000090266113030
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0900e+00,-1.2711e+00,-1.1255e+00,-1.2363e+00,-7.3661e-01,-1.1117e+00,-1.6723e+00,2.0905e-01,-2.2196e+00,-1.1255e+00,-2.0941e+00,-6.6885e-01,-2.1069e+00,-2.1488e+00,-5.6603e-01,-2.2196e+00,2.3700e+00,-3.0983e+00,-3.3532e+00,-2.7722e+00,-2.1463e+00,-5.6603e-01,1.4612e+00,-3.9320e-01,-3.3857e+00,4.5663e-01,-3.0355e+00,-2.1463e+00,-9.4429e-02,4.3560e-01,4.4590e-03,-1.7624e+00,1.2989e-01,-3.0355e+00,-1.3284e+00,-1.7778e+00,7.8084e-02,9.3726e-02,7.8084e-02,9.6526e-02,7.8011e-02,-1.2002e+00,7.8011e-02,-9.4237e-01,7.8084e-02,-2.5387e+00,7.8084e-02,-2.9281e+00,5.4286e-01,-5.4286e-01,5.8626e-01,-5.8626e-01,1.0867e-01,-1.0867e-01,2.0475e-01,-2.0475e-01,3.8825e-01,-3.8825e-01,3.8726e-01,-3.8726e-01}
> Gradient: {-7.0922e-06,-2.5663e-06,1.2511e-06,-4.1961e-08,1.9280e-06,1.0105e-05,5.1779e-07,-2.9990e-06,-1.5861e-06,1.2511e-06,1.0761e-06,5.3235e-06,3.1198e-07,8.4372e-07,4.5206e-08,-1.5861e-06,2.6408e-06,5.3417e-07,9.7638e-08,-4.8533e-07,3.2320e-07,4.5206e-08,8.6063e-06,-5.7972e-06,1.5885e-07,3.6218e-06,-7.6370e-07,3.2320e-07,9.1988e-06,-9.7492e-06,-5.7607e-06,7.6268e-07,7.6922e-06,-7.6370e-07,-1.3018e-06,2.1611e-06,1.5617e-07,1.8745e-07,1.5617e-07,1.9305e-07,1.5602e-07,-3.9826e-06,1.5602e-07,4.6460e-06,1.5617e-07,-1.2453e-07,1.5617e-07,1.1765e-06,3.0213e-05,-3.0213e-05,1.5539e-05,-1.5539e-05,-7.1986e-06,7.1986e-06,2.8739e-06,-2.8739e-06,1.9665e-05,-1.9665e-05,-4.6290e-05,4.6290e-05}
>>>> Re-trying (3/3).
After: gradient norm = 9.025420617976145E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5429,-0.5429}
Count Table 1:
---------------
h: {0.5863,-0.5863}
Count Table 2:
---------------
h: {0.1087,-0.1087}
Count Table 3:
---------------
h: {0.2047,-0.2047}
Count Table 4:
---------------
h: {0.3882,-0.3882}
Count Table 5:
---------------
h: {0.3873,-0.3873}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-1.2711,-2.0900,-1.1117,-0.7366,-1.1255,-1.2363,0.2091,-1.6723,-0.6689,-2.0941,-2.2196,-1.1255,-2.1488,-2.1069,-3.0983,2.3700,-0.5660,-2.2196,-2.7722,-3.3532,-0.3932,1.4612,-2.1463,-0.5660,0.4566,-3.3857,0.4356,-0.0944,-3.0355,-2.1463,-1.7624,0.0045,-1.7778,-1.3284,0.1299,-3.0355,-1.3284,-1.7778,0.0045,-1.7624,-3.0355,0.1299,-0.0944,0.4356,-3.3857,0.4566,-2.1463,-3.0355,1.4612,-0.3932,-3.3532,-2.7722,-0.5660,-2.1463,2.3700,-3.0983,-2.1069,-2.1488,-2.2196,-0.5660,-2.0941,-0.6689,-1.6723,0.2091,-1.1255,-2.2196,-0.7366,-1.1117,-2.0900,-1.2711,-1.2363,-1.1255}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0781,0.0937}
Activity(exp=1): {0.0781,0.0965}
Activity(exp=2): {0.0780,-1.2002}
Activity(exp=3): {0.0780,-0.9424}
Activity(exp=4): {0.0781,-2.5387}
Activity(exp=5): {0.0781,-2.9281}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;11;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component2-2-variation8).
>> Starting new optimization: component2-2-variation8. (2021-05-21 18:35:39.043).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[48,49]},{"h":[50,51]},{"h":[52,53]},{"h":[54,55]},{"h":[56,57]},{"h":[58,59]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[36,37],[38,39],[40,41],[42,43],[44,45],[46,47]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.673343881312914
gradient = {-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000}
gradient norm = 9.088522737300918E-5
Gradient = {-7.0250e-06,-2.4960e-06,1.2511e-06,-4.1857e-08,1.9527e-06,1.0361e-05,6.6393e-07,-2.8975e-06,-1.5861e-06,1.2511e-06,1.1035e-06,5.4672e-06,3.7188e-07,8.5765e-07,4.5241e-08,-1.5861e-06,2.9750e-06,5.4498e-07,1.0771e-07,-4.3248e-07,3.2320e-07,4.5241e-08,8.7813e-06,-5.6164e-06,1.6762e-07,3.7176e-06,-7.6370e-07,3.2320e-07,9.2597e-06,-9.4959e-06,-5.6025e-06,8.1256e-07,7.6917e-06,-7.6370e-07,-1.2340e-06,2.3045e-06,1.5617e-07,1.8745e-07,1.5617e-07,1.9305e-07,1.5602e-07,-3.7795e-06,1.5602e-07,4.6465e-06,1.5617e-07,-1.1818e-07,1.5617e-07,1.1760e-06,3.0184e-05,-3.0184e-05,1.5523e-05,-1.5523e-05,-1.1687e-05,1.1687e-05,2.8551e-06,-2.8551e-06,1.8895e-05,-1.8895e-05,-4.6255e-05,4.6255e-05}
pCurr = {7.0246e-06,2.4956e-06,-1.2512e-06,4.1776e-08,-1.9534e-06,-1.0363e-05,-6.6449e-07,2.8965e-06,1.5861e-06,-1.2512e-06,-1.1037e-06,-5.4685e-06,-3.7197e-07,-8.5772e-07,-4.5260e-08,1.5861e-06,-2.9778e-06,-5.4503e-07,-1.0775e-07,4.3241e-07,-3.2320e-07,-4.5260e-08,-8.7835e-06,5.6157e-06,-1.6767e-07,-3.7188e-06,7.6370e-07,-3.2320e-07,-9.2604e-06,9.4947e-06,5.6015e-06,-8.1289e-07,-7.6926e-06,7.6370e-07,1.2336e-06,-2.3050e-06,-1.5617e-07,-1.8745e-07,-1.5617e-07,-1.9305e-07,-1.5602e-07,3.7787e-06,-1.5602e-07,-4.6469e-06,-1.5617e-07,1.1837e-07,-1.5617e-07,-1.1765e-06,-3.0213e-05,3.0213e-05,-1.5539e-05,1.5539e-05,1.1699e-05,-1.1699e-05,-2.8566e-06,2.8566e-06,-1.8910e-05,1.8910e-05,4.6292e-05,-4.6292e-05}
grad*pCur = -8.253583803231142E-9
parameters = {-2.0900e+00,-1.2711e+00,-1.1255e+00,-1.2363e+00,-7.3661e-01,-1.1117e+00,-1.6723e+00,2.0905e-01,-2.2196e+00,-1.1255e+00,-2.0941e+00,-6.6885e-01,-2.1069e+00,-2.1488e+00,-5.6603e-01,-2.2196e+00,2.3700e+00,-3.0983e+00,-3.3532e+00,-2.7722e+00,-2.1463e+00,-5.6603e-01,1.4612e+00,-3.9320e-01,-3.3857e+00,4.5663e-01,-3.0355e+00,-2.1463e+00,-9.4429e-02,4.3560e-01,4.4590e-03,-1.7624e+00,1.2989e-01,-3.0355e+00,-1.3284e+00,-1.7778e+00,7.8084e-02,9.3726e-02,7.8084e-02,9.6526e-02,7.8011e-02,-1.2002e+00,7.8011e-02,-9.4237e-01,7.8084e-02,-2.5387e+00,7.8084e-02,-2.9281e+00,5.4286e-01,-5.4286e-01,5.8626e-01,-5.8626e-01,1.0867e-01,-1.0867e-01,2.0475e-01,-2.0475e-01,3.8825e-01,-3.8825e-01,3.8726e-01,-3.8726e-01}
|grad|/|x| = 7.609413024501902E-6
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0900e+00,-1.2711e+00,-1.1255e+00,-1.2363e+00,-7.3661e-01,-1.1117e+00,-1.6723e+00,2.0905e-01,-2.2196e+00,-1.1255e+00,-2.0941e+00,-6.6885e-01,-2.1069e+00,-2.1488e+00,-5.6603e-01,-2.2196e+00,2.3700e+00,-3.0983e+00,-3.3532e+00,-2.7722e+00,-2.1463e+00,-5.6603e-01,1.4612e+00,-3.9320e-01,-3.3857e+00,4.5663e-01,-3.0355e+00,-2.1463e+00,-9.4429e-02,4.3560e-01,4.4590e-03,-1.7624e+00,1.2989e-01,-3.0355e+00,-1.3284e+00,-1.7778e+00,7.8084e-02,9.3726e-02,7.8084e-02,9.6526e-02,7.8011e-02,-1.2002e+00,7.8011e-02,-9.4237e-01,7.8084e-02,-2.5387e+00,7.8084e-02,-2.9281e+00,5.4286e-01,-5.4286e-01,5.8626e-01,-5.8626e-01,1.0867e-01,-1.0867e-01,2.0475e-01,-2.0475e-01,3.8825e-01,-3.8825e-01,3.8726e-01,-3.8726e-01}
> Gradient: {-7.0250e-06,-2.4960e-06,1.2511e-06,-4.1857e-08,1.9527e-06,1.0361e-05,6.6393e-07,-2.8975e-06,-1.5861e-06,1.2511e-06,1.1035e-06,5.4672e-06,3.7188e-07,8.5765e-07,4.5241e-08,-1.5861e-06,2.9750e-06,5.4498e-07,1.0771e-07,-4.3248e-07,3.2320e-07,4.5241e-08,8.7813e-06,-5.6164e-06,1.6762e-07,3.7176e-06,-7.6370e-07,3.2320e-07,9.2597e-06,-9.4959e-06,-5.6025e-06,8.1256e-07,7.6917e-06,-7.6370e-07,-1.2340e-06,2.3045e-06,1.5617e-07,1.8745e-07,1.5617e-07,1.9305e-07,1.5602e-07,-3.7795e-06,1.5602e-07,4.6465e-06,1.5617e-07,-1.1818e-07,1.5617e-07,1.1760e-06,3.0184e-05,-3.0184e-05,1.5523e-05,-1.5523e-05,-1.1687e-05,1.1687e-05,2.8551e-06,-2.8551e-06,1.8895e-05,-1.8895e-05,-4.6255e-05,4.6255e-05}
>>>> Re-trying (1/3).
Starting Function Value: 3.673343881312914
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673343870381728 0.000237570916259 2.613966242109711 0.000026833687076
2 4 3.673343868747213 0.000069786701075 1.000000000000000 0.000024193576217
3 5 3.673343858520959 0.000651914095676 1.000000000000000 0.000035974769392
4 6 3.673343852356765 0.000730612866850 1.000000000000000 0.000016161182635
5 8 3.673343851954046 0.000080844988628 0.356088948268656 0.000012682819068
6 9 3.673343851629905 0.000055769600751 1.000000000000000 0.000009895634019
7 10 3.673343850953557 0.000131605117955 1.000000000000000 0.000013446954009
8 11 3.673343849683440 0.000305057964228 1.000000000000000 0.000020639344148
9 12 3.673343797148422 0.000446450781677 1.000000000000000 0.000019348043052
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0894e+00,-1.2706e+00,-1.1256e+00,-1.2362e+00,-7.3680e-01,-1.1126e+00,-1.6727e+00,2.0942e-01,-2.2193e+00,-1.1256e+00,-2.0941e+00,-6.6893e-01,-2.1069e+00,-2.1489e+00,-5.6602e-01,-2.2193e+00,2.3700e+00,-3.0983e+00,-3.3532e+00,-2.7721e+00,-2.1463e+00,-5.6602e-01,1.4608e+00,-3.9272e-01,-3.3857e+00,4.5667e-01,-3.0353e+00,-2.1463e+00,-9.5410e-02,4.3654e-01,4.6800e-03,-1.7624e+00,1.2974e-01,-3.0353e+00,-1.3282e+00,-1.7780e+00,7.8053e-02,9.3688e-02,7.8053e-02,9.6487e-02,7.7980e-02,-1.1999e+00,7.7980e-02,-9.4264e-01,7.8053e-02,-2.5387e+00,7.8053e-02,-2.9281e+00,5.4279e-01,-5.4279e-01,5.8623e-01,-5.8623e-01,1.0872e-01,-1.0872e-01,2.0472e-01,-2.0472e-01,3.8821e-01,-3.8821e-01,3.8735e-01,-3.8735e-01}
> Gradient: {9.8987e-07,1.2785e-07,4.6675e-07,-2.6302e-07,7.3943e-07,-3.7518e-07,2.5890e-06,8.2173e-07,-1.5863e-06,4.6675e-07,8.5723e-08,-6.9124e-07,1.4008e-07,6.2475e-07,-3.2238e-08,-1.5863e-06,1.3914e-06,3.5510e-07,4.2071e-08,-4.6882e-07,3.2032e-07,-3.2238e-08,-2.4384e-07,1.2753e-06,-1.1615e-07,-4.1641e-07,-7.7326e-07,3.2032e-07,1.5259e-07,1.7257e-06,2.6360e-07,1.2111e-07,1.1886e-06,-7.7326e-07,-2.5001e-08,1.1773e-07,1.5611e-07,1.8738e-07,1.5611e-07,1.9297e-07,1.5596e-07,-8.0664e-08,1.5596e-07,9.0525e-07,1.5611e-07,-2.1286e-07,1.5611e-07,1.5493e-07,-1.1043e-06,1.1043e-06,1.6061e-06,-1.6061e-06,-3.5240e-07,3.5240e-07,-3.8336e-07,3.8336e-07,3.2339e-06,-3.2339e-06,-1.2619e-05,1.2619e-05}
>>>> Re-trying (2/3).
Starting Function Value: 3.673343848182629
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.673343847660519 0.000053225488032 2.751591843069654 0.000004723665399
2 4 3.673343847602899 0.000013167936825 1.000000000000000 0.000004531073269
3 5 3.673343846869116 0.000262202407141 1.000000000000000 0.000008427226897
4 6 3.673343846445696 0.000259691233595 1.000000000000000 0.000007640954006
5 7 3.673343846367601 0.000170236394249 1.000000000000000 0.000012749411750
6 8 3.673343704454965 0.000034448690219 1.000000000000000 0.000006580590811
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0895e+00,-1.2706e+00,-1.1257e+00,-1.2362e+00,-7.3686e-01,-1.1125e+00,-1.6731e+00,2.0938e-01,-2.2190e+00,-1.1257e+00,-2.0941e+00,-6.6880e-01,-2.1070e+00,-2.1490e+00,-5.6601e-01,-2.2190e+00,2.3700e+00,-3.0984e+00,-3.3532e+00,-2.7720e+00,-2.1464e+00,-5.6601e-01,1.4609e+00,-3.9281e-01,-3.3857e+00,4.5677e-01,-3.0352e+00,-2.1464e+00,-9.5403e-02,4.3642e-01,4.7046e-03,-1.7624e+00,1.2966e-01,-3.0352e+00,-1.3282e+00,-1.7780e+00,7.8026e-02,9.3656e-02,7.8026e-02,9.6454e-02,7.7953e-02,-1.1999e+00,7.7953e-02,-9.4272e-01,7.8026e-02,-2.5387e+00,7.8026e-02,-2.9281e+00,5.4279e-01,-5.4279e-01,5.8622e-01,-5.8622e-01,1.0872e-01,-1.0872e-01,2.0472e-01,-2.0472e-01,3.8821e-01,-3.8821e-01,3.8738e-01,-3.8738e-01}
> Gradient: {-1.1867e-06,1.1369e-07,2.5104e-07,-2.8808e-07,9.8213e-08,1.5784e-06,-4.4192e-07,1.5731e-07,-1.5768e-06,2.5104e-07,2.7206e-07,1.9049e-06,2.1750e-07,6.0755e-07,-4.5699e-08,-1.5768e-06,2.1171e-07,3.6000e-07,6.6728e-08,-4.0880e-07,3.1585e-07,-4.5699e-08,1.0705e-06,-1.2244e-06,-6.2254e-08,1.0688e-06,-7.6607e-07,3.1585e-07,3.9234e-07,-1.1745e-06,5.8866e-07,3.6904e-07,-1.2125e-06,-7.6607e-07,2.7843e-07,5.1663e-07,1.5605e-07,1.8731e-07,1.5605e-07,1.9291e-07,1.5591e-07,2.3566e-07,1.5591e-07,-2.2624e-08,1.5605e-07,-8.3761e-08,1.5605e-07,7.7891e-08,-4.6843e-07,4.6843e-07,-3.8994e-07,3.8994e-07,2.1642e-06,-2.1642e-06,9.8666e-07,-9.8666e-07,1.8911e-06,-1.8911e-06,-4.1314e-07,4.1314e-07}
>>>> Re-trying (3/3).
After: gradient norm = 6.528947043530919E-6
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5428,-0.5428}
Count Table 1:
---------------
h: {0.5862,-0.5862}
Count Table 2:
---------------
h: {0.1087,-0.1087}
Count Table 3:
---------------
h: {0.2047,-0.2047}
Count Table 4:
---------------
h: {0.3882,-0.3882}
Count Table 5:
---------------
h: {0.3874,-0.3874}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-1.2706,-2.0895,-1.1125,-0.7369,-1.1257,-1.2362,0.2094,-1.6731,-0.6688,-2.0941,-2.2190,-1.1257,-2.1490,-2.1070,-3.0984,2.3700,-0.5660,-2.2190,-2.7720,-3.3532,-0.3928,1.4609,-2.1464,-0.5660,0.4568,-3.3857,0.4364,-0.0954,-3.0352,-2.1464,-1.7624,0.0047,-1.7780,-1.3282,0.1297,-3.0352,-1.3282,-1.7780,0.0047,-1.7624,-3.0352,0.1297,-0.0954,0.4364,-3.3857,0.4568,-2.1464,-3.0352,1.4609,-0.3928,-3.3532,-2.7720,-0.5660,-2.1464,2.3700,-3.0984,-2.1070,-2.1490,-2.2190,-0.5660,-2.0941,-0.6688,-1.6731,0.2094,-1.1257,-2.2190,-0.7369,-1.1125,-2.0895,-1.2706,-1.2362,-1.1257}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0780,0.0937}
Activity(exp=1): {0.0780,0.0965}
Activity(exp=2): {0.0780,-1.1999}
Activity(exp=3): {0.0780,-0.9427}
Activity(exp=4): {0.0780,-2.5387}
Activity(exp=5): {0.0780,-2.9281}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
The Likelihood DID NOT improve. Discarding fit component2-2-variation8.
> No varitions possible for Binding mode 2.
> Unfreezing component (component2-3-f0).
>> Starting new optimization: component2-3-f0. (2021-05-21 18:37:07.343).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[249,250]},{"h":[251,252]},{"h":[253,254]},{"h":[255,256]},{"h":[257,258]},{"h":[259,260]}],"bindingModeInteractions":[],"bindingModes":[{},{},{"mononucleotide":[1,0,5,4,2,3,7,6,11,10,8,9,13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14,10,11,6,7,9,8,4,5,0,1,3,2],"activity":[[237,238],[239,240],[241,242],[243,244],[245,246],[247,248]],"dinucleotide":[[43,42,47,46,44,45,37,36,41,40,38,39,67,66,71,70,68,69,61,60,65,64,62,63,49,48,53,52,50,51,55,54,59,58,56,57,79,78,83,82,80,81,73,72,77,76,74,75,103,102,107,106,104,105,97,96,101,100,98,99,85,84,89,88,86,87,91,90,95,94,92,93,115,114,119,118,116,117,109,108,113,112,110,111,139,138,143,142,140,141,133,132,137,136,134,135,121,120,125,124,122,123,127,126,131,130,128,129,151,150,155,154,152,153,145,144,149,148,146,147,175,174,179,178,176,177,169,168,173,172,170,171,157,156,161,160,158,159,163,162,167,166,164,165,187,186,191,190,188,189,181,180,185,184,182,183,211,210,215,214,212,213,205,204,209,208,206,207,193,192,197,196,194,195,199,198,203,202,200,201,223,222,220,226,224,225,217,216,221,220,218,219,234,236,216,222,231,227,235,234,217,223,232,228,228,227,219,225,229,230,232,231,218,224,233,229,208,214,184,190,202,196,209,215,185,191,203,197,204,210,180,186,198,192,205,211,181,187,199,193,207,213,183,189,201,195,206,212,182,188,200,194,172,178,148,154,166,160,173,179,149,155,167,161,168,174,144,150,162,156,169,175,145,151,163,157,171,177,147,153,165,159,170,176,146,152,164,158,136,142,112,118,130,124,137,143,113,119,131,125,132,138,108,114,126,120,133,139,109,115,127,121,135,141,111,117,129,123,134,140,110,116,128,122,100,106,76,82,94,88,101,107,77,83,95,89,96,102,72,78,90,84,97,103,73,79,91,85,99,105,75,81,93,87,98,104,74,80,92,86,64,70,40,46,58,52,65,71,41,47,59,53,60,66,36,42,54,48,61,67,37,43,55,49,63,69,39,45,57,51,62,68,38,44,56,50]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.673343841014609
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gradient norm = 0.006387148145774515
Starting Function Value: 3.673343841014609
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 3.670715586563168 1.000000000000000 156.56439731424743 0.016447674584179
2 4 3.670279860653302 0.127249357581936 0.187840327860455 0.010174659311856
3 5 3.670069081935098 0.049938057362934 1.000000000000000 0.006209385954702
4 6 3.669829321517531 0.058221738157061 1.000000000000000 0.005943799965274
5 7 3.669396525681895 0.183457863308899 1.000000000000000 0.009089401335694
6 8 3.669177005534794 0.273016362672384 1.000000000000000 0.013001766731412
7 9 3.668932353331670 0.096733415031538 1.000000000000000 0.004660430119782
8 10 3.668869726751107 0.036314289014551 1.000000000000000 0.003150411428713
9 11 3.668800633182361 0.053866388519679 1.000000000000000 0.003751669318193
10 12 3.668669251644965 0.117179903195048 1.000000000000000 0.005567595181543
11 13 3.668548828012009 0.195481070680341 1.000000000000000 0.008330848870252
12 14 3.668430183374780 0.103322681759159 1.000000000000000 0.004105820256376
13 15 3.668384562926547 0.028685038302147 1.000000000000000 0.002312367919197
14 16 3.668353676259930 0.029663811920774 1.000000000000000 0.002557526601734
15 17 3.668308639390172 0.049922324097525 1.000000000000000 0.003791705652747
16 18 3.668205302767303 0.141005706428254 1.000000000000000 0.005753674889837
17 19 3.668139912734921 0.228616951398765 1.000000000000000 0.008876252582227
18 20 3.668042577767184 0.053331843608020 1.000000000000000 0.003608823019159
19 21 3.668013376423859 0.027627332716545 1.000000000000000 0.001738320089274
20 22 3.667996795947377 0.023500086179224 1.000000000000000 0.001853114528663
21 23 3.667971074599178 0.044477637737223 1.000000000000000 0.002737719187783
22 24 3.667918171039366 0.104099005533991 1.000000000000000 0.003876488363692
23 25 3.667849547730022 0.148340004218755 1.000000000000000 0.003571284013740
24 27 3.667832012440194 0.060777275632577 0.237570195636126 0.004212887799022
25 28 3.667783907609358 0.115941148928841 1.000000000000000 0.001925400939204
26 29 3.667758720376980 0.053213692404098 1.000000000000000 0.001419670987890
27 30 3.667732560991691 0.062195140799292 1.000000000000000 0.001969690423857
28 31 3.667705681618063 0.073796323357581 1.000000000000000 0.001846436271504
29 32 3.667653210610665 0.154228265991221 1.000000000000000 0.001641085157135
30 33 3.667643725822779 0.274519336586392 1.000000000000000 0.006498711360872
31 34 3.667588315933353 0.028644011457337 1.000000000000000 0.001242324543443
32 35 3.667579102089937 0.017443140170631 1.000000000000000 0.000929313259207
33 36 3.667566566984710 0.050715422234270 1.000000000000000 0.001013468976171
34 37 3.667521919222412 0.147350107232843 1.000000000000000 0.001255595224671
35 38 3.667451110866697 0.304857569738523 1.000000000000000 0.001243313632114
36 39 3.667401574436020 0.381276597098712 1.000000000000000 0.001400886625690
37 40 3.667375018940526 0.325670614435409 1.000000000000000 0.001840735328341
38 41 3.667347242030155 0.089190079687587 1.000000000000000 0.000706931090305
39 42 3.667334421407864 0.047446731850636 1.000000000000000 0.000578688704770
40 43 3.667318645440976 0.084651941923028 1.000000000000000 0.000534421166609
41 44 3.667291848107041 0.190870807853548 1.000000000000000 0.000628232051425
42 45 3.667267136670026 0.289421972961403 1.000000000000000 0.000579409726545
43 46 3.667246149607659 0.139597988721892 1.000000000000000 0.000475044768874
44 47 3.667218053586760 0.207033264998260 1.000000000000000 0.000527435520351
45 48 3.667200234116231 0.194745885076376 1.000000000000000 0.000511919267775
46 49 3.667181682476136 0.162976262266652 1.000000000000000 0.000535310365952
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48 51 3.667127887251609 0.253684198608095 1.000000000000000 0.000578465767518
49 52 3.667102652829000 0.255513485250340 1.000000000000000 0.001110484945118
50 53 3.667091785095389 0.073448412092585 1.000000000000000 0.000369227838877
51 54 3.667088820281357 0.033744673775733 1.000000000000000 0.000271870187569
52 55 3.667086053024360 0.022402145927114 1.000000000000000 0.000352183309439
53 56 3.667077728105108 0.088935220193825 1.000000000000000 0.000529921928613
54 57 3.667068397189565 0.116311127849040 1.000000000000000 0.000503073410423
55 58 3.667060098456195 0.229443533744810 1.000000000000000 0.000643193432604
56 59 3.667051914303775 0.086342336945958 1.000000000000000 0.000220629038935
57 60 3.667048676294452 0.032178870442626 1.000000000000000 0.000207725333236
58 61 3.667044434195560 0.060834858530689 1.000000000000000 0.000336279269945
59 62 3.667036890208921 0.132242571415440 1.000000000000000 0.000444723925456
60 63 3.667020220185996 0.322868417771104 1.000000000000000 0.000537079771481
61 64 3.667015864661149 0.612465241722566 1.000000000000000 0.001513000720359
62 65 3.666995664782327 0.109403126697263 1.000000000000000 0.000447556636243
63 66 3.666989731866658 0.058909372101181 1.000000000000000 0.000240569869861
64 67 3.666985532055825 0.093710676596680 1.000000000000000 0.000358151230127
65 68 3.666975678392441 0.198735043118142 1.000000000000000 0.000515467513477
66 69 3.666953678488800 0.455895118582170 1.000000000000000 0.000661316687442
67 70 3.666921971201881 0.794854750870750 1.000000000000000 0.001107274093512
68 71 3.666894043489112 0.366731146940579 1.000000000000000 0.000608461678668
69 72 3.666875726569721 0.140529521046019 1.000000000000000 0.000326535435328
70 73 3.666865261321278 0.077924442739698 1.000000000000000 0.000470425046519
71 74 3.666848897556199 0.231478828111001 1.000000000000000 0.000722620530626
72 75 3.666820955249119 0.276578999370526 1.000000000000000 0.000694841565575
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78 81 3.666744328927900 0.180425867005559 1.000000000000000 0.000245665259910
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81 84 3.666710989751615 0.078608504596674 1.000000000000000 0.000202878392965
82 85 3.666703637273481 0.116365027100953 1.000000000000000 0.000181520430686
83 86 3.666695965041398 0.143477411911002 1.000000000000000 0.000194887289029
84 87 3.666686976285051 0.256877537946873 1.000000000000000 0.000345652516323
85 88 3.666681931241722 0.116554524691105 1.000000000000000 0.000154797320798
86 89 3.666678425256368 0.074411278895563 1.000000000000000 0.000162203216850
87 90 3.666673678986608 0.110584372025266 1.000000000000000 0.000212105612522
88 91 3.666666358713536 0.191976185095455 1.000000000000000 0.000177528908605
89 92 3.666664098710557 0.227574416977835 1.000000000000000 0.000358429201051
90 93 3.666658436457388 0.053392647507344 1.000000000000000 0.000154233900763
91 94 3.666655382931715 0.057137460321538 1.000000000000000 0.000108558633428
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94 97 3.666641638214741 0.236576405086662 1.000000000000000 0.000171606970765
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97 100 3.666618142160807 0.120890597237686 1.000000000000000 0.000145931189271
98 101 3.666617619670196 0.191966445647307 1.000000000000000 0.000156559185425
99 102 3.666601319791555 0.246797357300308 1.000000000000000 0.000197901628114
100 103 3.666595917904598 0.231993958067230 1.000000000000000 0.000247152840438
101 104 3.666590556771792 0.077834959627397 1.000000000000000 0.000160142286193
102 105 3.666586666827175 0.083697935677620 1.000000000000000 0.000157298346331
103 107 3.666585901727018 0.034888600524489 0.286135767869420 0.000585853878578
104 108 3.666583468428462 0.086539200745928 1.000000000000000 0.000310751379722
105 109 3.666581267884174 0.082163063536483 1.000000000000000 0.000143728275561
106 111 3.666581015167383 0.007331048520862 0.093464825049546 0.000141624323226
107 112 3.666577363382625 0.157626839540334 1.000000000000000 0.000814818227121
108 114 3.666575899159835 0.053271193325002 0.391499387313546 0.000247383258013
109 115 3.666574649201090 0.019999591523865 1.000000000000000 0.000161336599306
110 116 3.666571959097399 0.134911246730014 1.000000000000000 0.000225617061717
111 117 3.666571580614757 0.172921742135929 1.000000000000000 0.000569828453664
112 118 3.666568707888685 0.113284580506851 1.000000000000000 0.000203346157997
113 119 3.666566557310704 0.152439740864802 1.000000000000000 0.000540395105311
114 120 3.666564308276224 0.155074190901351 1.000000000000000 0.000938406866301
115 121 3.666560596926945 0.070857871183469 1.000000000000000 0.000673807624237
116 122 3.666553330786671 0.245313362525977 1.000000000000000 0.000407151603928
117 123 3.666550611215193 0.115087960205070 1.000000000000000 0.000338018648439
118 124 3.666545508981907 0.222363918467897 1.000000000000000 0.000378727773474
119 126 3.666544440720374 0.052548845205625 0.118182187700888 0.000831630159541
120 127 3.666539224220218 0.159760660291189 1.000000000000000 0.000522779405900
121 128 3.666531286815374 0.315013178546396 1.000000000000000 0.000816824320995
122 130 3.666521652169334 0.201453345069539 0.254840959332634 0.001186595665905
123 133 3.666508555339116 0.311303789445452 0.129542205825879 0.002749133073433
124 135 3.666495867269086 0.401074757762294 0.253826382645917 0.005569115112399
125 137 3.666473599989245 0.157873302354760 0.416797340237611 0.002819803744142
126 138 3.666448089948910 0.120869041203830 1.000000000000000 0.001946684813291
127 139 3.666401548846546 0.283058894421699 1.000000000000000 0.002572839381390
128 140 3.666398318248213 0.089413885889137 1.000000000000000 0.004513184165136
129 141 3.666368450311148 0.067728580705478 1.000000000000000 0.001626290786447
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131 143 3.666343265775980 0.167186321202859 1.000000000000000 0.003322824716373
132 144 3.666321216785797 0.180948001517384 1.000000000000000 0.001304005925015
133 145 3.666311152836072 0.123533671953943 1.000000000000000 0.001086703621018
134 146 3.666298272444110 0.066832915579315 1.000000000000000 0.001446176757134
135 147 3.666271017300416 0.164645939052173 1.000000000000000 0.001954202075742
136 149 3.666255179189779 0.130376293614426 0.456104764772800 0.001953889687548
137 150 3.666225334110378 0.117304037966514 1.000000000000000 0.001336031541859
138 151 3.666184657803667 0.165604047107050 1.000000000000000 0.001546380301228
139 152 3.666161598852040 0.122978157519995 1.000000000000000 0.001388600981047
140 153 3.666136968967616 0.131502517574876 1.000000000000000 0.001036903067100
141 154 3.666123235659521 0.193031985022124 1.000000000000000 0.001844584439745
142 155 3.666110995246244 0.145793466912649 1.000000000000000 0.000799917963889
143 156 3.666106046411359 0.057063909411258 1.000000000000000 0.000547373829420
144 157 3.666100596230906 0.072884916460230 1.000000000000000 0.000508986667202
145 158 3.666093847986836 0.098205244842442 1.000000000000000 0.000797324292864
146 159 3.666085007868727 0.086074141642370 1.000000000000000 0.000692651605186
147 160 3.666077180485796 0.104187324809348 1.000000000000000 0.000585548011840
148 161 3.666072663141374 0.075275180624522 1.000000000000000 0.000942925593289
149 162 3.666069032898380 0.030883452141559 1.000000000000000 0.000711709827152
150 163 3.666064140266074 0.068803758160528 1.000000000000000 0.000289874579119
151 164 3.666062320257391 0.034906056187606 1.000000000000000 0.000385463379701
152 165 3.666060511102518 0.040111883185934 1.000000000000000 0.000443558865205
153 166 3.666057844644675 0.038850125045028 1.000000000000000 0.000474900167230
154 167 3.666057404827600 0.078162722908762 1.000000000000000 0.000671942920988
155 168 3.666054442752910 0.033710822130564 1.000000000000000 0.000233977856940
156 169 3.666053785223846 0.016451219171801 1.000000000000000 0.000169361989600
157 170 3.666052892343191 0.020228125135347 1.000000000000000 0.000202375246959
158 171 3.666052043331482 0.020465465269255 1.000000000000000 0.000211622653117
159 172 3.666050658902275 0.040172765806568 1.000000000000000 0.000221567793876
160 173 3.666049823987547 0.041496673458803 1.000000000000000 0.000342645444005
161 174 3.666048767100927 0.021738595201008 1.000000000000000 0.000224914055781
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.0569e+00,-6.0976e-01,-8.0162e-01,-8.7859e-01,-3.9652e-01,-7.8617e-01,-1.0269e+00,4.9420e-02,-1.3318e+00,-8.0162e-01,-7.6089e-01,-6.5779e-01,-1.0528e+00,-9.6110e-01,-5.3879e-01,-1.3318e+00,1.0252e+00,-1.7417e+00,-1.1529e+00,-8.1396e-01,-1.3399e+00,-5.3879e-01,1.5966e-01,-9.1505e-01,-1.3904e+00,3.2441e-01,-1.7849e+00,-1.3399e+00,1.5997e-01,-5.7009e-01,-1.1503e-01,-7.9794e-01,8.9380e-02,-1.7849e+00,-7.5936e-01,-1.2331e+00,-2.1217e-01,-2.4339e-01,-9.4414e-02,0.0000e+00,3.5269e-01,-1.0746e-01,-2.7130e-01,-1.9775e-01,2.7693e-01,0.0000e+00,1.3479e-01,-9.4997e-02,0.0000e+00,0.0000e+00,0.0000e+00,-3.9657e-01,0.0000e+00,0.0000e+00,-1.2869e-01,8.7105e-02,3.4063e-02,0.0000e+00,-3.3807e-01,-8.8058e-02,3.7013e-01,1.2492e-01,-3.4256e-01,0.0000e+00,-1.4261e-01,-1.4130e-01,-1.8300e-01,2.0330e-01,-4.0704e-01,0.0000e+00,-1.4059e-02,1.4735e-02,2.3535e-01,2.4626e-01,-2.1149e-01,0.0000e+00,-3.1542e-03,-6.9200e-01,-1.2652e-01,2.7932e-01,-4.1908e-01,0.0000e+00,2.3092e-01,9.5500e-03,0.0000e+00,0.0000e+00,0.0000e+00,-5.3301e-01,0.0000e+00,0.0000e+00,-4.8289e-01,-1.3875e+00,1.0479e+00,0.0000e+00,5.2349e-01,-9.7477e-02,5.6473e-01,6.8112e-01,-7.4959e-01,0.0000e+00,-8.7871e-01,3.7520e-01,-4.8516e-01,-6.9225e-03,-2.7793e-03,0.0000e+00,2.9970e-01,-2.2191e-01,1.3643e+00,-4.5622e-01,-3.7308e-02,0.0000e+00,-1.0334e-01,-1.0619e+00,3.1152e-01,8.6045e-01,3.5510e-02,0.0000e+00,-5.4389e-01,-8.5136e-01,0.0000e+00,0.0000e+00,0.0000e+00,-3.3508e-01,0.0000e+00,0.0000e+00,-1.0776e-02,-3.2957e-02,1.3990e-03,0.0000e+00,-7.7673e-01,2.8605e-01,-7.5089e-01,-7.5080e-01,-5.4991e-01,0.0000e+00,1.4011e+00,8.2275e-01,-8.6029e-01,5.6325e-01,-1.7200e-02,0.0000e+00,-3.4335e-01,3.0951e-02,1.8272e+00,-9.7361e-01,-1.6923e-02,0.0000e+00,-4.5814e-01,-3.2469e-01,6.4993e-01,2.4223e-02,1.6154e-02,0.0000e+00,-2.6878e-02,-4.7971e-01,0.0000e+00,0.0000e+00,0.0000e+00,-5.6751e-01,0.0000e+00,0.0000e+00,-1.8608e-01,4.9476e-01,-7.7300e-03,0.0000e+00,7.2747e-01,-1.3635e+00,-1.0940e+00,4.2399e-02,-1.8396e-01,0.0000e+00,-4.3358e-01,1.3029e+00,-1.3690e+00,5.7231e-01,-5.0001e-01,0.0000e+00,3.8508e-01,1.3810e-01,3.1690e-01,3.4107e-01,-9.4378e-01,0.0000e+00,7.4833e-01,-6.3447e-01,1.7327e-02,-1.6863e-02,1.1274e-02,0.0000e+00,4.1135e-02,1.0720e-01,0.0000e+00,0.0000e+00,0.0000e+00,-6.9247e-01,0.0000e+00,0.0000e+00,-6.9563e-01,2.1188e-01,4.6086e-01,0.0000e+00,-3.7448e-01,-1.7014e-01,9.2530e-02,-2.7805e-02,1.8418e-01,0.0000e+00,7.4397e-02,-1.2936e-01,1.5224e-01,-6.7197e-01,3.3009e-01,0.0000e+00,-7.7067e-01,2.3344e-01,-2.9655e-01,4.5854e-01,-9.2502e-01,0.0000e+00,-1.1414e-01,4.4674e-01,2.1167e-01,2.3748e-01,-2.0413e-01,0.0000e+00,-2.0180e-01,0.0000e+00,0.0000e+00,0.0000e+00,4.6809e-02,2.6280e-01,1.7487e-01,-5.2678e-04,-8.6116e-01,-1.6098e-01,1.8170e-01,4.9426e-02,5.9327e-02,4.9426e-02,6.1099e-02,4.9380e-02,-1.1751e+00,4.9380e-02,-7.9355e-01,4.9426e-02,-2.0718e+00,4.9426e-02,-1.8187e+00,5.4286e-01,-5.4286e-01,5.8625e-01,-5.8625e-01,1.5375e-01,-1.5375e-01,2.9106e-01,-2.9106e-01,4.0459e-01,-4.0459e-01,4.2368e-01,-4.2368e-01}
> Gradient: {-1.6347e-05,-1.8722e-05,4.3843e-06,-1.8740e-06,-1.4623e-05,-2.2870e-05,-2.4167e-05,-2.1379e-05,4.7593e-08,4.3843e-06,-3.9146e-06,-2.5023e-05,8.0848e-06,-3.7193e-07,-5.4893e-08,4.7593e-08,-7.7840e-05,-2.0303e-07,-2.9356e-06,-8.5064e-06,-7.2406e-06,-5.4893e-08,-2.8262e-05,-2.3338e-05,-2.1524e-05,2.0295e-05,-6.7905e-06,-7.2406e-06,-1.3892e-05,-4.1185e-05,-3.7313e-05,-1.0968e-05,-9.1976e-06,-6.7905e-06,-3.9806e-07,-5.6702e-06,-5.4764e-06,-1.9263e-06,-2.1105e-07,0.0000e+00,-8.7333e-06,3.0092e-06,-3.7701e-07,3.1786e-06,-4.9605e-07,0.0000e+00,-5.1885e-06,-1.4010e-05,0.0000e+00,0.0000e+00,0.0000e+00,6.0045e-06,0.0000e+00,0.0000e+00,-3.5223e-06,-1.4630e-07,1.7599e-06,0.0000e+00,7.5949e-06,-5.7804e-06,-1.3442e-05,-1.5356e-05,9.2496e-07,0.0000e+00,1.5882e-07,1.4152e-05,1.0581e-06,-7.4297e-06,1.2651e-06,0.0000e+00,5.2680e-06,-2.1431e-05,-2.1918e-06,2.6733e-06,-2.7567e-06,0.0000e+00,-2.0013e-05,5.2868e-07,2.8188e-06,5.5851e-06,3.5035e-06,0.0000e+00,-2.9499e-05,-4.0884e-06,0.0000e+00,0.0000e+00,0.0000e+00,3.2428e-06,0.0000e+00,0.0000e+00,6.0083e-06,-3.1740e-06,-5.2755e-07,0.0000e+00,5.3033e-06,-1.6055e-06,3.3648e-06,-4.3545e-06,4.3382e-07,0.0000e+00,-8.5157e-06,8.1715e-06,1.1177e-06,1.9915e-06,1.0692e-07,0.0000e+00,-2.8527e-05,1.2507e-06,-5.4512e-07,1.2673e-05,-5.4082e-07,0.0000e+00,7.8572e-07,-1.2547e-06,7.9578e-06,3.4948e-07,1.3532e-06,0.0000e+00,4.0557e-06,-1.0995e-05,0.0000e+00,0.0000e+00,0.0000e+00,7.5995e-07,0.0000e+00,0.0000e+00,5.8941e-07,-5.5663e-07,-5.8000e-09,0.0000e+00,3.9872e-06,-7.7138e-07,9.9405e-06,-1.4107e-05,-4.7746e-06,0.0000e+00,-5.0208e-05,-2.2102e-05,-1.6051e-05,-2.8745e-06,-1.8286e-07,0.0000e+00,1.1014e-05,1.2352e-05,-1.9714e-06,-2.2669e-07,5.6074e-08,0.0000e+00,-4.3992e-06,8.4327e-06,-3.6011e-06,-6.4180e-07,-8.0056e-07,0.0000e+00,7.3188e-06,-6.7911e-06,0.0000e+00,0.0000e+00,0.0000e+00,-4.1509e-06,0.0000e+00,0.0000e+00,1.0690e-05,-3.8198e-06,1.5917e-07,0.0000e+00,-3.5428e-06,-2.7267e-06,-1.4037e-05,1.7069e-05,-4.7298e-06,0.0000e+00,6.8972e-06,-3.5565e-05,-7.7307e-06,7.2572e-06,2.8944e-06,0.0000e+00,-2.0030e-05,-5.1625e-06,-1.2169e-06,-1.0350e-05,-2.7993e-06,0.0000e+00,-8.1056e-07,-1.4732e-06,-1.9655e-05,9.5262e-06,4.1331e-06,0.0000e+00,1.3927e-05,1.1707e-05,0.0000e+00,0.0000e+00,0.0000e+00,-2.4207e-06,0.0000e+00,0.0000e+00,1.3135e-06,-3.1795e-06,-8.7110e-07,0.0000e+00,-1.1211e-06,-2.9271e-07,-7.9002e-06,8.4766e-06,-2.5398e-06,0.0000e+00,8.5728e-06,-2.0366e-05,-9.8609e-06,-1.2904e-05,-7.3074e-06,0.0000e+00,-1.9054e-05,7.3137e-06,-4.1338e-06,8.2193e-06,2.1367e-06,0.0000e+00,-8.5558e-06,-1.8121e-05,2.0361e-06,-8.6885e-07,1.8138e-06,0.0000e+00,-1.2426e-06,0.0000e+00,0.0000e+00,0.0000e+00,-4.6839e-06,-1.6970e-06,-4.7114e-06,1.9473e-08,-6.9761e-07,4.6443e-08,8.7415e-07,9.8852e-08,1.1865e-07,9.8852e-08,1.2220e-07,9.8759e-08,1.4630e-06,9.8759e-08,-3.6642e-05,9.8852e-08,-3.2384e-06,9.8852e-08,7.3220e-07,3.1031e-05,-3.1031e-05,1.3515e-05,-1.3515e-05,6.2494e-05,-6.2494e-05,6.8571e-05,-6.8571e-05,1.6108e-05,-1.6108e-05,-2.8336e-06,2.8336e-06}
>>>> Re-trying (1/3).
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.0569e+00,-6.0976e-01,-8.0162e-01,-8.7859e-01,-3.9652e-01,-7.8617e-01,-1.0269e+00,4.9420e-02,-1.3318e+00,-8.0162e-01,-7.6089e-01,-6.5779e-01,-1.0528e+00,-9.6110e-01,-5.3879e-01,-1.3318e+00,1.0252e+00,-1.7417e+00,-1.1529e+00,-8.1396e-01,-1.3399e+00,-5.3879e-01,1.5966e-01,-9.1505e-01,-1.3904e+00,3.2441e-01,-1.7849e+00,-1.3399e+00,1.5997e-01,-5.7009e-01,-1.1503e-01,-7.9794e-01,8.9380e-02,-1.7849e+00,-7.5936e-01,-1.2331e+00,-2.1217e-01,-2.4339e-01,-9.4414e-02,0.0000e+00,3.5269e-01,-1.0746e-01,-2.7130e-01,-1.9775e-01,2.7693e-01,0.0000e+00,1.3479e-01,-9.4997e-02,0.0000e+00,0.0000e+00,0.0000e+00,-3.9657e-01,0.0000e+00,0.0000e+00,-1.2869e-01,8.7105e-02,3.4063e-02,0.0000e+00,-3.3807e-01,-8.8058e-02,3.7013e-01,1.2492e-01,-3.4256e-01,0.0000e+00,-1.4261e-01,-1.4130e-01,-1.8300e-01,2.0330e-01,-4.0704e-01,0.0000e+00,-1.4059e-02,1.4735e-02,2.3535e-01,2.4626e-01,-2.1149e-01,0.0000e+00,-3.1542e-03,-6.9200e-01,-1.2652e-01,2.7932e-01,-4.1908e-01,0.0000e+00,2.3092e-01,9.5500e-03,0.0000e+00,0.0000e+00,0.0000e+00,-5.3301e-01,0.0000e+00,0.0000e+00,-4.8289e-01,-1.3875e+00,1.0479e+00,0.0000e+00,5.2349e-01,-9.7477e-02,5.6473e-01,6.8112e-01,-7.4959e-01,0.0000e+00,-8.7871e-01,3.7520e-01,-4.8516e-01,-6.9225e-03,-2.7793e-03,0.0000e+00,2.9970e-01,-2.2191e-01,1.3643e+00,-4.5622e-01,-3.7308e-02,0.0000e+00,-1.0334e-01,-1.0619e+00,3.1152e-01,8.6045e-01,3.5510e-02,0.0000e+00,-5.4389e-01,-8.5136e-01,0.0000e+00,0.0000e+00,0.0000e+00,-3.3508e-01,0.0000e+00,0.0000e+00,-1.0776e-02,-3.2957e-02,1.3990e-03,0.0000e+00,-7.7673e-01,2.8605e-01,-7.5089e-01,-7.5080e-01,-5.4991e-01,0.0000e+00,1.4011e+00,8.2275e-01,-8.6029e-01,5.6325e-01,-1.7200e-02,0.0000e+00,-3.4335e-01,3.0951e-02,1.8272e+00,-9.7361e-01,-1.6923e-02,0.0000e+00,-4.5814e-01,-3.2469e-01,6.4993e-01,2.4223e-02,1.6154e-02,0.0000e+00,-2.6878e-02,-4.7971e-01,0.0000e+00,0.0000e+00,0.0000e+00,-5.6751e-01,0.0000e+00,0.0000e+00,-1.8608e-01,4.9476e-01,-7.7300e-03,0.0000e+00,7.2747e-01,-1.3635e+00,-1.0940e+00,4.2399e-02,-1.8396e-01,0.0000e+00,-4.3358e-01,1.3029e+00,-1.3690e+00,5.7231e-01,-5.0001e-01,0.0000e+00,3.8508e-01,1.3810e-01,3.1690e-01,3.4107e-01,-9.4378e-01,0.0000e+00,7.4833e-01,-6.3447e-01,1.7327e-02,-1.6863e-02,1.1274e-02,0.0000e+00,4.1135e-02,1.0720e-01,0.0000e+00,0.0000e+00,0.0000e+00,-6.9247e-01,0.0000e+00,0.0000e+00,-6.9563e-01,2.1188e-01,4.6086e-01,0.0000e+00,-3.7448e-01,-1.7014e-01,9.2530e-02,-2.7805e-02,1.8418e-01,0.0000e+00,7.4397e-02,-1.2936e-01,1.5224e-01,-6.7197e-01,3.3009e-01,0.0000e+00,-7.7067e-01,2.3344e-01,-2.9655e-01,4.5854e-01,-9.2502e-01,0.0000e+00,-1.1414e-01,4.4674e-01,2.1167e-01,2.3748e-01,-2.0413e-01,0.0000e+00,-2.0180e-01,0.0000e+00,0.0000e+00,0.0000e+00,4.6809e-02,2.6280e-01,1.7487e-01,-5.2678e-04,-8.6116e-01,-1.6098e-01,1.8170e-01,4.9426e-02,5.9327e-02,4.9426e-02,6.1099e-02,4.9380e-02,-1.1751e+00,4.9380e-02,-7.9355e-01,4.9426e-02,-2.0718e+00,4.9426e-02,-1.8187e+00,5.4286e-01,-5.4286e-01,5.8625e-01,-5.8625e-01,1.5375e-01,-1.5375e-01,2.9106e-01,-2.9106e-01,4.0459e-01,-4.0459e-01,4.2368e-01,-4.2368e-01}
> Gradient: {-1.6347e-05,-1.8722e-05,4.3843e-06,-1.8740e-06,-1.4623e-05,-2.2870e-05,-2.4167e-05,-2.1379e-05,4.7593e-08,4.3843e-06,-3.9146e-06,-2.5023e-05,8.0848e-06,-3.7193e-07,-5.4893e-08,4.7593e-08,-7.7840e-05,-2.0303e-07,-2.9356e-06,-8.5064e-06,-7.2406e-06,-5.4893e-08,-2.8262e-05,-2.3338e-05,-2.1524e-05,2.0295e-05,-6.7905e-06,-7.2406e-06,-1.3892e-05,-4.1185e-05,-3.7313e-05,-1.0968e-05,-9.1976e-06,-6.7905e-06,-3.9806e-07,-5.6702e-06,-5.4764e-06,-1.9263e-06,-2.1105e-07,0.0000e+00,-8.7333e-06,3.0092e-06,-3.7701e-07,3.1786e-06,-4.9605e-07,0.0000e+00,-5.1885e-06,-1.4010e-05,0.0000e+00,0.0000e+00,0.0000e+00,6.0045e-06,0.0000e+00,0.0000e+00,-3.5223e-06,-1.4630e-07,1.7599e-06,0.0000e+00,7.5949e-06,-5.7804e-06,-1.3442e-05,-1.5356e-05,9.2496e-07,0.0000e+00,1.5882e-07,1.4152e-05,1.0581e-06,-7.4297e-06,1.2651e-06,0.0000e+00,5.2680e-06,-2.1431e-05,-2.1918e-06,2.6733e-06,-2.7567e-06,0.0000e+00,-2.0013e-05,5.2868e-07,2.8188e-06,5.5851e-06,3.5035e-06,0.0000e+00,-2.9499e-05,-4.0884e-06,0.0000e+00,0.0000e+00,0.0000e+00,3.2428e-06,0.0000e+00,0.0000e+00,6.0083e-06,-3.1740e-06,-5.2755e-07,0.0000e+00,5.3033e-06,-1.6055e-06,3.3648e-06,-4.3545e-06,4.3382e-07,0.0000e+00,-8.5157e-06,8.1715e-06,1.1177e-06,1.9915e-06,1.0692e-07,0.0000e+00,-2.8527e-05,1.2507e-06,-5.4512e-07,1.2673e-05,-5.4082e-07,0.0000e+00,7.8572e-07,-1.2547e-06,7.9578e-06,3.4948e-07,1.3532e-06,0.0000e+00,4.0557e-06,-1.0995e-05,0.0000e+00,0.0000e+00,0.0000e+00,7.5995e-07,0.0000e+00,0.0000e+00,5.8941e-07,-5.5663e-07,-5.8000e-09,0.0000e+00,3.9872e-06,-7.7138e-07,9.9405e-06,-1.4107e-05,-4.7746e-06,0.0000e+00,-5.0208e-05,-2.2102e-05,-1.6051e-05,-2.8745e-06,-1.8286e-07,0.0000e+00,1.1014e-05,1.2352e-05,-1.9714e-06,-2.2669e-07,5.6074e-08,0.0000e+00,-4.3992e-06,8.4327e-06,-3.6011e-06,-6.4180e-07,-8.0056e-07,0.0000e+00,7.3188e-06,-6.7911e-06,0.0000e+00,0.0000e+00,0.0000e+00,-4.1509e-06,0.0000e+00,0.0000e+00,1.0690e-05,-3.8198e-06,1.5917e-07,0.0000e+00,-3.5428e-06,-2.7267e-06,-1.4037e-05,1.7069e-05,-4.7298e-06,0.0000e+00,6.8972e-06,-3.5565e-05,-7.7307e-06,7.2572e-06,2.8944e-06,0.0000e+00,-2.0030e-05,-5.1625e-06,-1.2169e-06,-1.0350e-05,-2.7993e-06,0.0000e+00,-8.1056e-07,-1.4732e-06,-1.9655e-05,9.5262e-06,4.1331e-06,0.0000e+00,1.3927e-05,1.1707e-05,0.0000e+00,0.0000e+00,0.0000e+00,-2.4207e-06,0.0000e+00,0.0000e+00,1.3135e-06,-3.1795e-06,-8.7110e-07,0.0000e+00,-1.1211e-06,-2.9271e-07,-7.9002e-06,8.4766e-06,-2.5398e-06,0.0000e+00,8.5728e-06,-2.0366e-05,-9.8609e-06,-1.2904e-05,-7.3074e-06,0.0000e+00,-1.9054e-05,7.3137e-06,-4.1338e-06,8.2193e-06,2.1367e-06,0.0000e+00,-8.5558e-06,-1.8121e-05,2.0361e-06,-8.6885e-07,1.8138e-06,0.0000e+00,-1.2426e-06,0.0000e+00,0.0000e+00,0.0000e+00,-4.6839e-06,-1.6970e-06,-4.7114e-06,1.9473e-08,-6.9761e-07,4.6443e-08,8.7415e-07,9.8852e-08,1.1865e-07,9.8852e-08,1.2220e-07,9.8759e-08,1.4630e-06,9.8759e-08,-3.6642e-05,9.8852e-08,-3.2384e-06,9.8852e-08,7.3220e-07,3.1031e-05,-3.1031e-05,1.3515e-05,-1.3515e-05,6.2494e-05,-6.2494e-05,6.8571e-05,-6.8571e-05,1.6108e-05,-1.6108e-05,-2.8336e-06,2.8336e-06}
>>>> Re-trying (2/3).
Starting Function Value: 3.6660488264604494
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.666048778732836 0.000389720299412 1.732753416910799 0.000120753009735
2 4 3.666048754677890 0.000236371026078 1.000000000000000 0.000125401952009
3 5 3.666048191116330 0.004896668784115 1.000000000000000 0.000295437654063
4 6 3.666048036175048 0.005171037786907 1.000000000000000 0.000316084134289
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.0571e+00,-6.0912e-01,-8.0220e-01,-8.7858e-01,-3.9683e-01,-7.8638e-01,-1.0261e+00,4.9014e-02,-1.3318e+00,-8.0220e-01,-7.6145e-01,-6.5755e-01,-1.0544e+00,-9.6147e-01,-5.3883e-01,-1.3318e+00,1.0269e+00,-1.7419e+00,-1.1536e+00,-8.1358e-01,-1.3392e+00,-5.3883e-01,1.5834e-01,-9.1462e-01,-1.3895e+00,3.2076e-01,-1.7842e+00,-1.3392e+00,1.5979e-01,-5.6912e-01,-1.1438e-01,-7.9777e-01,8.9030e-02,-1.7842e+00,-7.6063e-01,-1.2335e+00,-2.1230e-01,-2.4370e-01,-9.4394e-02,0.0000e+00,3.5311e-01,-1.0789e-01,-2.7148e-01,-1.9849e-01,2.7698e-01,0.0000e+00,1.3514e-01,-9.4005e-02,0.0000e+00,0.0000e+00,0.0000e+00,-3.9731e-01,0.0000e+00,0.0000e+00,-1.2837e-01,8.7035e-02,3.3890e-02,0.0000e+00,-3.3883e-01,-8.7539e-02,3.7101e-01,1.2574e-01,-3.4265e-01,0.0000e+00,-1.4276e-01,-1.4317e-01,-1.8340e-01,2.0322e-01,-4.0716e-01,0.0000e+00,-1.4769e-02,1.5679e-02,2.3532e-01,2.4591e-01,-2.1122e-01,0.0000e+00,-2.4899e-03,-6.9206e-01,-1.2701e-01,2.7861e-01,-4.1944e-01,0.0000e+00,2.3175e-01,9.8925e-03,0.0000e+00,0.0000e+00,0.0000e+00,-5.3334e-01,0.0000e+00,0.0000e+00,-4.8349e-01,-1.3872e+00,1.0479e+00,0.0000e+00,5.2283e-01,-9.7321e-02,5.6404e-01,6.8145e-01,-7.4964e-01,0.0000e+00,-8.7826e-01,3.7430e-01,-4.8534e-01,-7.1989e-03,-2.8043e-03,0.0000e+00,3.0051e-01,-2.2210e-01,1.3637e+00,-4.5750e-01,-3.7256e-02,0.0000e+00,-1.0363e-01,-1.0618e+00,3.1062e-01,8.6027e-01,3.5376e-02,0.0000e+00,-5.4440e-01,-8.5032e-01,0.0000e+00,0.0000e+00,0.0000e+00,-3.3520e-01,0.0000e+00,0.0000e+00,-1.0835e-02,-3.2903e-02,1.3996e-03,0.0000e+00,-7.7712e-01,2.8612e-01,-7.5211e-01,-7.4963e-01,-5.4945e-01,0.0000e+00,1.4023e+00,8.2320e-01,-8.5873e-01,5.6348e-01,-1.7182e-02,0.0000e+00,-3.4451e-01,2.9643e-02,1.8267e+00,-9.7364e-01,-1.6929e-02,0.0000e+00,-4.5789e-01,-3.2554e-01,6.5014e-01,2.4136e-02,1.6232e-02,0.0000e+00,-2.7722e-02,-4.7908e-01,0.0000e+00,0.0000e+00,0.0000e+00,-5.6711e-01,0.0000e+00,0.0000e+00,-1.8714e-01,4.9511e-01,-7.7457e-03,0.0000e+00,7.2779e-01,-1.3632e+00,-1.0929e+00,3.9863e-02,-1.8350e-01,0.0000e+00,-4.3487e-01,1.3041e+00,-1.3683e+00,5.7102e-01,-5.0029e-01,0.0000e+00,3.8645e-01,1.3796e-01,3.1647e-01,3.4195e-01,-9.4353e-01,0.0000e+00,7.4795e-01,-6.3433e-01,1.8616e-02,-1.8063e-02,1.0596e-02,0.0000e+00,3.9493e-02,1.0585e-01,0.0000e+00,0.0000e+00,0.0000e+00,-6.9223e-01,0.0000e+00,0.0000e+00,-6.9576e-01,2.1219e-01,4.6094e-01,0.0000e+00,-3.7437e-01,-1.7011e-01,9.2806e-02,-2.8843e-02,1.8412e-01,0.0000e+00,7.3316e-02,-1.2764e-01,1.5188e-01,-6.7100e-01,3.3018e-01,0.0000e+00,-7.6913e-01,2.3225e-01,-2.9663e-01,4.5674e-01,-9.2524e-01,0.0000e+00,-1.1378e-01,4.4798e-01,2.1127e-01,2.3743e-01,-2.0431e-01,0.0000e+00,-2.0173e-01,0.0000e+00,0.0000e+00,0.0000e+00,4.6642e-02,2.6297e-01,1.7533e-01,-5.2870e-04,-8.6116e-01,-1.6104e-01,1.8150e-01,4.9416e-02,5.9315e-02,4.9416e-02,6.1087e-02,4.9370e-02,-1.1766e+00,4.9370e-02,-7.9218e-01,4.9416e-02,-2.0716e+00,4.9416e-02,-1.8188e+00,5.4263e-01,-5.4263e-01,5.8615e-01,-5.8615e-01,1.5336e-01,-1.5336e-01,2.9071e-01,-2.9071e-01,4.0450e-01,-4.0450e-01,4.2368e-01,-4.2368e-01}
> Gradient: {2.8877e-05,1.7074e-05,4.3372e-06,2.4088e-06,2.4150e-05,3.9334e-05,3.1154e-05,3.2259e-05,2.1686e-07,4.3372e-06,1.0580e-05,3.7634e-05,1.9776e-05,6.5474e-06,1.8799e-07,2.1686e-07,8.5120e-05,4.0471e-06,1.2041e-05,2.7665e-06,-6.9712e-06,1.8799e-07,7.2555e-05,3.5316e-05,6.6913e-07,7.2901e-07,-6.5983e-06,-6.9712e-06,3.8802e-05,8.9265e-05,5.1249e-05,1.4207e-05,2.2870e-05,-6.5983e-06,1.6281e-05,1.7888e-05,1.8913e-05,8.9354e-06,-1.9187e-07,0.0000e+00,-2.2340e-06,6.4624e-06,7.0782e-06,1.2922e-05,-4.2927e-07,0.0000e+00,-1.7403e-06,1.0726e-06,0.0000e+00,0.0000e+00,0.0000e+00,5.9567e-06,0.0000e+00,0.0000e+00,-2.6184e-06,1.4410e-06,1.7622e-06,0.0000e+00,7.6868e-06,-4.0838e-06,1.3805e-06,5.8064e-07,9.5822e-07,0.0000e+00,2.5412e-06,1.9749e-05,8.8076e-06,8.0794e-06,1.3116e-06,0.0000e+00,7.3397e-06,1.5396e-05,3.7936e-06,4.5719e-06,-2.4699e-06,0.0000e+00,2.6980e-05,6.8500e-07,4.6433e-06,7.6762e-06,3.3837e-06,0.0000e+00,1.9185e-05,-2.9305e-06,0.0000e+00,0.0000e+00,0.0000e+00,3.4108e-06,0.0000e+00,0.0000e+00,5.9995e-06,-3.1732e-06,-5.8185e-07,0.0000e+00,5.2094e-06,-1.4971e-06,6.2122e-06,-3.2488e-06,4.8551e-07,0.0000e+00,4.6266e-07,9.6818e-06,2.1593e-06,3.8134e-06,1.8515e-07,0.0000e+00,2.9872e-05,2.5663e-06,8.0034e-06,1.3132e-05,-5.2260e-07,0.0000e+00,3.3029e-06,-1.1082e-06,9.7537e-06,3.2398e-06,1.3828e-06,0.0000e+00,5.3761e-06,-1.0113e-05,0.0000e+00,0.0000e+00,0.0000e+00,1.0025e-06,0.0000e+00,0.0000e+00,6.0878e-07,-5.3282e-07,-5.9597e-09,0.0000e+00,4.0356e-06,-6.9470e-07,1.4114e-05,-7.7461e-06,-4.5613e-06,0.0000e+00,4.5874e-05,3.4030e-05,-1.5613e-05,-1.3376e-06,-1.7567e-07,0.0000e+00,1.1863e-05,1.3768e-05,7.6467e-06,1.9065e-07,6.6218e-08,0.0000e+00,1.5452e-07,8.8081e-06,2.7328e-07,1.7074e-06,-7.9486e-07,0.0000e+00,1.0744e-05,-5.1739e-06,0.0000e+00,0.0000e+00,0.0000e+00,-3.8828e-06,0.0000e+00,0.0000e+00,1.0729e-05,-3.8931e-06,1.6068e-07,0.0000e+00,-3.3035e-06,-2.6905e-06,-6.6087e-06,-6.6106e-06,-4.5876e-06,0.0000e+00,2.2806e-05,6.5454e-05,-6.4991e-06,8.6775e-06,2.9253e-06,0.0000e+00,8.5377e-06,2.2241e-05,9.1610e-06,-6.4365e-06,-1.6732e-06,0.0000e+00,5.7635e-06,-1.2737e-06,-1.6435e-05,9.3716e-06,-6.7920e-06,0.0000e+00,4.5827e-06,9.3444e-06,0.0000e+00,0.0000e+00,0.0000e+00,-2.2302e-06,0.0000e+00,0.0000e+00,1.3420e-06,-3.1486e-06,-7.1538e-07,0.0000e+00,-1.0878e-06,-2.7304e-07,1.0913e-05,1.4727e-05,8.9649e-06,0.0000e+00,1.4381e-05,-1.0047e-05,4.6261e-05,2.2289e-06,2.2899e-05,0.0000e+00,-5.4469e-06,2.2696e-05,9.8276e-06,1.8871e-05,2.2137e-06,0.0000e+00,8.4358e-06,5.3170e-06,5.7039e-06,1.5822e-06,1.8542e-06,0.0000e+00,-2.3141e-07,0.0000e+00,0.0000e+00,0.0000e+00,1.1350e-05,-1.6655e-06,-4.6703e-06,1.9706e-08,1.1363e-06,8.9643e-07,2.9060e-06,9.8832e-08,1.1863e-07,9.8832e-08,1.2217e-07,9.8740e-08,3.4362e-05,9.8740e-08,2.0031e-05,9.8832e-08,8.1166e-07,9.8832e-08,2.2711e-07,-7.4353e-05,7.4353e-05,-3.5663e-05,3.5663e-05,-8.4445e-05,8.4445e-05,-8.3117e-05,8.3117e-05,-2.2661e-05,2.2661e-05,1.8695e-05,-1.8695e-05}
>>>> Re-trying (3/3).
After: gradient norm = 3.1607249718263694E-4
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5426,-0.5426}
Count Table 1:
---------------
h: {0.5861,-0.5861}
Count Table 2:
---------------
h: {0.1534,-0.1534}
Count Table 3:
---------------
h: {0.2907,-0.2907}
Count Table 4:
---------------
h: {0.4045,-0.4045}
Count Table 5:
---------------
h: {0.4237,-0.4237}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.8802}
Activity(exp=1): {-0.0000,1.0372}
Activity(exp=2): {-0.0000,-0.0000}
Activity(exp=3): {-0.0000,-0.0000}
Activity(exp=4): {-0.0000,0.2185}
Activity(exp=5): {-0.0000,0.0446}
Binding mode 1:
---------------
Mononucleotide: {-0.6456,-0.9703,-0.2689,-0.6460,-0.7197,-0.7896,-0.0990,-0.5821,-0.6527,-1.0189,-0.9678,-0.7197,-0.8126,-1.0237,-1.7014,0.4832,-0.0179,-0.9678,-0.9417,-0.7268,-1.4019,-0.7108,-0.2410,-0.0179,0.4132,-1.4394,-0.7872,-0.6336,-1.3521,-0.2410,-1.0914,0.0497,-1.3751,-0.4723,0.2010,-1.3521,-0.4723,-1.3751,0.0497,-1.0914,-1.3521,0.2010,-0.6336,-0.7872,-1.4394,0.4132,-0.2410,-1.3521,-0.7108,-1.4019,-0.7268,-0.9417,-0.0179,-0.2410,0.4832,-1.7014,-1.0237,-0.8126,-0.9678,-0.0179,-1.0189,-0.6527,-0.5821,-0.0990,-0.7197,-0.9678,-0.6460,-0.2689,-0.9703,-0.6456,-0.7896,-0.7197}
Dinucleotide(d=1): {-0.2494,-0.3675,0.0634,-0.0564,-0.0358,0.0000,-0.2792,-0.4087,-0.2042,-0.2276,0.1492,0.0000,-0.0264,0.0648,-0.3501,0.0136,0.0291,0.0000,0.2834,0.2621,0.0965,-0.5967,-0.6915,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,0.1726,-0.1330,-0.2583,-0.1520,-0.4191,0.0000,-0.2466,-0.4153,-0.6294,0.7179,0.4743,0.0000,-0.1357,-0.1316,-0.0195,0.0045,-0.2999,0.0000,-0.4001,-0.2097,-0.7305,0.3031,0.3845,0.0000,0.6190,0.0429,0.2128,-1.1747,-0.7191,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.6495,-0.3102,-0.5351,0.6326,0.1424,0.0000,0.0558,0.2101,-0.8115,-0.6330,0.3657,0.0000,-0.0981,0.2719,-0.2057,-0.5459,-0.4461,0.0000,0.1398,-0.2292,-1.4139,-0.7996,0.6012,0.0000,-0.4267,-1.1169,2.2366,1.8635,-2.0732,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-0.6128,0.1369,-1.2074,-0.5959,1.3111,0.0000,-0.8165,0.2395,-0.5931,0.0428,0.1853,0.0000,-0.3631,0.2089,-0.6133,-0.3221,0.3625,0.0000,0.9115,-0.6639,-0.8098,-0.2466,-0.5931,0.0000,-0.1238,-1.5692,1.9498,0.2093,-1.1770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,0.8054,0.3450,-0.7209,-0.3171,-0.1301,0.0000,-0.8261,0.7737,-0.1115,0.4674,0.1099,0.0000,0.3643,-1.0716,0.4189,-0.2900,-0.8612,0.0000,-0.6413,0.7106,-0.5063,-0.6133,0.2630,0.0000,-0.0019,0.4750,-0.3983,-0.7154,0.0069,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0134,-0.8379,-0.7782,0.6790,0.6826,0.0000,0.0980,0.2135,-0.6003,-0.8436,0.0398,0.0000,0.9602,-0.8851,0.6487,-0.6003,-0.0817,0.0000,-0.8674,0.6505,-0.8851,0.2135,-0.4803,0.0000,0.1494,-0.8674,0.9602,0.0980,-0.8195,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1907,-0.8195,-0.4803,-0.0817,0.0398,-0.0112,0.0000,-0.7154,-0.6133,-0.2900,0.4674,0.6790,0.0000,-0.3983,-0.5063,0.4189,-0.1115,-0.7782,0.0000,0.4750,0.7106,-1.0716,0.7737,-0.8379,0.0000,-0.0019,-0.6413,0.3643,-0.8261,0.0134,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.3524,0.0069,0.2630,-0.8612,0.1099,0.6826,0.0000,0.2093,-0.2466,-0.3221,0.0428,-0.3171,0.0000,1.9498,-0.8098,-0.6133,-0.5931,-0.7209,0.0000,-1.5692,-0.6639,0.2089,0.2395,0.3450,0.0000,-0.1238,0.9115,-0.3631,-0.8165,0.8054,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2412,-1.1770,-0.5931,0.3625,0.1853,-0.1301,0.0000,1.8635,-0.7996,-0.5459,-0.6330,-0.5959,0.0000,2.2366,-1.4139,-0.2057,-0.8115,-1.2074,0.0000,-1.1169,-0.2292,0.2719,0.2101,0.1369,0.0000,-0.4267,0.1398,-0.0981,0.0558,-0.6128,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0178,-2.0732,0.6012,-0.4461,0.3657,1.3111,0.0000,-1.1747,0.3031,0.0045,0.7179,0.6326,0.0000,0.2128,-0.7305,-0.0195,-0.6294,-0.5351,0.0000,0.0429,-0.2097,-0.1316,-0.4153,-0.3102,0.0000,0.6190,-0.4001,-0.1357,-0.2466,-0.6495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9680,-0.7191,0.3845,-0.2999,0.4743,0.1424,0.0000,-0.5967,0.0136,-0.2276,-0.0564,-0.1520,0.0000,0.0965,-0.3501,-0.2042,0.0634,-0.2583,0.0000,0.2621,0.0648,-0.4087,-0.3675,-0.1330,0.0000,0.2834,-0.0264,-0.2792,-0.2494,0.1726,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7198,-0.6915,0.0291,0.1492,-0.0358,-0.4191,0.0000}
Activity(exp=0): {0.0000,-1.4412}
Activity(exp=1): {0.0000,-1.6459}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-0.6004}
Activity(exp=5): {0.0000,-0.4198}
Binding mode 2:
---------------
Mononucleotide: {-0.6091,-1.0571,-0.7864,-0.3968,-0.8022,-0.8786,0.0490,-1.0261,-0.6575,-0.7615,-1.3318,-0.8022,-0.9615,-1.0544,-1.7419,1.0269,-0.5388,-1.3318,-0.8136,-1.1536,-0.9146,0.1583,-1.3392,-0.5388,0.3208,-1.3895,-0.5691,0.1598,-1.7842,-1.3392,-0.7978,-0.1144,-1.2335,-0.7606,0.0890,-1.7842,-0.7606,-1.2335,-0.1144,-0.7978,-1.7842,0.0890,0.1598,-0.5691,-1.3895,0.3208,-1.3392,-1.7842,0.1583,-0.9146,-1.1536,-0.8136,-0.5388,-1.3392,1.0269,-1.7419,-1.0544,-0.9615,-1.3318,-0.5388,-0.7615,-0.6575,-1.0261,0.0490,-0.8022,-1.3318,-0.3968,-0.7864,-1.0571,-0.6091,-0.8786,-0.8022}
Dinucleotide(d=1): {-0.1985,-0.2715,-0.0940,0.1351,0.2770,0.0000,-0.2437,-0.2123,-0.1079,0.3531,-0.0944,0.0000,0.2032,-0.1834,0.0157,-0.0148,-0.4072,0.0000,0.1257,0.3710,-0.1432,-0.1428,-0.3426,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3973,0.0870,-0.1284,-0.0875,-0.3388,0.0339,0.0000,0.2786,-0.1270,0.0099,0.2318,-0.4194,0.0000,0.2459,0.2353,-0.6921,-0.0025,-0.2112,0.0000,-0.0072,-0.4853,-0.2221,0.3005,-0.0028,0.0000,0.6814,0.5640,0.3743,-0.8783,-0.7496,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5333,-1.3872,-0.4835,-0.0973,0.5228,1.0479,0.0000,0.8603,0.3106,-0.8503,-0.5444,0.0354,0.0000,-0.4575,1.3637,-1.0618,-0.1036,-0.0373,0.0000,0.5635,-0.8587,0.0296,-0.3445,-0.0172,0.0000,-0.7496,-0.7521,0.8232,1.4023,-0.5495,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3352,-0.0329,-0.0108,0.2861,-0.7771,0.0014,0.0000,0.0241,0.6501,-0.4791,-0.0277,0.0162,0.0000,-0.9736,1.8267,-0.3255,-0.4579,-0.0169,0.0000,0.5710,-1.3683,0.1380,0.3864,-0.5003,0.0000,0.0399,-1.0929,1.3041,-0.4349,-0.1835,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5671,0.4951,-0.1871,-1.3632,0.7278,-0.0077,0.0000,-0.0181,0.0186,0.1058,0.0395,0.0106,0.0000,0.3419,0.3165,-0.6343,0.7479,-0.9435,0.0000,-0.6710,0.1519,0.2322,-0.7691,0.3302,0.0000,-0.0288,0.0928,-0.1276,0.0733,0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6922,0.2122,-0.6958,-0.1701,-0.3744,0.4609,0.0000,0.2374,0.2113,-0.1138,-0.2017,-0.2043,0.0000,0.4567,-0.2966,0.4480,-0.1138,-0.9252,0.0000,-0.8612,0.1815,-0.2966,0.2113,0.2630,0.0000,-0.1610,-0.8612,0.4567,0.2374,0.1753,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0466,0.1753,0.2630,-0.9252,-0.2043,-0.0005,0.0000,0.0733,-0.7691,0.7479,0.0395,-0.3744,0.0000,-0.1276,0.2322,-0.6343,0.1058,-0.1701,0.0000,0.0928,0.1519,0.3165,0.0186,-0.6958,0.0000,-0.0288,-0.6710,0.3419,-0.0181,0.2122,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6922,0.1841,0.3302,-0.9435,0.0106,0.4609,0.0000,-0.4349,0.3864,-0.4579,-0.0277,0.7278,0.0000,1.3041,0.1380,-0.3255,-0.4791,-1.3632,0.0000,-1.0929,-1.3683,1.8267,0.6501,-0.1871,0.0000,0.0399,0.5710,-0.9736,0.0241,0.4951,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5671,-0.1835,-0.5003,-0.0169,0.0162,-0.0077,0.0000,1.4023,-0.3445,-0.1036,-0.5444,-0.7771,0.0000,0.8232,0.0296,-1.0618,-0.8503,0.2861,0.0000,-0.7521,-0.8587,1.3637,0.3106,-0.0108,0.0000,-0.7496,0.5635,-0.4575,0.8603,-0.0329,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3352,-0.5495,-0.0172,-0.0373,0.0354,0.0014,0.0000,-0.8783,0.3005,-0.0025,0.2318,0.5228,0.0000,0.3743,-0.2221,-0.6921,0.0099,-0.0973,0.0000,0.5640,-0.4853,0.2353,-0.1270,-0.4835,0.0000,0.6814,-0.0072,0.2459,0.2786,-1.3872,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5333,-0.7496,-0.0028,-0.2112,-0.4194,1.0479,0.0000,-0.1428,-0.0148,0.3531,0.1351,-0.3388,0.0000,-0.1432,0.0157,-0.1079,-0.0940,-0.0875,0.0000,0.3710,-0.1834,-0.2123,-0.2715,-0.1284,0.0000,0.1257,0.2032,-0.2437,-0.1985,0.0870,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3973,-0.3426,-0.4072,-0.0944,0.2770,0.0339,0.0000}
Activity(exp=0): {0.0494,0.0593}
Activity(exp=1): {0.0494,0.0611}
Activity(exp=2): {0.0494,-1.1766}
Activity(exp=3): {0.0494,-0.7922}
Activity(exp=4): {0.0494,-2.0716}
Activity(exp=5): {0.0494,-1.8188}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
> Optimizing the full model (component2-4-all).
>> Starting new optimization: component2-4-all. (2021-05-21 18:48:49.939).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[510,511]},{"h":[512,513]},{"h":[514,515]},{"h":[516,517]},{"h":[518,519]},{"h":[520,521]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5],[6,7],[8,9],[10,11]]},{"mononucleotide":[13,12,17,16,14,15,19,18,23,22,20,21,25,24,29,28,26,27,31,30,35,34,32,33,37,36,41,40,38,39,43,42,47,46,44,45,46,47,42,43,45,44,40,41,36,37,39,38,34,35,30,31,33,32,28,29,24,25,27,26,22,23,18,19,21,20,16,17,12,13,15,14],"activity":[[249,250],[251,252],[253,254],[255,256],[257,258],[259,260]],"dinucleotide":[[55,54,59,58,56,57,49,48,53,52,50,51,79,78,83,82,80,81,73,72,77,76,74,75,61,60,65,64,62,63,67,66,71,70,68,69,91,90,95,94,92,93,85,84,89,88,86,87,115,114,119,118,116,117,109,108,113,112,110,111,97,96,101,100,98,99,103,102,107,106,104,105,127,126,131,130,128,129,121,120,125,124,122,123,151,150,155,154,152,153,145,144,149,148,146,147,133,132,137,136,134,135,139,138,143,142,140,141,163,162,167,166,164,165,157,156,161,160,158,159,187,186,191,190,188,189,181,180,185,184,182,183,169,168,173,172,170,171,175,174,179,178,176,177,199,198,203,202,200,201,193,192,197,196,194,195,223,222,227,226,224,225,217,216,221,220,218,219,205,204,209,208,206,207,211,210,215,214,212,213,235,234,232,238,236,237,229,228,233,232,230,231,246,248,228,234,243,239,247,246,229,235,244,240,240,239,231,237,241,242,244,243,230,236,245,241,220,226,196,202,214,208,221,227,197,203,215,209,216,222,192,198,210,204,217,223,193,199,211,205,219,225,195,201,213,207,218,224,194,200,212,206,184,190,160,166,178,172,185,191,161,167,179,173,180,186,156,162,174,168,181,187,157,163,175,169,183,189,159,165,177,171,182,188,158,164,176,170,148,154,124,130,142,136,149,155,125,131,143,137,144,150,120,126,138,132,145,151,121,127,139,133,147,153,123,129,141,135,146,152,122,128,140,134,112,118,88,94,106,100,113,119,89,95,107,101,108,114,84,90,102,96,109,115,85,91,103,97,111,117,87,93,105,99,110,116,86,92,104,98,76,82,52,58,70,64,77,83,53,59,71,65,72,78,48,54,66,60,73,79,49,55,67,61,75,81,51,57,69,63,74,80,50,56,68,62]]},{"mononucleotide":[262,261,266,265,263,264,268,267,272,271,269,270,274,273,278,277,275,276,280,279,284,283,281,282,286,285,290,289,287,288,292,291,296,295,293,294,295,296,291,292,294,293,289,290,285,286,288,287,283,284,279,280,282,281,277,278,273,274,276,275,271,272,267,268,270,269,265,266,261,262,264,263],"activity":[[498,499],[500,501],[502,503],[504,505],[506,507],[508,509]],"dinucleotide":[[304,303,308,307,305,306,298,297,302,301,299,300,328,327,332,331,329,330,322,321,326,325,323,324,310,309,314,313,311,312,316,315,320,319,317,318,340,339,344,343,341,342,334,333,338,337,335,336,364,363,368,367,365,366,358,357,362,361,359,360,346,345,350,349,347,348,352,351,356,355,353,354,376,375,380,379,377,378,370,369,374,373,371,372,400,399,404,403,401,402,394,393,398,397,395,396,382,381,386,385,383,384,388,387,392,391,389,390,412,411,416,415,413,414,406,405,410,409,407,408,436,435,440,439,437,438,430,429,434,433,431,432,418,417,422,421,419,420,424,423,428,427,425,426,448,447,452,451,449,450,442,441,446,445,443,444,472,471,476,475,473,474,466,465,470,469,467,468,454,453,458,457,455,456,460,459,464,463,461,462,484,483,481,487,485,486,478,477,482,481,479,480,495,497,477,483,492,488,496,495,478,484,493,489,489,488,480,486,490,491,493,492,479,485,494,490,469,475,445,451,463,457,470,476,446,452,464,458,465,471,441,447,459,453,466,472,442,448,460,454,468,474,444,450,462,456,467,473,443,449,461,455,433,439,409,415,427,421,434,440,410,416,428,422,429,435,405,411,423,417,430,436,406,412,424,418,432,438,408,414,426,420,431,437,407,413,425,419,397,403,373,379,391,385,398,404,374,380,392,386,393,399,369,375,387,381,394,400,370,376,388,382,396,402,372,378,390,384,395,401,371,377,389,383,361,367,337,343,355,349,362,368,338,344,356,350,357,363,333,339,351,345,358,364,334,340,352,346,360,366,336,342,354,348,359,365,335,341,353,347,325,331,301,307,319,313,326,332,302,308,320,314,321,327,297,303,315,309,322,328,298,304,316,310,324,330,300,306,318,312,323,329,299,305,317,311]]},{}]}
Value and gradient before optimization:
=======================================
value = 3.6660481416374577
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gradient norm = 0.009117673239447897
Starting Function Value: 3.6660481416374577
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
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13 15 3.665192862109655 0.025998857286471 1.000000000000000 0.002899983729367
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429 451 3.656915408645194 0.010641574955279 0.381541000634582 0.000230404045198
430 452 3.656915198676377 0.013197944121563 1.000000000000000 0.000114521440176
431 453 3.656915013060340 0.012809252963999 1.000000000000000 0.000091436286804
432 454 3.656914804143920 0.016167246773489 1.000000000000000 0.000111238109424
433 455 3.656914527416811 0.019844179815164 1.000000000000000 0.000099304673586
434 457 3.656914406514713 0.019577870863523 0.341485662002503 0.000190793275716
435 458 3.656914138182529 0.022313518340807 1.000000000000000 0.000091504852554
436 459 3.656913938962004 0.017860194196070 1.000000000000000 0.000093103433451
437 460 3.656913623898780 0.029538629717659 1.000000000000000 0.000118668685884
438 462 3.656913477786419 0.023736883591385 0.443316229513813 0.000238742579630
439 463 3.656913212382933 0.027796289246569 1.000000000000000 0.000128210254876
440 464 3.656912991947998 0.018997205714438 1.000000000000000 0.000083177115854
441 465 3.656912790910067 0.022271998809657 1.000000000000000 0.000110178373528
442 466 3.656912570490218 0.024088754871424 1.000000000000000 0.000112272208147
443 467 3.656912289054554 0.028409563581015 1.000000000000000 0.000094705705870
444 468 3.656911934685299 0.030493747231628 1.000000000000000 0.000117692976460
445 469 3.656911599357800 0.041663805111366 1.000000000000000 0.000092049089833
446 470 3.656911389645952 0.027155191906880 1.000000000000000 0.000103923455759
447 471 3.656911284459333 0.047602994534062 1.000000000000000 0.000226389401025
448 472 3.656911109792186 0.007823996351952 1.000000000000000 0.000080668100385
449 473 3.656910983070096 0.008521059960360 1.000000000000000 0.000078439910124
450 474 3.656910826855799 0.017933901532050 1.000000000000000 0.000102258876162
451 475 3.656910611093577 0.024341049912541 1.000000000000000 0.000125379336403
452 477 3.656910495616464 0.019528613227336 0.190314951263839 0.000161982040487
453 478 3.656910184189426 0.036003337181074 1.000000000000000 0.000088904376817
454 479 3.656909950995018 0.023543403383831 1.000000000000000 0.000089831804281
455 480 3.656909631438649 0.034948035182095 1.000000000000000 0.000117526428036
456 481 3.656909475788714 0.051346744935818 1.000000000000000 0.000181020081890
457 482 3.656909099613155 0.019570493529573 1.000000000000000 0.000083552042871
458 483 3.656908823217695 0.014812296297697 1.000000000000000 0.000085708766193
459 484 3.656908501184833 0.034496844976667 1.000000000000000 0.000099713533069
460 486 3.656908393822291 0.021705898828577 0.267232433657435 0.000165630879648
461 487 3.656908212309410 0.033411463707829 1.000000000000000 0.000093228407674
462 488 3.656908047588441 0.031621019072782 1.000000000000000 0.000070820500786
463 489 3.656907844108744 0.033290926327059 1.000000000000000 0.000105702677854
464 490 3.656907520659729 0.041847625390072 1.000000000000000 0.000140082806766
465 491 3.656907054386277 0.055508571709014 1.000000000000000 0.000187436484947
466 493 3.656906866294078 0.034591054970377 0.367658301992451 0.000192743733100
467 494 3.656906621632697 0.017314678123326 1.000000000000000 0.000080681294032
468 495 3.656906495624510 0.012324989339835 1.000000000000000 0.000065405093438
469 496 3.656906367342603 0.009075551330748 1.000000000000000 0.000088030767472
470 497 3.656906145273974 0.024447129960193 1.000000000000000 0.000098757489671
471 499 3.656906033306229 0.028286708318996 0.352725731410048 0.000148991448100
472 500 3.656905860668041 0.025800911091689 1.000000000000000 0.000079352718868
473 501 3.656905716565275 0.026738849526710 1.000000000000000 0.000069509255658
474 502 3.656905635183010 0.013806121237920 1.000000000000000 0.000087334630845
475 503 3.656905491414332 0.020021344813195 1.000000000000000 0.000125262443122
476 504 3.656905349106204 0.032956600871798 1.000000000000000 0.000101925008683
477 505 3.656905196927860 0.007711607119841 1.000000000000000 0.000065074958202
478 506 3.656905031051701 0.014608832408586 1.000000000000000 0.000087330423431
479 507 3.656905003237695 0.024191257336851 1.000000000000000 0.000227248566569
480 508 3.656904885066054 0.008767390996484 1.000000000000000 0.000100692428264
481 509 3.656904797666696 0.018380700189547 1.000000000000000 0.000068015610160
482 510 3.656904729741298 0.022063342414169 1.000000000000000 0.000087305944000
483 511 3.656904648511583 0.018986750233295 1.000000000000000 0.000084606715801
484 512 3.656904518924355 0.030714828416586 1.000000000000000 0.000079509880263
485 514 3.656904438547410 0.019592415547160 0.338660489311908 0.000122085250894
486 515 3.656904319030688 0.009591098457708 1.000000000000000 0.000092564205149
487 516 3.656904141701997 0.023047769242714 1.000000000000000 0.000066598471938
488 518 3.656904083410236 0.011148685364647 0.375770592367600 0.000102882266684
489 519 3.656904004227716 0.010578028446167 1.000000000000000 0.000079952087294
490 520 3.656903849366417 0.031599220330725 1.000000000000000 0.000071016684129
491 521 3.656903749385242 0.025199379685886 1.000000000000000 0.000067507501758
492 522 3.656903672182448 0.057127411707419 1.000000000000000 0.000198838293001
493 523 3.656903477784581 0.014062064665413 1.000000000000000 0.000065584717885
494 524 3.656903386664340 0.006441369961938 1.000000000000000 0.000059780879208
495 525 3.656903268791455 0.013957955553605 1.000000000000000 0.000082120181268
496 526 3.656903123616130 0.023280818807074 1.000000000000000 0.000101792883756
497 527 3.656902943556196 0.038396570858913 1.000000000000000 0.000068884785774
498 528 3.656902756409335 0.037550199023921 1.000000000000000 0.000082028615886
499 529 3.656902562358492 0.039288987032290 1.000000000000000 0.000079805958667
500 530 3.656902453693212 0.035555091126902 1.000000000000000 0.000096971502558
>>> Maximum iteration count reached.
After: gradient norm = 9.697150255823326E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6214,-0.6214}
Count Table 3:
---------------
h: {0.6336,-0.6336}
Count Table 4:
---------------
h: {0.8389,-0.8389}
Count Table 5:
---------------
h: {0.9827,-0.9827}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,0.0000}
Activity(exp=5): {0.0000,0.0000}
==================================
== Starts fiting Binding mode 3 ==
==================================
> Optimizing h (component3-0-h).
>> Starting new optimization: component3-0-h. (2021-05-21 19:29:27.613).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]},{"h":[6,7]},{"h":[8,9]},{"h":[10,11]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{}]}
Value and gradient before optimization:
=======================================
value = 4.387896173450695
gradient = {0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.3677,0.3677,-0.3021,0.3021}
gradient norm = 0.6730203322489482
Starting Function Value: 4.387896173450695
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 3.862519438394367 1.000000000000000 1.485839211808690 0.355104945856295
2 3 3.720507804127612 1.125587683451966 1.000000000000000 0.109056274403633
3 4 3.705908591649905 0.263534786991224 1.000000000000000 0.001070390549083
4 5 3.705907258636385 0.002565630193738 1.000000000000000 0.000028941594190
5 6 3.705907225370345 0.000070371353583 1.000000000000000 0.000000857596166
Gradient = {-1.0988e-09,1.0988e-09,3.4646e-08,-3.4646e-08,6.5205e-09,-6.5205e-09,5.1202e-11,-5.1202e-11,-2.0527e-07,2.0527e-07,-5.6952e-07,5.6952e-07}
pCurr = {2.8882e-09,-2.8882e-09,-8.9850e-08,8.9850e-08,-1.7092e-08,1.7092e-08,-1.1016e-10,1.1016e-10,4.8481e-07,-4.8481e-07,1.4584e-06,-1.4584e-06}
grad*pCur = -1.866640902551569E-12
parameters = {9.6665e-02,-9.6665e-02,-1.1076e-02,1.1076e-02,6.2140e-01,-6.2140e-01,6.3351e-01,-6.3351e-01,1.8690e+00,-1.8690e+00,1.8140e+00,-1.8140e+00}
|grad|/|x| = 2.2024857276223578E-7
>>>> Exception caugth. Parameters reverted.
> Parameter: {9.6665e-02,-9.6665e-02,-1.1076e-02,1.1076e-02,6.2140e-01,-6.2140e-01,6.3351e-01,-6.3351e-01,1.8690e+00,-1.8690e+00,1.8140e+00,-1.8140e+00}
> Gradient: {-1.0988e-09,1.0988e-09,3.4646e-08,-3.4646e-08,6.5205e-09,-6.5205e-09,5.1202e-11,-5.1202e-11,-2.0527e-07,2.0527e-07,-5.6952e-07,5.6952e-07}
>>>> Re-trying (1/3).
Gradient = {-1.0987e-09,1.0987e-09,3.4642e-08,-3.4642e-08,6.9063e-09,-6.9063e-09,5.1195e-11,-5.1195e-11,-2.0503e-07,2.0503e-07,-5.6946e-07,5.6946e-07}
pCurr = {1.0988e-09,-1.0988e-09,-3.4646e-08,3.4646e-08,-6.5205e-09,6.5205e-09,-5.1202e-11,5.1202e-11,2.0527e-07,-2.0527e-07,5.6952e-07,-5.6952e-07}
grad*pCur = -7.353045200827682E-13
parameters = {9.6665e-02,-9.6665e-02,-1.1076e-02,1.1076e-02,6.2140e-01,-6.2140e-01,6.3351e-01,-6.3351e-01,1.8690e+00,-1.8690e+00,1.8140e+00,-1.8140e+00}
|grad|/|x| = 2.2019875481470734E-7
>>>> Exception caugth. Parameters reverted.
> Parameter: {9.6665e-02,-9.6665e-02,-1.1076e-02,1.1076e-02,6.2140e-01,-6.2140e-01,6.3351e-01,-6.3351e-01,1.8690e+00,-1.8690e+00,1.8140e+00,-1.8140e+00}
> Gradient: {-1.0987e-09,1.0987e-09,3.4642e-08,-3.4642e-08,6.9063e-09,-6.9063e-09,5.1195e-11,-5.1195e-11,-2.0503e-07,2.0503e-07,-5.6946e-07,5.6946e-07}
>>>> Re-trying (2/3).
>>>> Exception caugth. Parameters reverted.
> Parameter: {9.6665e-02,-9.6665e-02,-1.1076e-02,1.1076e-02,6.2140e-01,-6.2140e-01,6.3351e-01,-6.3351e-01,1.8690e+00,-1.8690e+00,1.8140e+00,-1.8140e+00}
> Gradient: {-1.0988e-09,1.0988e-09,3.4646e-08,-3.4646e-08,6.5205e-09,-6.5205e-09,5.1202e-11,-5.1202e-11,-2.0527e-07,2.0527e-07,-5.6952e-07,5.6952e-07}
>>>> Re-trying (3/3).
After: gradient norm = 8.575961661089979E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6214,-0.6214}
Count Table 3:
---------------
h: {0.6335,-0.6335}
Count Table 4:
---------------
h: {1.8690,-1.8690}
Count Table 5:
---------------
h: {1.8140,-1.8140}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {4.3723,4.3510}
Activity(exp=1): {4.3723,4.1885}
Activity(exp=2): {4.3799,5.4065}
Activity(exp=3): {4.3799,5.2368}
Activity(exp=4): {4.3809,5.4934}
Activity(exp=5): {4.3809,5.6125}
> Initial optimization (component3-1-f1).
>> Starting new optimization: component3-1-f1. (2021-05-21 19:31:35.319).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[84,85]},{"h":[86,87]},{"h":[88,89]},{"h":[90,91]},{"h":[92,93]},{"h":[94,95]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[72,73],[74,75],[76,77],[78,79],[80,81],[82,83]]}]}
Value and gradient before optimization:
=======================================
value = 3.705907207805773
gradient = {0.0036,0.0060,0.0128,0.0074,-0.0006,-0.0008,0.0024,0.0071,0.0112,0.0090,-0.0007,-0.0006,0.0051,0.0053,0.0080,0.0121,-0.0013,-0.0007,0.0054,0.0027,0.0064,0.0165,-0.0013,-0.0013,0.0011,0.0049,0.0228,0.0022,-0.0013,-0.0013,0.0034,0.0172,0.0066,0.0043,-0.0018,-0.0013,0.0182,0.0057,0.0014,0.0059,-0.0011,-0.0018,0.0030,0.0066,0.0076,0.0140,-0.0016,-0.0011,0.0048,0.0213,0.0052,0.0015,-0.0028,-0.0016,0.0176,0.0084,0.0028,0.0032,-0.0008,-0.0028,0.0094,0.0120,0.0043,0.0038,-0.0004,-0.0008,0.0097,0.0103,0.0060,0.0035,-0.0007,-0.0004,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0103,0.0000,0.0181,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 0.06833751582651189
Starting Function Value: 3.705907207805773
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.703299890773788 0.078205382570083 1.144398967744493 0.051276583992524
2 4 3.701439935991615 0.045693860287947 1.000000000000000 0.049317250206169
3 6 3.671339544391934 1.091392069377750 0.365541179341703 0.059956810472026
4 7 3.666685460184326 0.770820808432878 1.000000000000000 0.107622401625298
5 8 3.661950992379996 0.245496896186260 1.000000000000000 0.039049749903585
6 9 3.660038603984952 0.131410070810608 1.000000000000000 0.021591732593153
7 10 3.657739326393140 0.363710892189390 1.000000000000000 0.018663280870468
8 11 3.656888093414616 0.196331198942673 1.000000000000000 0.015107610157480
9 12 3.656252794581722 0.170754821846036 1.000000000000000 0.005868448735681
10 13 3.655925054017628 0.203407630732538 1.000000000000000 0.006158865036548
11 14 3.655590896307565 0.228529435046260 1.000000000000000 0.004443909566658
12 15 3.655383928655825 0.352323797286312 1.000000000000000 0.006353061722355
13 16 3.655160716456033 0.219696766169396 1.000000000000000 0.002043727850532
14 17 3.654863006476994 0.570370236977124 1.000000000000000 0.002304661166678
15 19 3.654842012491012 0.061337186439216 0.037850757080291 0.004171072902050
16 20 3.654599950572883 0.686054295477268 1.000000000000000 0.002739533496869
17 21 3.654584819149659 0.223666255368606 1.000000000000000 0.000903700816768
18 22 3.654577041292856 0.045724162175407 1.000000000000000 0.002293743639977
19 23 3.654543703326781 0.104630135409050 1.000000000000000 0.003156150986764
20 24 3.654377043950171 0.811455319065227 1.000000000000000 0.003623892409505
21 25 3.654335465078462 0.217120676191765 1.000000000000000 0.003006123863470
22 26 3.654300808932797 0.117750855166407 1.000000000000000 0.001824878573138
23 27 3.654273629682471 0.055077751273294 1.000000000000000 0.002974752912590
24 28 3.654215750450619 0.178013059035595 1.000000000000000 0.005412046191838
25 29 3.654175927957044 0.099026774078706 1.000000000000000 0.006314250607464
26 30 3.654083320626114 0.247556447936192 1.000000000000000 0.007095831665751
27 31 3.653994427251976 0.265009732575169 1.000000000000000 0.005938622489083
28 33 3.653951492821403 0.250560404577457 0.494572059252010 0.004876794983973
29 34 3.653913792003471 0.098835861666803 1.000000000000000 0.001235626735590
30 35 3.653910069992296 0.083233497813583 1.000000000000000 0.000796585491459
31 36 3.653908512581046 0.004544781688142 1.000000000000000 0.000663173087059
32 37 3.653905267631016 0.010634839591594 1.000000000000000 0.000953385726733
33 38 3.653897134926571 0.034596817720134 1.000000000000000 0.001944700778804
34 39 3.653875606386610 0.083916440962719 1.000000000000000 0.003417871864247
35 40 3.653830038316162 0.201141682979033 1.000000000000000 0.005128213026685
36 41 3.653767436553180 0.345888245210130 1.000000000000000 0.005536105126976
37 42 3.653722599834513 0.261533862327877 1.000000000000000 0.003159278556258
38 43 3.653706729044801 0.153096060591087 1.000000000000000 0.001868967186526
39 44 3.653701376597330 0.032040640845891 1.000000000000000 0.000765593061344
40 45 3.653700006896823 0.017392069275589 1.000000000000000 0.000619979529328
41 46 3.653697040350579 0.066739347980817 1.000000000000000 0.000822196375346
42 47 3.653693440111708 0.026878991805850 1.000000000000000 0.001037803711532
43 48 3.653677628288397 0.109566204827615 1.000000000000000 0.002062637593635
44 49 3.653649911464917 0.172939249000057 1.000000000000000 0.002751077258843
45 50 3.653598812972483 0.335449457136066 1.000000000000000 0.003619316115413
46 51 3.653544824302773 0.370528335989095 1.000000000000000 0.002416926514199
47 52 3.653516935885756 0.200232037077953 1.000000000000000 0.000559661944508
48 53 3.653513716522039 0.175993452332161 1.000000000000000 0.000606325167858
49 54 3.653507087172272 0.050380369221711 1.000000000000000 0.000479877622540
50 55 3.653484269255916 0.203838303611874 1.000000000000000 0.001684964552480
51 56 3.653439565055300 0.430992805139297 1.000000000000000 0.002510758893084
52 57 3.653405443935479 0.412238360753777 1.000000000000000 0.001897559703016
53 58 3.653382400900546 0.268041686375308 1.000000000000000 0.002027953804399
54 59 3.653363908519407 0.207561766310968 1.000000000000000 0.000443288433325
55 60 3.653355204147282 0.099326989389996 1.000000000000000 0.001305211314728
56 61 3.653347712987487 0.063198435810524 1.000000000000000 0.001930553491548
57 62 3.653329840498839 0.169983155059708 1.000000000000000 0.002810923460571
58 63 3.653307204327611 0.182720627650174 1.000000000000000 0.003142360196247
59 64 3.653271509964441 0.246718874184519 1.000000000000000 0.002247089517321
60 65 3.653250192406805 0.154294800818355 1.000000000000000 0.000652015686223
61 66 3.653245728814386 0.077949190032896 1.000000000000000 0.000442697468228
62 67 3.653244611834575 0.055882656393327 1.000000000000000 0.000415585492229
63 68 3.653227499906781 0.119710130872356 1.000000000000000 0.000556905086716
64 69 3.653202611275569 0.558209182865705 1.000000000000000 0.001239179473005
65 70 3.653185815572717 0.175450234933900 1.000000000000000 0.000589318361353
66 71 3.653184377744164 0.034788312959212 1.000000000000000 0.000213841934976
67 72 3.653183781538993 0.020792888225971 1.000000000000000 0.000209624254674
68 73 3.653182618135729 0.025526539245315 1.000000000000000 0.000372203127501
69 74 3.653178834215321 0.068995016568127 1.000000000000000 0.000809668098302
70 75 3.653172067352300 0.111006469443092 1.000000000000000 0.001270693470747
71 76 3.653161521483286 0.167755112284709 1.000000000000000 0.001444000959959
72 77 3.653149590225892 0.165669964821593 1.000000000000000 0.000919722811182
73 78 3.653141031866190 0.161085002744452 1.000000000000000 0.000208011753231
74 79 3.653138530285472 0.084243310398720 1.000000000000000 0.000557887839368
75 80 3.653135307308470 0.108663297590868 1.000000000000000 0.000868044266083
76 81 3.653129906664020 0.169457065224625 1.000000000000000 0.001015850842982
77 82 3.653123281403714 0.162833601738917 1.000000000000000 0.000700921155308
78 83 3.653119541776691 0.059583413048204 1.000000000000000 0.000299649222700
79 84 3.653118211722771 0.082466520717794 1.000000000000000 0.000149429884202
80 85 3.653117712463759 0.028647103012049 1.000000000000000 0.000242759543274
81 86 3.653117004195740 0.028182358094799 1.000000000000000 0.000395373393589
82 87 3.653115465778334 0.030970611547787 1.000000000000000 0.000613693135734
83 88 3.653112721400372 0.063588174235852 1.000000000000000 0.000793488638759
84 89 3.653109171608556 0.120780947080343 1.000000000000000 0.000686808549037
85 90 3.653105590817023 0.141713308827249 1.000000000000000 0.000326937201508
86 91 3.653102708976040 0.178434185739180 1.000000000000000 0.000249837480778
87 92 3.653101283278439 0.095391524417447 1.000000000000000 0.000502343882247
88 93 3.653098931022947 0.137548953580747 1.000000000000000 0.000697680598502
89 94 3.653095856343616 0.147667283883372 1.000000000000000 0.000697573039512
90 95 3.653088364061471 0.286068393850880 1.000000000000000 0.000522312700408
91 96 3.653080874432266 0.402153572650608 1.000000000000000 0.000329434931034
92 97 3.653078607981071 0.058249793399811 1.000000000000000 0.000334691999399
93 98 3.653076930329892 0.109979626375976 1.000000000000000 0.000327500295951
94 99 3.653073919037119 0.185058999720359 1.000000000000000 0.000216808142969
95 100 3.653069899579872 0.374201866916942 1.000000000000000 0.000206813112119
96 101 3.653066467869385 0.374027403802500 1.000000000000000 0.000391818042884
97 102 3.653063527966991 0.344235219326616 1.000000000000000 0.000488405322525
98 103 3.653060658809049 0.192951944965945 1.000000000000000 0.000456062900532
99 104 3.653054077084970 0.325532122135517 1.000000000000000 0.000277071291582
100 105 3.653046350437249 0.367340040382873 1.000000000000000 0.000268519149701
101 106 3.653043097188133 0.117238244034997 1.000000000000000 0.000397654374595
102 107 3.653040311954507 0.147622857592899 1.000000000000000 0.000391619602914
103 108 3.653036905050060 0.305989166535365 1.000000000000000 0.000280141308082
104 109 3.653033465074215 0.502413572881576 1.000000000000000 0.000179568023188
105 110 3.653031395261024 0.379006960950595 1.000000000000000 0.000371227941692
106 111 3.653029214132466 0.333394327133853 1.000000000000000 0.000541427814599
107 112 3.653026845335087 0.192065786654228 1.000000000000000 0.000546600147338
108 113 3.653025075596772 0.245749961271438 1.000000000000000 0.000478052177973
109 114 3.653017658274631 0.287802798621413 1.000000000000000 0.001470439138540
110 116 3.653016061517626 0.070304275652061 0.284096915362798 0.001085874713355
111 117 3.653013618824572 0.172907559221937 1.000000000000000 0.000191626149678
112 118 3.653013457600018 0.026275185497570 1.000000000000000 0.000129661534991
113 119 3.653013050620093 0.085489499019717 1.000000000000000 0.000103713562843
114 120 3.653012262878718 0.164770893996882 1.000000000000000 0.000104513367721
115 121 3.653010563328508 0.449911455881799 1.000000000000000 0.000188965083209
116 122 3.653009414175918 0.272094282652491 1.000000000000000 0.000551964931678
117 123 3.653007825395969 0.238418467123044 1.000000000000000 0.000254151542792
118 124 3.653006647211030 0.123105250621127 1.000000000000000 0.000144484671146
119 125 3.653005988396242 0.211676571624148 1.000000000000000 0.000101151646613
120 126 3.653005600652366 0.153262550003610 1.000000000000000 0.000106079732781
121 127 3.653004547052686 0.120186405113297 1.000000000000000 0.000210939919060
122 128 3.653001562501353 0.255466902014920 1.000000000000000 0.000434447498502
123 129 3.652997657681793 0.287118284136054 1.000000000000000 0.000675305357002
124 130 3.652992703297808 0.427279698463162 1.000000000000000 0.000410357889571
125 131 3.652987137827974 0.999212460032901 1.000000000000000 0.000519158391263
126 132 3.652986613666201 0.460127568152535 1.000000000000000 0.000414753041915
127 133 3.652986035177700 0.125420961607458 1.000000000000000 0.000148640421352
128 134 3.652985818386984 0.021271223603251 1.000000000000000 0.000139969537359
129 135 3.652985122784052 0.035900348851122 1.000000000000000 0.000228322497163
130 136 3.652983402508549 0.058298609955491 1.000000000000000 0.000396126025641
131 137 3.652979875891194 0.202336167819154 1.000000000000000 0.000828636906691
132 138 3.652974670766407 0.331753922545893 1.000000000000000 0.000919019895082
133 139 3.652965953314298 0.892196099479321 1.000000000000000 0.000755936187852
134 141 3.652962784682857 0.192771302043173 0.389412991816654 0.000710144877280
135 142 3.652960815895944 0.114635102603056 1.000000000000000 0.000161014456566
136 143 3.652960477476560 0.047553846335457 1.000000000000000 0.000207925235923
137 144 3.652959872364350 0.040652029408916 1.000000000000000 0.000281896000614
138 145 3.652957515845698 0.157933810305809 1.000000000000000 0.000516434461840
139 146 3.652952685036226 0.312944563148788 1.000000000000000 0.000787624548522
140 147 3.652943237949862 0.706219196389632 1.000000000000000 0.001228689303809
141 149 3.652937919964562 0.555946568697475 0.385188126495236 0.001508009877570
142 150 3.652927448644345 0.685566517408407 1.000000000000000 0.000771972380617
143 151 3.652919353367465 0.662633691944458 1.000000000000000 0.000540252397055
144 152 3.652918660984871 0.219146148033782 1.000000000000000 0.000846742016917
145 153 3.652917707340465 0.046602897832412 1.000000000000000 0.000202752853952
146 154 3.652917499553726 0.045107535308704 1.000000000000000 0.000182336314511
147 155 3.652916963672404 0.092384008187061 1.000000000000000 0.000291742864015
148 156 3.652915875761788 0.125293976841639 1.000000000000000 0.000449301949427
149 157 3.652913158461570 0.203128734909662 1.000000000000000 0.000685292005626
150 158 3.652909908335488 0.378937692369181 1.000000000000000 0.001408394477905
151 159 3.652903733902813 0.317407490954740 1.000000000000000 0.000764752787994
152 160 3.652898124980730 0.618224966885353 1.000000000000000 0.000423735479149
153 161 3.652897017214527 0.156644389755223 1.000000000000000 0.000190436483485
154 162 3.652896690804817 0.088283433054916 1.000000000000000 0.000156740575785
155 163 3.652896218164703 0.033848638854504 1.000000000000000 0.000256493845146
156 164 3.652895161588233 0.114383909858759 1.000000000000000 0.000427006050858
157 166 3.652892120067393 0.030054858086803 0.184187603002930 0.000474719760900
158 167 3.652886595255687 0.537500005583425 1.000000000000000 0.000839670371804
159 168 3.652881765807249 0.352795749778655 1.000000000000000 0.000929414532910
160 170 3.652879385249375 0.466479073957601 0.221226708418035 0.000603693229803
161 171 3.652875105558928 0.304016894885181 1.000000000000000 0.000302704284573
162 172 3.652873438627494 0.196787226096693 1.000000000000000 0.000146030270502
163 173 3.652872757873182 0.071183783840796 1.000000000000000 0.000187069159117
164 175 3.652872734605185 0.001237104217566 0.022553821584627 0.000187727908942
165 176 3.652870204534899 0.130515233849175 1.000000000000000 0.000391039098254
166 177 3.652868428973248 0.147857061136106 1.000000000000000 0.000471000405225
167 178 3.652865090490226 0.255670275241371 1.000000000000000 0.000470983466355
168 179 3.652862277346480 0.241287241521188 1.000000000000000 0.000383612000687
169 180 3.652860311214074 0.140110651641656 1.000000000000000 0.000166710745938
170 181 3.652859690710765 0.058625938560701 1.000000000000000 0.000092500022146
171 182 3.652859308088129 0.053152275035638 1.000000000000000 0.000125543123540
172 183 3.652858640844114 0.050294910096930 1.000000000000000 0.000237319158612
173 184 3.652857737834439 0.072257560274436 1.000000000000000 0.000217920228526
174 185 3.652855561874158 0.200326937067699 1.000000000000000 0.000256403159230
175 186 3.652854284737822 0.217535247579330 1.000000000000000 0.000323532741126
176 187 3.652853364864227 0.152103334027191 1.000000000000000 0.000091603195950
177 188 3.652853098116422 0.015041659699198 1.000000000000000 0.000082659140630
178 189 3.652852678733057 0.023120397500891 1.000000000000000 0.000090332411242
179 190 3.652851406793564 0.080381094263309 1.000000000000000 0.000223541239825
180 191 3.652849969547406 0.105305047463471 1.000000000000000 0.000314929205178
181 192 3.652848048355160 0.177963686678008 1.000000000000000 0.000298190813456
182 194 3.652847760955776 0.052634714304167 0.147026177673369 0.000325132344130
183 195 3.652846575513066 0.155053527773239 1.000000000000000 0.000139948836244
184 196 3.652846163073691 0.063077521802995 1.000000000000000 0.000063302429257
185 197 3.652845942721525 0.032025219470722 1.000000000000000 0.000121217626789
186 198 3.652845667955330 0.031636734956661 1.000000000000000 0.000180826131723
187 199 3.652844940222253 0.070191360043819 1.000000000000000 0.000272735121876
188 200 3.652843654769583 0.125202440071269 1.000000000000000 0.000344569435631
189 201 3.652841743145628 0.238411604354193 1.000000000000000 0.000313180593847
190 203 3.652840667926649 0.202369985224427 0.312239275563390 0.000344708061418
191 204 3.652839326995138 0.100018392656367 1.000000000000000 0.000211050558101
192 205 3.652839045139923 0.085381939654503 1.000000000000000 0.000100151647849
193 206 3.652838235611276 0.041719702357465 1.000000000000000 0.000103961542620
194 207 3.652837718696882 0.076266396960477 1.000000000000000 0.000137061618825
195 208 3.652836864903142 0.143202383802939 1.000000000000000 0.000196352942780
196 209 3.652835640969556 0.156375943059080 1.000000000000000 0.000242364094123
197 210 3.652834386580161 0.208502973492100 1.000000000000000 0.000212332607371
198 211 3.652833848590452 0.149046211558066 1.000000000000000 0.000124576786784
199 212 3.652833318231725 0.133263747024361 1.000000000000000 0.000124514582564
200 214 3.652833309844651 0.002007529993048 0.022891745880104 0.000123955213834
201 215 3.652832400823406 0.134915793295707 1.000000000000000 0.000060078566986
202 216 3.652831905388567 0.050884234256923 1.000000000000000 0.000092203323603
203 217 3.652830872861390 0.113067488652183 1.000000000000000 0.000158601445547
204 218 3.652830148558622 0.173165175549352 1.000000000000000 0.000129544009090
205 219 3.652829670156802 0.154782012359218 1.000000000000000 0.000108358925147
206 220 3.652829494207913 0.084838584776922 1.000000000000000 0.000054689521418
207 221 3.652829416765633 0.016745342603330 1.000000000000000 0.000082789504308
208 222 3.652829317517817 0.014876075161538 1.000000000000000 0.000129581162267
209 223 3.652828552028435 0.026783126861627 1.000000000000000 0.000149836558619
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0107e-01,-9.9541e-01,-6.0099e-01,-3.3425e-01,-5.5423e-01,-6.0598e-01,4.0067e-01,-4.2810e-01,-3.7496e-01,-5.0547e-01,-1.8298e+00,-5.5423e-01,2.0185e-01,1.8297e-01,-2.4239e+00,1.5611e+00,-1.0466e+00,-1.8298e+00,-2.0389e-01,5.9649e-01,-3.1400e+00,1.7297e+00,-1.2901e+00,-1.0466e+00,1.0704e-02,-5.1807e-01,-2.6565e-01,1.1665e-01,-1.4079e+00,-1.2901e+00,-4.2950e-01,6.8258e-01,-1.3501e+00,-3.7567e-02,-8.1186e-01,-1.4079e+00,8.7471e-01,-4.0351e-01,-2.7895e+00,4.4544e-01,-6.6970e-01,-8.1186e-01,-4.5800e-01,-3.4080e-01,-1.0433e+00,-1.1660e-01,-7.2604e-01,-6.6970e-01,-5.3725e-01,-4.7871e-01,-8.7198e-01,-5.0634e-01,-2.3410e-01,-7.2604e-01,-1.8468e-01,-7.1665e-01,-7.7486e-01,-4.5428e-01,-9.8985e-01,-2.3410e-01,-3.9120e-01,-5.5164e-01,-2.4237e-01,-2.6516e-01,-8.5172e-01,-9.8985e-01,-7.5908e-01,-1.7172e-01,-5.4640e-01,-3.6607e-01,-5.9695e-01,-8.5172e-01,9.1064e-02,9.0619e-02,9.1064e-02,8.7236e-02,9.1223e-02,1.1260e-01,9.1223e-02,1.0907e-01,9.1242e-02,-1.8864e+00,9.1242e-02,-1.1325e+00,9.6793e-02,-9.6793e-02,-1.1061e-02,1.1061e-02,6.2135e-01,-6.2135e-01,6.3352e-01,-6.3352e-01,8.8965e-01,-8.8965e-01,1.0835e+00,-1.0835e+00}
> Gradient: {-5.6473e-06,-2.4926e-06,-3.1947e-06,1.3481e-07,-3.6727e-06,-4.1406e-07,-4.6025e-06,5.5548e-07,-1.1079e-06,-4.3135e-06,-2.1454e-06,-3.6727e-06,-5.5090e-06,1.2176e-06,7.8013e-07,-1.1372e-05,1.6172e-06,-2.1454e-06,-3.7751e-06,-3.3767e-06,-1.5647e-06,-9.2391e-06,9.2697e-07,1.6172e-06,-3.5929e-06,-3.6128e-06,-3.8581e-06,-4.4438e-06,-8.3080e-07,9.2697e-07,-4.1330e-06,-6.9403e-06,-4.8233e-06,-1.9905e-06,3.3065e-06,-8.3080e-07,-4.2728e-06,-4.0639e-06,-2.4420e-06,-8.7259e-06,7.8669e-07,3.3065e-06,-3.7665e-06,-4.2513e-06,-8.8197e-07,-3.5884e-06,-3.7099e-06,7.8669e-07,-4.6366e-07,-4.2898e-06,2.4232e-06,-6.1634e-06,-3.2079e-06,-3.7099e-06,-7.4954e-06,-1.3251e-06,-3.9495e-06,1.7070e-06,-1.1407e-06,-3.2079e-06,-2.0614e-06,-8.8707e-06,-2.2754e-06,-5.3598e-06,4.4215e-06,-1.1407e-06,-5.7358e-06,-8.2358e-06,-2.3867e-06,-2.8376e-06,-5.1197e-07,4.4215e-06,1.8213e-07,1.8124e-07,1.8213e-07,1.7447e-07,1.8245e-07,2.2521e-07,1.8245e-07,2.1814e-07,1.8248e-07,-3.6660e-06,1.8248e-07,-1.1075e-05,5.8297e-05,-5.8297e-05,9.5814e-06,-9.5814e-06,-2.1373e-05,2.1373e-05,3.8262e-06,-3.8262e-06,5.1744e-05,-5.1744e-05,6.2889e-05,-6.2889e-05}
>>>> Re-trying (1/3).
Gradient = {-5.6394e-06,-2.4891e-06,-3.1839e-06,1.4198e-07,-3.6719e-06,-4.1311e-07,-4.5911e-06,5.6114e-07,-1.0993e-06,-4.3088e-06,-2.1454e-06,-3.6719e-06,-5.5036e-06,1.2234e-06,7.8072e-07,-1.1353e-05,1.6172e-06,-2.1454e-06,-3.7718e-06,-3.3699e-06,-1.5645e-06,-9.2185e-06,9.2704e-07,1.6172e-06,-3.5840e-06,-3.6070e-06,-3.8512e-06,-4.4345e-06,-8.3067e-07,9.2704e-07,-4.1283e-06,-6.9235e-06,-4.8213e-06,-1.9834e-06,3.3068e-06,-8.3067e-07,-4.2577e-06,-4.0594e-06,-2.4417e-06,-8.7157e-06,7.8728e-07,3.3068e-06,-3.7596e-06,-4.2430e-06,-8.7769e-07,-3.5784e-06,-3.7089e-06,7.8728e-07,-4.5678e-07,-4.2820e-06,2.4282e-06,-6.1556e-06,-3.2053e-06,-3.7089e-06,-7.4867e-06,-1.3181e-06,-3.9446e-06,1.7146e-06,-1.1403e-06,-3.2053e-06,-2.0553e-06,-8.8605e-06,-2.2686e-06,-5.3527e-06,4.4219e-06,-1.1403e-06,-5.7304e-06,-8.2216e-06,-2.3823e-06,-2.8317e-06,-5.1125e-07,4.4219e-06,1.8213e-07,1.8124e-07,1.8213e-07,1.7447e-07,1.8245e-07,2.2521e-07,1.8245e-07,2.1814e-07,1.8248e-07,-3.6563e-06,1.8248e-07,-1.1053e-05,5.8174e-05,-5.8174e-05,6.9372e-06,-6.9372e-06,-2.1328e-05,2.1328e-05,3.8187e-06,-3.8187e-06,5.1643e-05,-5.1643e-05,6.2770e-05,-6.2770e-05}
pCurr = {5.6473e-06,2.4926e-06,3.1947e-06,-1.3480e-07,3.6727e-06,4.1406e-07,4.6025e-06,-5.5548e-07,1.1079e-06,4.3135e-06,2.1454e-06,3.6727e-06,5.5090e-06,-1.2176e-06,-7.8013e-07,1.1372e-05,-1.6172e-06,2.1454e-06,3.7751e-06,3.3767e-06,1.5647e-06,9.2392e-06,-9.2697e-07,-1.6172e-06,3.5929e-06,3.6128e-06,3.8581e-06,4.4438e-06,8.3080e-07,-9.2697e-07,4.1330e-06,6.9403e-06,4.8233e-06,1.9905e-06,-3.3065e-06,8.3080e-07,4.2728e-06,4.0639e-06,2.4420e-06,8.7259e-06,-7.8669e-07,-3.3065e-06,3.7665e-06,4.2513e-06,8.8197e-07,3.5884e-06,3.7099e-06,-7.8669e-07,4.6366e-07,4.2898e-06,-2.4232e-06,6.1634e-06,3.2079e-06,3.7099e-06,7.4954e-06,1.3251e-06,3.9495e-06,-1.7070e-06,1.1407e-06,3.2079e-06,2.0614e-06,8.8707e-06,2.2754e-06,5.3598e-06,-4.4215e-06,1.1407e-06,5.7358e-06,8.2358e-06,2.3867e-06,2.8376e-06,5.1197e-07,-4.4215e-06,-1.8213e-07,-1.8124e-07,-1.8213e-07,-1.7447e-07,-1.8245e-07,-2.2521e-07,-1.8245e-07,-2.1814e-07,-1.8248e-07,3.6660e-06,-1.8248e-07,1.1075e-05,-5.8297e-05,5.8297e-05,-6.9524e-06,6.9524e-06,2.1373e-05,-2.1373e-05,-3.8262e-06,3.8262e-06,-5.1744e-05,5.1744e-05,-6.2889e-05,6.2889e-05}
grad*pCur = -2.2402944616773493E-8
parameters = {-2.0107e-01,-9.9541e-01,-6.0099e-01,-3.3425e-01,-5.5423e-01,-6.0598e-01,4.0067e-01,-4.2810e-01,-3.7496e-01,-5.0547e-01,-1.8298e+00,-5.5423e-01,2.0185e-01,1.8297e-01,-2.4239e+00,1.5611e+00,-1.0466e+00,-1.8298e+00,-2.0389e-01,5.9649e-01,-3.1400e+00,1.7297e+00,-1.2901e+00,-1.0466e+00,1.0704e-02,-5.1807e-01,-2.6565e-01,1.1665e-01,-1.4079e+00,-1.2901e+00,-4.2950e-01,6.8258e-01,-1.3501e+00,-3.7567e-02,-8.1186e-01,-1.4079e+00,8.7471e-01,-4.0351e-01,-2.7895e+00,4.4544e-01,-6.6970e-01,-8.1186e-01,-4.5800e-01,-3.4080e-01,-1.0433e+00,-1.1660e-01,-7.2604e-01,-6.6970e-01,-5.3725e-01,-4.7871e-01,-8.7198e-01,-5.0634e-01,-2.3410e-01,-7.2604e-01,-1.8468e-01,-7.1665e-01,-7.7486e-01,-4.5428e-01,-9.8985e-01,-2.3410e-01,-3.9120e-01,-5.5164e-01,-2.4237e-01,-2.6516e-01,-8.5172e-01,-9.8985e-01,-7.5908e-01,-1.7172e-01,-5.4640e-01,-3.6607e-01,-5.9695e-01,-8.5172e-01,9.1064e-02,9.0619e-02,9.1064e-02,8.7236e-02,9.1223e-02,1.1260e-01,9.1223e-02,1.0907e-01,9.1242e-02,-1.8864e+00,9.1242e-02,-1.1325e+00,9.6792e-02,-9.6792e-02,-1.1061e-02,1.1061e-02,6.2135e-01,-6.2135e-01,6.3352e-01,-6.3352e-01,8.8965e-01,-8.8965e-01,1.0835e+00,-1.0835e+00}
|grad|/|x| = 1.7116210528191516E-5
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0107e-01,-9.9541e-01,-6.0099e-01,-3.3425e-01,-5.5423e-01,-6.0598e-01,4.0067e-01,-4.2810e-01,-3.7496e-01,-5.0547e-01,-1.8298e+00,-5.5423e-01,2.0185e-01,1.8297e-01,-2.4239e+00,1.5611e+00,-1.0466e+00,-1.8298e+00,-2.0389e-01,5.9649e-01,-3.1400e+00,1.7297e+00,-1.2901e+00,-1.0466e+00,1.0704e-02,-5.1807e-01,-2.6565e-01,1.1665e-01,-1.4079e+00,-1.2901e+00,-4.2950e-01,6.8258e-01,-1.3501e+00,-3.7567e-02,-8.1186e-01,-1.4079e+00,8.7471e-01,-4.0351e-01,-2.7895e+00,4.4544e-01,-6.6970e-01,-8.1186e-01,-4.5800e-01,-3.4080e-01,-1.0433e+00,-1.1660e-01,-7.2604e-01,-6.6970e-01,-5.3725e-01,-4.7871e-01,-8.7198e-01,-5.0634e-01,-2.3410e-01,-7.2604e-01,-1.8468e-01,-7.1665e-01,-7.7486e-01,-4.5428e-01,-9.8985e-01,-2.3410e-01,-3.9120e-01,-5.5164e-01,-2.4237e-01,-2.6516e-01,-8.5172e-01,-9.8985e-01,-7.5908e-01,-1.7172e-01,-5.4640e-01,-3.6607e-01,-5.9695e-01,-8.5172e-01,9.1064e-02,9.0619e-02,9.1064e-02,8.7236e-02,9.1223e-02,1.1260e-01,9.1223e-02,1.0907e-01,9.1242e-02,-1.8864e+00,9.1242e-02,-1.1325e+00,9.6793e-02,-9.6793e-02,-1.1061e-02,1.1061e-02,6.2135e-01,-6.2135e-01,6.3352e-01,-6.3352e-01,8.8965e-01,-8.8965e-01,1.0835e+00,-1.0835e+00}
> Gradient: {-5.6394e-06,-2.4891e-06,-3.1839e-06,1.4198e-07,-3.6719e-06,-4.1311e-07,-4.5911e-06,5.6114e-07,-1.0993e-06,-4.3088e-06,-2.1454e-06,-3.6719e-06,-5.5036e-06,1.2234e-06,7.8072e-07,-1.1353e-05,1.6172e-06,-2.1454e-06,-3.7718e-06,-3.3699e-06,-1.5645e-06,-9.2185e-06,9.2704e-07,1.6172e-06,-3.5840e-06,-3.6070e-06,-3.8512e-06,-4.4345e-06,-8.3067e-07,9.2704e-07,-4.1283e-06,-6.9235e-06,-4.8213e-06,-1.9834e-06,3.3068e-06,-8.3067e-07,-4.2577e-06,-4.0594e-06,-2.4417e-06,-8.7157e-06,7.8728e-07,3.3068e-06,-3.7596e-06,-4.2430e-06,-8.7769e-07,-3.5784e-06,-3.7089e-06,7.8728e-07,-4.5678e-07,-4.2820e-06,2.4282e-06,-6.1556e-06,-3.2053e-06,-3.7089e-06,-7.4867e-06,-1.3181e-06,-3.9446e-06,1.7146e-06,-1.1403e-06,-3.2053e-06,-2.0553e-06,-8.8605e-06,-2.2686e-06,-5.3527e-06,4.4219e-06,-1.1403e-06,-5.7304e-06,-8.2216e-06,-2.3823e-06,-2.8317e-06,-5.1125e-07,4.4219e-06,1.8213e-07,1.8124e-07,1.8213e-07,1.7447e-07,1.8245e-07,2.2521e-07,1.8245e-07,2.1814e-07,1.8248e-07,-3.6563e-06,1.8248e-07,-1.1053e-05,5.8174e-05,-5.8174e-05,6.9372e-06,-6.9372e-06,-2.1328e-05,2.1328e-05,3.8187e-06,-3.8187e-06,5.1643e-05,-5.1643e-05,6.2770e-05,-6.2770e-05}
>>>> Re-trying (2/3).
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.0107e-01,-9.9541e-01,-6.0099e-01,-3.3425e-01,-5.5423e-01,-6.0598e-01,4.0067e-01,-4.2810e-01,-3.7496e-01,-5.0547e-01,-1.8298e+00,-5.5423e-01,2.0185e-01,1.8297e-01,-2.4239e+00,1.5611e+00,-1.0466e+00,-1.8298e+00,-2.0389e-01,5.9649e-01,-3.1400e+00,1.7297e+00,-1.2901e+00,-1.0466e+00,1.0704e-02,-5.1807e-01,-2.6565e-01,1.1665e-01,-1.4079e+00,-1.2901e+00,-4.2950e-01,6.8258e-01,-1.3501e+00,-3.7567e-02,-8.1186e-01,-1.4079e+00,8.7471e-01,-4.0351e-01,-2.7895e+00,4.4544e-01,-6.6970e-01,-8.1186e-01,-4.5800e-01,-3.4080e-01,-1.0433e+00,-1.1660e-01,-7.2604e-01,-6.6970e-01,-5.3725e-01,-4.7871e-01,-8.7198e-01,-5.0634e-01,-2.3410e-01,-7.2604e-01,-1.8468e-01,-7.1665e-01,-7.7486e-01,-4.5428e-01,-9.8985e-01,-2.3410e-01,-3.9120e-01,-5.5164e-01,-2.4237e-01,-2.6516e-01,-8.5172e-01,-9.8985e-01,-7.5908e-01,-1.7172e-01,-5.4640e-01,-3.6607e-01,-5.9695e-01,-8.5172e-01,9.1064e-02,9.0619e-02,9.1064e-02,8.7236e-02,9.1223e-02,1.1260e-01,9.1223e-02,1.0907e-01,9.1242e-02,-1.8864e+00,9.1242e-02,-1.1325e+00,9.6793e-02,-9.6793e-02,-1.1061e-02,1.1061e-02,6.2135e-01,-6.2135e-01,6.3352e-01,-6.3352e-01,8.8965e-01,-8.8965e-01,1.0835e+00,-1.0835e+00}
> Gradient: {-5.6473e-06,-2.4926e-06,-3.1947e-06,1.3480e-07,-3.6727e-06,-4.1406e-07,-4.6025e-06,5.5548e-07,-1.1079e-06,-4.3135e-06,-2.1454e-06,-3.6727e-06,-5.5090e-06,1.2176e-06,7.8013e-07,-1.1372e-05,1.6172e-06,-2.1454e-06,-3.7751e-06,-3.3767e-06,-1.5647e-06,-9.2392e-06,9.2697e-07,1.6172e-06,-3.5929e-06,-3.6128e-06,-3.8581e-06,-4.4438e-06,-8.3080e-07,9.2697e-07,-4.1330e-06,-6.9403e-06,-4.8233e-06,-1.9905e-06,3.3065e-06,-8.3080e-07,-4.2728e-06,-4.0639e-06,-2.4420e-06,-8.7259e-06,7.8669e-07,3.3065e-06,-3.7665e-06,-4.2513e-06,-8.8197e-07,-3.5884e-06,-3.7099e-06,7.8669e-07,-4.6366e-07,-4.2898e-06,2.4232e-06,-6.1634e-06,-3.2079e-06,-3.7099e-06,-7.4954e-06,-1.3251e-06,-3.9495e-06,1.7070e-06,-1.1407e-06,-3.2079e-06,-2.0614e-06,-8.8707e-06,-2.2754e-06,-5.3598e-06,4.4215e-06,-1.1407e-06,-5.7358e-06,-8.2358e-06,-2.3867e-06,-2.8376e-06,-5.1197e-07,4.4215e-06,1.8213e-07,1.8124e-07,1.8213e-07,1.7447e-07,1.8245e-07,2.2521e-07,1.8245e-07,2.1814e-07,1.8248e-07,-3.6660e-06,1.8248e-07,-1.1075e-05,5.8297e-05,-5.8297e-05,6.9524e-06,-6.9524e-06,-2.1373e-05,2.1373e-05,3.8262e-06,-3.8262e-06,5.1744e-05,-5.1744e-05,6.2889e-05,-6.2889e-05}
>>>> Re-trying (3/3).
After: gradient norm = 1.498230373225234E-4
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0968,-0.0968}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6214,-0.6214}
Count Table 3:
---------------
h: {0.6335,-0.6335}
Count Table 4:
---------------
h: {0.8896,-0.8896}
Count Table 5:
---------------
h: {1.0835,-1.0835}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.2011,-0.9954,-0.6010,-0.3343,-0.5542,-0.6060,0.4007,-0.4281,-0.3750,-0.5055,-1.8298,-0.5542,0.2018,0.1830,-2.4239,1.5611,-1.0466,-1.8298,-0.2039,0.5965,-3.1400,1.7297,-1.2901,-1.0466,0.0107,-0.5181,-0.2656,0.1166,-1.4079,-1.2901,-0.4295,0.6826,-1.3501,-0.0376,-0.8119,-1.4079,0.8747,-0.4035,-2.7895,0.4454,-0.6697,-0.8119,-0.4580,-0.3408,-1.0433,-0.1166,-0.7260,-0.6697,-0.5372,-0.4787,-0.8720,-0.5063,-0.2341,-0.7260,-0.1847,-0.7166,-0.7749,-0.4543,-0.9899,-0.2341,-0.3912,-0.5516,-0.2424,-0.2652,-0.8517,-0.9899,-0.7591,-0.1717,-0.5464,-0.3661,-0.5969,-0.8517}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0911,0.0906}
Activity(exp=1): {0.0911,0.0872}
Activity(exp=2): {0.0912,0.1126}
Activity(exp=3): {0.0912,0.1091}
Activity(exp=4): {0.0912,-1.8864}
Activity(exp=5): {0.0912,-1.1325}
Suggested variations:
key=12;3;0, description = Initial model.
> Optimizing variation "Initial model." (component3-2-variation0).
>> Starting new optimization: component3-2-variation0. (2021-05-21 19:41:56.262).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[84,85]},{"h":[86,87]},{"h":[88,89]},{"h":[90,91]},{"h":[92,93]},{"h":[94,95]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[72,73],[74,75],[76,77],[78,79],[80,81],[82,83]]}]}
Value and gradient before optimization:
=======================================
value = 3.6528291101132075
gradient = {-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0001,-0.0001,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0001,-0.0001,0.0001,-0.0001}
gradient norm = 1.4982316985015555E-4
Starting Function Value: 3.6528291101132075
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.652829082760777 0.000345085386788 2.303284512891447 0.000021399123239
2 4 3.652829081726262 0.000052599340278 1.000000000000000 0.000020290975368
3 5 3.652829072185434 0.000636156066363 1.000000000000000 0.000052571669021
4 6 3.652829054398493 0.001436293265091 1.000000000000000 0.000101542411197
5 7 3.652829010930692 0.003995719404134 1.000000000000000 0.000167391952798
6 8 3.652828984108625 0.007105714256017 1.000000000000000 0.000196521598007
7 9 3.652828846493875 0.010225842285437 1.000000000000000 0.000171358491038
8 11 3.652828830446076 0.002619692054817 0.220725039024903 0.000181832264238
9 12 3.652828767853709 0.007335606481432 1.000000000000000 0.000057832879352
10 13 3.652828759204226 0.000584741448602 1.000000000000000 0.000025086862476
11 14 3.652828754302299 0.000793892598998 1.000000000000000 0.000037434781649
12 15 3.652828746272443 0.000847197367220 1.000000000000000 0.000051697570514
13 18 3.652828727928184 0.001736434486092 0.660000000000000 0.000071030127518
14 19 3.652825909966905 0.004857053133208 1.000000000000000 0.000074648159034
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9901e-01,-9.9409e-01,-6.0330e-01,-3.3966e-01,-5.4780e-01,-6.0673e-01,3.9803e-01,-4.3374e-01,-3.7993e-01,-5.0188e-01,-1.8253e+00,-5.4780e-01,2.0788e-01,1.7664e-01,-2.4261e+00,1.5642e+00,-1.0501e+00,-1.8253e+00,-1.9908e-01,5.9683e-01,-3.1368e+00,1.7286e+00,-1.2922e+00,-1.0501e+00,1.0340e-02,-5.1665e-01,-2.6487e-01,1.1696e-01,-1.4064e+00,-1.2922e+00,-4.2679e-01,6.8225e-01,-1.3423e+00,-4.0302e-02,-8.1931e-01,-1.4064e+00,8.7333e-01,-4.0032e-01,-2.7846e+00,4.5036e-01,-6.7229e-01,-8.1931e-01,-4.5702e-01,-3.4036e-01,-1.0454e+00,-1.1796e-01,-7.1979e-01,-6.7229e-01,-5.4201e-01,-4.7732e-01,-8.7981e-01,-5.0165e-01,-2.3223e-01,-7.1979e-01,-1.7908e-01,-7.2003e-01,-7.7197e-01,-4.6151e-01,-9.8799e-01,-2.3223e-01,-3.9188e-01,-5.4634e-01,-2.4139e-01,-2.6159e-01,-8.6142e-01,-9.8799e-01,-7.5259e-01,-1.7020e-01,-5.4475e-01,-3.6518e-01,-5.9647e-01,-8.6142e-01,9.0671e-02,9.0228e-02,9.0671e-02,8.6859e-02,9.0829e-02,1.1212e-01,9.0829e-02,1.0860e-01,9.0848e-02,-1.8869e+00,9.0848e-02,-1.1319e+00,9.6678e-02,-9.6678e-02,-1.1069e-02,1.1069e-02,6.2142e-01,-6.2142e-01,6.3352e-01,-6.3352e-01,8.8965e-01,-8.8965e-01,1.0838e+00,-1.0838e+00}
> Gradient: {6.6784e-06,7.9066e-07,7.6296e-07,2.2950e-06,-1.8970e-06,1.2746e-06,8.4073e-06,1.3123e-06,1.2131e-06,2.9561e-06,-2.0873e-06,-1.8970e-06,-8.6243e-07,-1.3981e-06,8.3228e-07,1.1727e-05,1.5685e-06,-2.0873e-06,-1.8228e-06,-8.9032e-08,-1.5164e-06,1.0709e-05,9.3112e-07,1.5685e-06,2.5255e-06,1.6036e-06,3.4524e-07,5.0657e-06,-6.9089e-07,9.3112e-07,2.7777e-06,3.6631e-06,-3.1168e-06,4.0199e-06,3.1272e-06,-6.9089e-07,1.9614e-06,-3.1470e-07,-2.2949e-06,6.1979e-06,1.1033e-06,3.1272e-06,3.8633e-06,2.8521e-06,6.8844e-07,3.2054e-06,-1.9322e-06,1.1033e-06,3.5729e-06,1.7521e-06,-8.7615e-08,4.6513e-06,1.8238e-06,-1.9322e-06,4.7456e-06,1.4255e-06,1.5847e-06,9.9155e-07,-7.9093e-07,1.8238e-06,1.7025e-06,4.9001e-06,-2.0346e-06,2.5834e-06,3.5441e-06,-7.9093e-07,-3.3611e-07,6.1726e-06,-4.0198e-07,1.4930e-06,-5.6696e-07,3.5441e-06,1.8134e-07,1.8046e-07,1.8134e-07,1.7372e-07,1.8166e-07,2.2423e-07,1.8166e-07,2.1720e-07,1.8170e-07,2.6116e-06,1.8170e-07,7.8366e-06,6.0069e-06,-6.0069e-06,3.4567e-06,-3.4567e-06,1.2721e-05,-1.2721e-05,1.9246e-06,-1.9246e-06,2.0554e-05,-2.0554e-05,4.1296e-05,-4.1296e-05}
>>>> Re-trying (1/3).
Starting Function Value: 3.652828684281938
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 4 3.652828682996110 0.000017859817595 0.239922424103087 0.000069635935112
2 5 3.652828667758738 0.000366984742989 1.000000000000000 0.000048326377375
3 6 3.652828659197573 0.000303298944369 1.000000000000000 0.000060777966941
4 7 3.652828635638545 0.001134734000896 1.000000000000000 0.000063812245288
5 9 3.652828599111408 0.000164936154853 0.186898275681682 0.000054099877379
6 10 3.652828577515375 0.001209254976095 1.000000000000000 0.000033150179498
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9966e-01,-9.9420e-01,-6.0342e-01,-3.3982e-01,-5.4760e-01,-6.0690e-01,3.9724e-01,-4.3393e-01,-3.8014e-01,-5.0215e-01,-1.8250e+00,-5.4760e-01,2.0798e-01,1.7671e-01,-2.4262e+00,1.5631e+00,-1.0503e+00,-1.8250e+00,-1.9887e-01,5.9674e-01,-3.1366e+00,1.7276e+00,-1.2923e+00,-1.0503e+00,1.0119e-02,-5.1684e-01,-2.6498e-01,1.1654e-01,-1.4063e+00,-1.2923e+00,-4.2707e-01,6.8190e-01,-1.3419e+00,-4.0672e-02,-8.1971e-01,-1.4063e+00,8.7327e-01,-4.0033e-01,-2.7843e+00,4.4974e-01,-6.7245e-01,-8.1971e-01,-4.5738e-01,-3.4065e-01,-1.0455e+00,-1.1821e-01,-7.1959e-01,-6.7245e-01,-5.4235e-01,-4.7749e-01,-8.7982e-01,-5.0206e-01,-2.3248e-01,-7.1959e-01,-1.7954e-01,-7.2018e-01,-7.7218e-01,-4.6151e-01,-9.8790e-01,-2.3248e-01,-3.9200e-01,-5.4687e-01,-2.4113e-01,-2.6182e-01,-8.6186e-01,-9.8790e-01,-7.5253e-01,-1.7078e-01,-5.4470e-01,-3.6530e-01,-5.9642e-01,-8.6186e-01,9.0649e-02,9.0206e-02,9.0649e-02,8.6838e-02,9.0807e-02,1.1209e-01,9.0807e-02,1.0857e-01,9.0826e-02,-1.8872e+00,9.0826e-02,-1.1327e+00,9.6674e-02,-9.6674e-02,-1.1066e-02,1.1066e-02,6.2142e-01,-6.2142e-01,6.3352e-01,-6.3352e-01,8.8942e-01,-8.8942e-01,1.0833e+00,-1.0833e+00}
> Gradient: {-3.3003e-07,-5.1599e-07,-3.2019e-06,-3.2442e-06,-1.7533e-06,1.0749e-06,-1.4672e-06,-6.4625e-07,-1.1219e-06,-9.0756e-07,-2.0744e-06,-1.7533e-06,-3.0085e-06,-1.8311e-06,8.6941e-07,-3.6491e-06,1.5987e-06,-2.0744e-06,-2.8636e-06,-1.0063e-06,-1.4973e-06,-5.3016e-06,9.7511e-07,1.5987e-06,-3.0722e-06,-9.4676e-07,-1.3439e-06,-3.0835e-06,-6.2377e-07,9.7511e-07,-5.3441e-07,-5.4665e-06,-3.2999e-06,-1.4740e-06,3.3036e-06,-6.2377e-07,-7.8687e-06,-1.3432e-06,-2.2606e-06,-1.2587e-06,1.3326e-06,3.3036e-06,-1.4600e-06,-1.8849e-06,-4.7624e-07,-3.8730e-06,-1.7334e-06,1.3326e-06,-1.2904e-06,-2.3935e-06,-1.6743e-06,-1.9406e-06,9.3723e-07,-1.7334e-06,-1.6197e-06,-2.0069e-06,-2.2784e-07,-4.4086e-06,-7.6922e-07,9.3723e-07,-2.5381e-06,-1.0591e-06,-4.8946e-06,-2.2617e-06,3.5521e-06,-7.6922e-07,-3.0054e-06,-3.5393e-06,-2.0401e-06,-2.3087e-06,-6.2931e-07,3.5521e-06,1.8130e-07,1.8041e-07,1.8130e-07,1.7368e-07,1.8161e-07,2.2418e-07,1.8161e-07,2.1714e-07,1.8165e-07,-2.3023e-06,1.8165e-07,-5.1249e-06,4.0579e-06,-4.0579e-06,4.6420e-06,-4.6420e-06,1.0350e-05,-1.0350e-05,7.6435e-07,-7.6435e-07,5.6438e-06,-5.6438e-06,1.1659e-05,-1.1659e-05}
>>>> Re-trying (2/3).
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-1.9966e-01,-9.9420e-01,-6.0342e-01,-3.3982e-01,-5.4760e-01,-6.0690e-01,3.9724e-01,-4.3393e-01,-3.8014e-01,-5.0215e-01,-1.8250e+00,-5.4760e-01,2.0798e-01,1.7671e-01,-2.4262e+00,1.5631e+00,-1.0503e+00,-1.8250e+00,-1.9887e-01,5.9674e-01,-3.1366e+00,1.7276e+00,-1.2923e+00,-1.0503e+00,1.0119e-02,-5.1684e-01,-2.6498e-01,1.1654e-01,-1.4063e+00,-1.2923e+00,-4.2707e-01,6.8190e-01,-1.3419e+00,-4.0672e-02,-8.1971e-01,-1.4063e+00,8.7327e-01,-4.0033e-01,-2.7843e+00,4.4974e-01,-6.7245e-01,-8.1971e-01,-4.5738e-01,-3.4065e-01,-1.0455e+00,-1.1821e-01,-7.1959e-01,-6.7245e-01,-5.4235e-01,-4.7749e-01,-8.7982e-01,-5.0206e-01,-2.3248e-01,-7.1959e-01,-1.7954e-01,-7.2018e-01,-7.7218e-01,-4.6151e-01,-9.8790e-01,-2.3248e-01,-3.9200e-01,-5.4687e-01,-2.4113e-01,-2.6182e-01,-8.6186e-01,-9.8790e-01,-7.5253e-01,-1.7078e-01,-5.4470e-01,-3.6530e-01,-5.9642e-01,-8.6186e-01,9.0649e-02,9.0206e-02,9.0649e-02,8.6838e-02,9.0807e-02,1.1209e-01,9.0807e-02,1.0857e-01,9.0826e-02,-1.8872e+00,9.0826e-02,-1.1327e+00,9.6674e-02,-9.6674e-02,-1.1066e-02,1.1066e-02,6.2142e-01,-6.2142e-01,6.3352e-01,-6.3352e-01,8.8942e-01,-8.8942e-01,1.0833e+00,-1.0833e+00}
> Gradient: {-3.3002e-07,-5.1599e-07,-3.2019e-06,-3.2439e-06,-1.7533e-06,1.0749e-06,-1.4671e-06,-6.4624e-07,-1.1219e-06,-9.0734e-07,-2.0744e-06,-1.7533e-06,-3.0085e-06,-1.8311e-06,8.6941e-07,-3.6488e-06,1.5987e-06,-2.0744e-06,-2.8636e-06,-1.0063e-06,-1.4973e-06,-5.3012e-06,9.7511e-07,1.5987e-06,-3.0722e-06,-9.4664e-07,-1.3439e-06,-3.0833e-06,-6.2377e-07,9.7511e-07,-5.3440e-07,-5.4664e-06,-3.2999e-06,-1.4738e-06,3.3036e-06,-6.2377e-07,-7.8687e-06,-1.3431e-06,-2.2606e-06,-1.2584e-06,1.3326e-06,3.3036e-06,-1.4600e-06,-1.8846e-06,-4.7624e-07,-3.8729e-06,-1.7334e-06,1.3326e-06,-1.2904e-06,-2.3933e-06,-1.6743e-06,-1.9404e-06,9.3723e-07,-1.7334e-06,-1.6196e-06,-2.0068e-06,-2.2784e-07,-4.4084e-06,-7.6922e-07,9.3723e-07,-2.5380e-06,-1.0590e-06,-4.8946e-06,-2.2615e-06,3.5521e-06,-7.6922e-07,-3.0053e-06,-3.5391e-06,-2.0401e-06,-2.3085e-06,-6.2931e-07,3.5521e-06,1.8130e-07,1.8041e-07,1.8130e-07,1.7368e-07,1.8161e-07,2.2418e-07,1.8161e-07,2.1714e-07,1.8165e-07,-2.3019e-06,1.8165e-07,-5.1249e-06,4.0579e-06,-4.0579e-06,4.6420e-06,-4.6420e-06,1.0350e-05,-1.0350e-05,7.6435e-07,-7.6435e-07,5.6436e-06,-5.6436e-06,1.1659e-05,-1.1659e-05}
>>>> Re-trying (3/3).
After: gradient norm = 3.31423356172144E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6214,-0.6214}
Count Table 3:
---------------
h: {0.6335,-0.6335}
Count Table 4:
---------------
h: {0.8894,-0.8894}
Count Table 5:
---------------
h: {1.0833,-1.0833}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.1997,-0.9942,-0.6034,-0.3398,-0.5476,-0.6069,0.3972,-0.4339,-0.3801,-0.5022,-1.8250,-0.5476,0.2080,0.1767,-2.4262,1.5631,-1.0503,-1.8250,-0.1989,0.5967,-3.1366,1.7276,-1.2923,-1.0503,0.0101,-0.5168,-0.2650,0.1165,-1.4063,-1.2923,-0.4271,0.6819,-1.3419,-0.0407,-0.8197,-1.4063,0.8733,-0.4003,-2.7843,0.4497,-0.6725,-0.8197,-0.4574,-0.3406,-1.0455,-0.1182,-0.7196,-0.6725,-0.5423,-0.4775,-0.8798,-0.5021,-0.2325,-0.7196,-0.1795,-0.7202,-0.7722,-0.4615,-0.9879,-0.2325,-0.3920,-0.5469,-0.2411,-0.2618,-0.8619,-0.9879,-0.7525,-0.1708,-0.5447,-0.3653,-0.5964,-0.8619}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0906,0.0902}
Activity(exp=1): {0.0906,0.0868}
Activity(exp=2): {0.0908,0.1121}
Activity(exp=3): {0.0908,0.1086}
Activity(exp=4): {0.0908,-1.8872}
Activity(exp=5): {0.0908,-1.1327}
The Likelihood DID improve.
Suggested variations:
key=12;4;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component3-2-variation1).
>> Starting new optimization: component3-2-variation1. (2021-05-21 19:43:51.47).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[84,85]},{"h":[86,87]},{"h":[88,89]},{"h":[90,91]},{"h":[92,93]},{"h":[94,95]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[72,73],[74,75],[76,77],[78,79],[80,81],[82,83]]}]}
Value and gradient before optimization:
=======================================
value = 3.6528095258349493
gradient = {0.0003,0.0001,0.0003,0.0002,0.0000,0.0000,0.0004,0.0001,0.0003,0.0001,-0.0000,0.0000,0.0002,0.0002,0.0000,0.0006,0.0000,-0.0000,0.0001,0.0002,0.0000,0.0006,0.0000,0.0000,0.0003,0.0002,0.0002,0.0002,0.0000,0.0000,0.0002,0.0005,0.0001,0.0002,0.0000,0.0000,0.0005,0.0001,0.0000,0.0003,0.0000,0.0000,0.0003,0.0002,0.0001,0.0003,0.0000,0.0000,0.0002,0.0004,0.0001,0.0002,0.0000,0.0000,0.0002,0.0004,0.0001,0.0002,0.0000,0.0000,0.0003,0.0003,0.0001,0.0002,0.0000,0.0000,0.0001,0.0004,0.0002,0.0002,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0002,0.0000,0.0007,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0017,0.0017,-0.0029,0.0029}
gradient norm = 0.005135725870530885
Starting Function Value: 3.6528095258349493
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.652777783179515 0.012380622296478 2.410685968953088 0.000503444874018
2 4 3.652777640984004 0.001205287315399 1.000000000000000 0.000470996162068
3 5 3.652770711213181 0.026200193123446 1.000000000000000 0.000267869934695
4 6 3.652768123047177 0.013320376402662 1.000000000000000 0.000407164748814
5 7 3.652757868260888 0.112939460593230 1.000000000000000 0.000997055463201
6 10 3.652757245467225 0.003310726846732 0.092065026065208 0.000693497357921
7 11 3.652756365393346 0.004407789854366 1.000000000000000 0.000121644613435
8 12 3.652756326339166 0.001446518141152 1.000000000000000 0.000086066068313
9 15 3.652756319583061 0.000894571306876 0.660000000000000 0.000083578931182
10 16 3.652756132588262 0.003738958861260 1.000000000000000 0.000192572155108
11 17 3.652755889057877 0.005847565418088 1.000000000000000 0.000323803806199
12 18 3.652755268831102 0.015883594152747 1.000000000000000 0.000501793109547
13 19 3.652754205166453 0.031819318203702 1.000000000000000 0.000622340645068
14 20 3.652753509033063 0.038530256246318 1.000000000000000 0.000630475948387
15 21 3.652752921101492 0.007077386959248 1.000000000000000 0.000243130483112
16 22 3.652752781220583 0.004049859072169 1.000000000000000 0.000074191663066
17 23 3.652752775776930 0.000770106461157 1.000000000000000 0.000066352320685
18 24 3.652752734754457 0.001304591012388 1.000000000000000 0.000116665797475
19 25 3.652752619119644 0.003610462027602 1.000000000000000 0.000231649816876
20 26 3.652752391668982 0.009076548509148 1.000000000000000 0.000383908612571
21 29 3.652752068582828 0.012816917617544 0.660000000000000 0.000461966633059
22 30 3.652751429459020 0.033620082553819 1.000000000000000 0.000424810007363
23 32 3.652751413273609 0.001175132432158 0.033031842739761 0.000421177464856
24 33 3.652751181540714 0.013983589189060 1.000000000000000 0.000218382337133
25 34 3.652751106277580 0.002912541015892 1.000000000000000 0.000043229573460
26 36 3.652751106008156 0.000038022755017 0.019004141678580 0.000042692818406
27 37 3.652751088462514 0.003284301222061 1.000000000000000 0.000052720711336
28 38 3.652751077344683 0.000998425299198 1.000000000000000 0.000069118258681
29 39 3.652751002583788 0.004304088346357 1.000000000000000 0.000143271386744
30 40 3.652750887153343 0.006926877276217 1.000000000000000 0.000210530210223
31 43 3.652750725921189 0.010674383167645 0.660000000000000 0.000233182537703
32 44 3.652750439328565 0.027723594440057 1.000000000000000 0.000175708902286
33 45 3.652750318822687 0.017752100718206 1.000000000000000 0.000075356591329
34 46 3.652750190193609 0.013909996403431 1.000000000000000 0.000073994174343
35 47 3.652750148460428 0.004899809540488 1.000000000000000 0.000124578359568
36 48 3.652750059989596 0.008815520834277 1.000000000000000 0.000186139610787
37 49 3.652749912624865 0.015018961767046 1.000000000000000 0.000219333448144
38 50 3.652749709921477 0.023479495346408 1.000000000000000 0.000174053471773
39 51 3.652749577300091 0.018602485519643 1.000000000000000 0.000061332241175
40 52 3.652749535965929 0.006547942538636 1.000000000000000 0.000035987055646
41 53 3.652749522318968 0.002147609853660 1.000000000000000 0.000061708819323
42 54 3.652749497536921 0.002799759262709 1.000000000000000 0.000088735494831
43 55 3.652749377432282 0.005249662044958 1.000000000000000 0.000119008702979
44 56 3.652749146389626 0.013179556305592 1.000000000000000 0.000130750680338
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.3792e-01,-9.9034e-01,-6.0181e-01,-3.1199e-01,-6.0484e-01,-6.2091e-01,3.6752e-01,-4.4949e-01,-4.1230e-01,-4.6607e-01,-1.8026e+00,-6.0484e-01,1.7168e-01,1.1897e-01,-2.4485e+00,1.6047e+00,-1.0728e+00,-1.8026e+00,-2.7871e-01,5.6440e-01,-3.1325e+00,1.8049e+00,-1.3138e+00,-1.0728e+00,-4.1016e-03,-6.0216e-01,-2.5412e-01,1.5866e-01,-1.4130e+00,-1.3138e+00,-4.6859e-01,6.9647e-01,-1.3377e+00,-2.3646e-02,-8.8208e-01,-1.4130e+00,8.9107e-01,-3.8288e-01,-2.7454e+00,4.2781e-01,-7.3706e-01,-8.8208e-01,-5.0875e-01,-3.1503e-01,-1.0702e+00,-9.2879e-02,-7.0457e-01,-7.3706e-01,-5.8318e-01,-5.1479e-01,-8.4916e-01,-5.4975e-01,-2.2704e-01,-7.0457e-01,-1.5669e-01,-8.1777e-01,-7.4639e-01,-4.9793e-01,-9.8268e-01,-2.2704e-01,-4.3795e-01,-5.5753e-01,-2.1064e-01,-2.7220e-01,-9.0680e-01,-9.8268e-01,-7.6090e-01,-1.6862e-01,-5.6630e-01,-3.9446e-01,-5.7072e-01,-9.0680e-01,8.8451e-02,8.8018e-02,8.8451e-02,8.4732e-02,8.8605e-02,1.0937e-01,8.8605e-02,1.0594e-01,8.8623e-02,-1.9303e+00,8.8623e-02,-1.1724e+00,9.6683e-02,-9.6683e-02,-1.1222e-02,1.1222e-02,6.2149e-01,-6.2149e-01,6.3352e-01,-6.3352e-01,8.8956e-01,-8.8956e-01,1.0836e+00,-1.0836e+00}
> Gradient: {4.4842e-06,1.0325e-07,4.0056e-06,5.3723e-06,-6.8726e-07,-9.7710e-07,6.2896e-06,-6.8641e-07,5.0177e-06,4.1471e-06,-1.7797e-06,-6.8726e-07,9.6185e-07,-1.1635e-06,1.6165e-06,1.1017e-05,1.5272e-06,-1.7797e-06,-8.2539e-07,1.5717e-06,-4.2023e-07,8.8839e-06,1.4425e-06,1.5272e-06,7.7960e-08,-5.1634e-07,6.8076e-06,4.1382e-06,2.2967e-07,1.4425e-06,8.8826e-07,1.3308e-05,-3.1209e-06,-2.4814e-06,3.3563e-06,2.2967e-07,1.7706e-06,1.1991e-06,-3.6863e-06,8.0308e-06,1.5091e-06,3.3563e-06,2.2531e-06,4.2850e-06,6.2321e-07,3.3959e-06,1.1326e-07,1.5091e-06,1.6287e-06,5.0438e-06,4.6298e-07,4.3211e-06,6.0971e-07,1.1326e-07,2.3392e-06,4.1836e-06,1.0558e-06,4.3728e-06,-3.8142e-07,6.0971e-07,9.4262e-07,3.3980e-06,1.5392e-06,4.8034e-06,1.9992e-06,-3.8142e-07,-1.1834e-06,7.4174e-06,8.6448e-07,4.2033e-06,-9.9998e-07,1.9992e-06,1.7690e-07,1.7604e-07,1.7690e-07,1.6946e-07,1.7721e-07,2.1874e-07,1.7721e-07,2.1188e-07,1.7725e-07,5.2668e-06,1.7725e-07,7.5644e-06,7.8941e-06,-7.8941e-06,-6.8987e-05,6.8987e-05,4.2519e-05,-4.2519e-05,1.0762e-06,-1.0762e-06,1.1520e-05,-1.1520e-05,-3.5445e-05,3.5445e-05}
>>>> Re-trying (1/3).
Starting Function Value: 3.652749343595102
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.652749315403413 0.000290445694883 2.220226288556973 0.000025349881533
2 4 3.652749314027747 0.000059191764632 1.000000000000000 0.000023768883006
3 5 3.652749283502824 0.000772656644714 1.000000000000000 0.000048194925288
4 7 3.652749276261608 0.000062661963719 0.055377800930338 0.000048361662921
5 8 3.652749272274128 0.002987351349472 1.000000000000000 0.000097175072850
6 9 3.652749262487859 0.003074821664124 1.000000000000000 0.000093310081486
7 11 3.652749258834712 0.000082548315649 0.133835886303821 0.000084075293011
8 12 3.652749206282624 0.001022298675790 1.000000000000000 0.000047902287339
Gradient = {-1.7017e-06,-1.2487e-06,-8.4613e-07,-6.0433e-07,-5.5949e-07,-1.1892e-06,-2.0989e-06,-2.6977e-06,1.0659e-06,-8.4573e-08,-1.7748e-06,-5.5949e-07,-9.3801e-07,-2.4186e-06,1.5201e-06,-4.1867e-06,1.5271e-06,-1.7748e-06,-1.8349e-06,-3.5587e-07,-4.4236e-07,-6.6044e-06,1.4394e-06,1.5271e-06,-3.6859e-06,-3.3799e-06,2.1751e-06,-3.0501e-06,2.3055e-07,1.4394e-06,-3.9365e-07,-1.7333e-06,-3.2339e-06,-4.5127e-06,3.3721e-06,2.3055e-07,-4.4820e-06,-1.1255e-06,-3.6260e-06,-1.9030e-06,1.4934e-06,3.3721e-06,-1.3218e-06,-2.0266e-06,-1.1311e-06,-3.3111e-06,2.6343e-08,1.4934e-06,-1.1224e-06,-2.0698e-06,-1.0977e-06,-1.8725e-06,-1.3485e-07,2.6343e-08,-1.7999e-06,-1.3057e-06,-1.1853e-06,-1.4059e-06,-4.3926e-07,-1.3485e-07,-2.8183e-06,-2.3507e-06,-2.1823e-06,-3.1889e-07,1.9599e-06,-4.3926e-07,-2.7185e-06,-2.6966e-06,-1.9438e-06,2.9790e-07,-1.0485e-06,1.9599e-06,1.7676e-07,1.7590e-07,1.7676e-07,1.6933e-07,1.7707e-07,2.1857e-07,1.7707e-07,2.1171e-07,1.7711e-07,-1.6947e-06,1.7711e-07,-3.9251e-06,3.6431e-06,-3.6431e-06,1.0915e-05,-1.0915e-05,2.2749e-05,-2.2749e-05,-1.2794e-06,1.2794e-06,-4.6732e-06,4.6732e-06,-1.7620e-05,1.7620e-05}
pCurr = {-8.9057e-06,9.3590e-05,-9.6166e-07,-1.0204e-04,7.2880e-05,1.1398e-04,-6.1465e-06,2.2816e-04,-1.6942e-04,-1.0826e-04,1.5132e-04,7.2880e-05,8.1083e-05,2.1993e-04,-1.2721e-04,-1.7681e-05,-1.2862e-04,1.5132e-04,1.5726e-04,1.3470e-05,3.8575e-05,2.1917e-04,-1.2103e-04,-1.2862e-04,3.1857e-04,2.2737e-04,-3.4235e-04,1.1362e-04,-1.7353e-05,-1.2103e-04,7.7312e-05,-3.6746e-04,3.0152e-04,4.6626e-04,-2.8144e-04,-1.7353e-05,4.2305e-04,3.2696e-05,3.1368e-04,-1.9070e-04,-1.1846e-04,-2.8144e-04,8.0540e-05,-1.9470e-05,6.6144e-05,1.5523e-04,1.4844e-05,-1.1846e-04,9.8783e-05,-5.4113e-05,9.2114e-05,-1.2434e-05,3.9633e-05,1.4844e-05,1.2754e-04,-4.7101e-05,5.5429e-05,-3.9685e-05,4.3013e-05,3.9633e-05,2.1561e-04,7.2426e-05,1.0579e-04,-1.0820e-04,-1.6010e-04,4.3013e-05,2.6082e-04,-5.1548e-05,1.3223e-04,-1.1783e-04,1.0498e-04,-1.6010e-04,-1.4996e-05,-1.4923e-05,-1.4996e-05,-1.4366e-05,-1.5022e-05,-1.8543e-05,-1.5022e-05,-1.7961e-05,-1.5025e-05,-2.3724e-04,-1.5025e-05,3.6083e-04,5.2958e-06,-5.2958e-06,9.8151e-06,-9.8151e-06,3.5423e-05,-3.5423e-05,-1.8083e-06,1.8083e-06,9.5082e-06,-9.5082e-06,6.9829e-05,-6.9829e-05}
grad*pCur = -2.052373645045742E-8
parameters = {-2.3845e-01,-9.9002e-01,-6.0218e-01,-3.1292e-01,-6.0450e-01,-6.2040e-01,3.6681e-01,-4.4861e-01,-4.1335e-01,-4.6689e-01,-1.8019e+00,-6.0450e-01,1.7190e-01,1.1990e-01,-2.4491e+00,1.6035e+00,-1.0733e+00,-1.8019e+00,-2.7806e-01,5.6434e-01,-3.1324e+00,1.8047e+00,-1.3143e+00,-1.0733e+00,-2.9831e-03,-6.0133e-01,-2.5597e-01,1.5859e-01,-1.4131e+00,-1.3143e+00,-4.6838e-01,6.9375e-01,-1.3363e+00,-2.1762e-02,-8.8336e-01,-1.4131e+00,8.9240e-01,-3.8288e-01,-2.7439e+00,4.2624e-01,-7.3759e-01,-8.8336e-01,-5.0869e-01,-3.1559e-01,-1.0700e+00,-9.2710e-02,-7.0450e-01,-7.3759e-01,-5.8298e-01,-5.1555e-01,-8.4888e-01,-5.5029e-01,-2.2690e-01,-7.0450e-01,-1.5648e-01,-8.1838e-01,-7.4631e-01,-4.9855e-01,-9.8248e-01,-2.2690e-01,-4.3729e-01,-5.5763e-01,-2.1045e-01,-2.7308e-01,-9.0753e-01,-9.8248e-01,-7.5985e-01,-1.6962e-01,-5.6592e-01,-3.9530e-01,-5.7024e-01,-9.0753e-01,8.8382e-02,8.7950e-02,8.8382e-02,8.4666e-02,8.8536e-02,1.0929e-01,8.8536e-02,1.0586e-01,8.8555e-02,-1.9320e+00,8.8555e-02,-1.1716e+00,9.6673e-02,-9.6673e-02,-1.1053e-02,1.1053e-02,6.2145e-01,-6.2145e-01,6.3351e-01,-6.3351e-01,8.8927e-01,-8.8927e-01,1.0834e+00,-1.0834e+00}
|grad|/|x| = 5.45169393081166E-6
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.3845e-01,-9.9002e-01,-6.0218e-01,-3.1292e-01,-6.0450e-01,-6.2040e-01,3.6681e-01,-4.4861e-01,-4.1334e-01,-4.6689e-01,-1.8019e+00,-6.0450e-01,1.7190e-01,1.1990e-01,-2.4491e+00,1.6035e+00,-1.0733e+00,-1.8019e+00,-2.7806e-01,5.6434e-01,-3.1324e+00,1.8047e+00,-1.3143e+00,-1.0733e+00,-2.9873e-03,-6.0133e-01,-2.5597e-01,1.5858e-01,-1.4131e+00,-1.3143e+00,-4.6838e-01,6.9376e-01,-1.3363e+00,-2.1768e-02,-8.8336e-01,-1.4131e+00,8.9239e-01,-3.8288e-01,-2.7439e+00,4.2625e-01,-7.3759e-01,-8.8336e-01,-5.0869e-01,-3.1559e-01,-1.0700e+00,-9.2712e-02,-7.0450e-01,-7.3759e-01,-5.8298e-01,-5.1555e-01,-8.4888e-01,-5.5029e-01,-2.2690e-01,-7.0450e-01,-1.5648e-01,-8.1838e-01,-7.4631e-01,-4.9855e-01,-9.8248e-01,-2.2690e-01,-4.3729e-01,-5.5763e-01,-2.1045e-01,-2.7308e-01,-9.0753e-01,-9.8248e-01,-7.5985e-01,-1.6962e-01,-5.6592e-01,-3.9530e-01,-5.7025e-01,-9.0753e-01,8.8382e-02,8.7950e-02,8.8382e-02,8.4667e-02,8.8536e-02,1.0929e-01,8.8536e-02,1.0586e-01,8.8555e-02,-1.9320e+00,8.8555e-02,-1.1716e+00,9.6673e-02,-9.6673e-02,-1.1053e-02,1.1053e-02,6.2145e-01,-6.2145e-01,6.3351e-01,-6.3351e-01,8.8927e-01,-8.8927e-01,1.0834e+00,-1.0834e+00}
> Gradient: {-1.7017e-06,-1.2487e-06,-8.4613e-07,-6.0433e-07,-5.5949e-07,-1.1892e-06,-2.0989e-06,-2.6977e-06,1.0659e-06,-8.4573e-08,-1.7748e-06,-5.5949e-07,-9.3801e-07,-2.4186e-06,1.5201e-06,-4.1867e-06,1.5271e-06,-1.7748e-06,-1.8349e-06,-3.5587e-07,-4.4236e-07,-6.6044e-06,1.4394e-06,1.5271e-06,-3.6859e-06,-3.3799e-06,2.1751e-06,-3.0501e-06,2.3055e-07,1.4394e-06,-3.9365e-07,-1.7333e-06,-3.2339e-06,-4.5127e-06,3.3721e-06,2.3055e-07,-4.4820e-06,-1.1255e-06,-3.6260e-06,-1.9030e-06,1.4934e-06,3.3721e-06,-1.3218e-06,-2.0266e-06,-1.1311e-06,-3.3111e-06,2.6343e-08,1.4934e-06,-1.1224e-06,-2.0698e-06,-1.0977e-06,-1.8725e-06,-1.3485e-07,2.6343e-08,-1.7999e-06,-1.3057e-06,-1.1853e-06,-1.4059e-06,-4.3926e-07,-1.3485e-07,-2.8183e-06,-2.3507e-06,-2.1823e-06,-3.1889e-07,1.9599e-06,-4.3926e-07,-2.7185e-06,-2.6966e-06,-1.9438e-06,2.9790e-07,-1.0485e-06,1.9599e-06,1.7676e-07,1.7590e-07,1.7676e-07,1.6933e-07,1.7707e-07,2.1857e-07,1.7707e-07,2.1171e-07,1.7711e-07,-1.6947e-06,1.7711e-07,-3.9251e-06,3.6431e-06,-3.6431e-06,1.0915e-05,-1.0915e-05,2.2749e-05,-2.2749e-05,-1.2794e-06,1.2794e-06,-4.6732e-06,4.6732e-06,-1.7620e-05,1.7620e-05}
>>>> Re-trying (2/3).
Starting Function Value: 3.652749224093967
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.652749219641091 0.000138465433160 2.890685136662826 0.000026385963623
2 4 3.652749218059838 0.000070935043566 1.000000000000000 0.000025458030674
3 5 3.652749208481890 0.001999090074105 1.000000000000000 0.000101926614355
4 7 3.652749207033653 0.000148050499045 0.338905418309616 0.000060894464439
5 8 3.652749200193965 0.000428192792705 1.000000000000000 0.000014812493264
6 9 3.652749199417607 0.000061170212830 1.000000000000000 0.000015846440606
7 10 3.652749175151326 0.002639025795917 1.000000000000000 0.000076211320754
8 11 3.652749136298431 0.005092063887634 1.000000000000000 0.000133062256905
9 12 3.652749060399019 0.013020777624671 1.000000000000000 0.000183941816540
10 15 3.652749012163999 0.011471693861975 0.660000000000000 0.000212741990884
Gradient = {-4.9622e-06,-9.3346e-07,-4.0159e-06,-4.0347e-06,-8.5314e-08,-1.1042e-06,-6.5303e-06,1.3192e-08,-3.2085e-06,-3.5698e-06,-1.7550e-06,-8.5314e-08,-2.0046e-06,-2.3544e-06,1.3477e-06,-1.1936e-05,1.4458e-06,-1.7550e-06,-2.3917e-06,-3.0285e-06,-4.8280e-07,-1.2137e-05,1.3376e-06,1.4458e-06,-2.5171e-06,-3.0312e-06,-4.7966e-06,-6.3781e-06,1.2911e-07,1.3376e-06,-9.9281e-07,-1.2219e-05,-2.9747e-06,-2.2932e-06,3.0943e-06,1.2911e-07,-3.9999e-06,-2.5160e-06,-3.4997e-06,-9.3861e-06,1.0510e-06,3.0943e-06,-3.9126e-06,-5.3667e-06,-1.9056e-06,-4.5064e-06,-6.1612e-07,1.0510e-06,-2.5891e-06,-5.1299e-06,-3.0571e-07,-5.8125e-06,-8.0305e-07,-6.1612e-07,-2.8457e-06,-4.5853e-06,-1.7732e-06,-4.6301e-06,-6.1906e-07,-8.0305e-07,-2.5352e-06,-5.6970e-06,-2.4923e-06,-5.2873e-06,1.4951e-06,-6.1906e-07,-1.5193e-06,-8.5725e-06,-1.2110e-06,-4.2067e-06,-1.1215e-06,1.4951e-06,1.7577e-07,1.7491e-07,1.7577e-07,1.6838e-07,1.7608e-07,2.1735e-07,1.7608e-07,2.1052e-07,1.7611e-07,-3.7528e-06,1.7611e-07,-1.0856e-05,-6.5693e-06,6.5693e-06,1.3897e-04,-1.3897e-04,-6.4234e-06,6.4234e-06,1.6282e-06,-1.6282e-06,-1.4058e-05,1.4058e-05,4.8596e-05,-4.8596e-05}
pCurr = {-6.2934e-04,1.0211e-03,-6.3073e-04,-1.8345e-03,7.7949e-04,1.4875e-03,-1.4280e-03,2.4146e-03,-2.2185e-03,-1.6029e-03,2.2490e-03,7.7949e-04,3.3234e-04,2.9319e-03,-1.8878e-03,-1.3678e-03,-1.9108e-03,2.2490e-03,1.9650e-03,2.9864e-04,5.6970e-04,1.2172e-03,-1.7928e-03,-1.9108e-03,2.1337e-03,3.3051e-03,-3.1705e-03,1.1991e-04,-2.4859e-04,-1.7928e-03,-7.9970e-04,-1.6141e-03,4.0384e-03,3.1322e-03,-4.1614e-03,-2.4859e-04,7.4381e-04,1.1209e-03,4.6006e-03,-2.2294e-04,-1.7341e-03,-4.1614e-03,-4.3690e-04,5.0819e-04,9.9277e-04,9.1021e-04,1.0668e-04,-1.7341e-03,-5.1985e-04,5.2199e-04,4.9703e-04,-2.5079e-04,-8.2105e-06,1.0668e-04,-3.6689e-04,1.3902e-05,6.7315e-04,-5.5899e-04,5.9388e-04,-8.2105e-06,1.2935e-03,8.7406e-04,1.2132e-03,-1.3627e-03,-2.4183e-03,5.9388e-04,2.2783e-03,-3.2331e-04,1.1456e-03,-1.8047e-03,1.3161e-03,-2.4183e-03,-2.2333e-04,-2.2224e-04,-2.2333e-04,-2.1394e-04,-2.2372e-04,-2.7615e-04,-2.2372e-04,-2.6749e-04,-2.2377e-04,-3.8628e-04,-2.2377e-04,-8.9538e-05,1.2164e-05,-1.2164e-05,-2.0252e-04,2.0252e-04,7.3741e-05,-7.3741e-05,6.8010e-06,-6.8010e-06,9.9725e-05,-9.9725e-05,7.3760e-05,-7.3760e-05}
grad*pCur = -1.128219629517323E-7
parameters = {-2.3989e-01,-9.8773e-01,-6.0361e-01,-3.1705e-01,-6.0275e-01,-6.1708e-01,3.6357e-01,-4.4315e-01,-4.1833e-01,-4.7052e-01,-1.7969e+00,-6.0275e-01,1.7264e-01,1.2645e-01,-2.4533e+00,1.6003e+00,-1.0776e+00,-1.7969e+00,-2.7369e-01,5.6497e-01,-3.1311e+00,1.8073e+00,-1.3183e+00,-1.0776e+00,1.8195e-03,-5.9395e-01,-2.6314e-01,1.5881e-01,-1.4136e+00,-1.3183e+00,-4.7015e-01,6.9000e-01,-1.3273e+00,-1.4729e-02,-8.9261e-01,-1.4136e+00,8.9411e-01,-3.8040e-01,-2.7337e+00,4.2562e-01,-7.4145e-01,-8.9261e-01,-5.0970e-01,-3.1450e-01,-1.0678e+00,-9.0678e-02,-7.0427e-01,-7.4145e-01,-5.8415e-01,-5.1443e-01,-8.4774e-01,-5.5092e-01,-2.2691e-01,-7.0427e-01,-1.5729e-01,-8.1840e-01,-7.4481e-01,-4.9984e-01,-9.8116e-01,-2.2691e-01,-4.3438e-01,-5.5573e-01,-2.0774e-01,-2.7619e-01,-9.1291e-01,-9.8116e-01,-7.5474e-01,-1.7042e-01,-5.6333e-01,-3.9939e-01,-5.6732e-01,-9.1291e-01,8.7886e-02,8.7456e-02,8.7886e-02,8.4191e-02,8.8039e-02,1.0867e-01,8.8039e-02,1.0526e-01,8.8057e-02,-1.9329e+00,8.8057e-02,-1.1718e+00,9.6651e-02,-9.6651e-02,-1.0782e-02,1.0782e-02,6.2138e-01,-6.2138e-01,6.3352e-01,-6.3352e-01,8.8933e-01,-8.8933e-01,1.0838e+00,-1.0838e+00}
|grad|/|x| = 2.4099900526556476E-5
>>>> Exception caugth. Parameters reverted.
> Parameter: {-2.3989e-01,-9.8773e-01,-6.0361e-01,-3.1705e-01,-6.0275e-01,-6.1708e-01,3.6357e-01,-4.4315e-01,-4.1833e-01,-4.7052e-01,-1.7969e+00,-6.0275e-01,1.7264e-01,1.2645e-01,-2.4533e+00,1.6003e+00,-1.0776e+00,-1.7969e+00,-2.7369e-01,5.6497e-01,-3.1311e+00,1.8073e+00,-1.3183e+00,-1.0776e+00,1.8195e-03,-5.9395e-01,-2.6314e-01,1.5881e-01,-1.4136e+00,-1.3183e+00,-4.7015e-01,6.9000e-01,-1.3273e+00,-1.4729e-02,-8.9261e-01,-1.4136e+00,8.9411e-01,-3.8040e-01,-2.7337e+00,4.2562e-01,-7.4145e-01,-8.9261e-01,-5.0970e-01,-3.1450e-01,-1.0678e+00,-9.0678e-02,-7.0427e-01,-7.4145e-01,-5.8415e-01,-5.1443e-01,-8.4774e-01,-5.5092e-01,-2.2691e-01,-7.0427e-01,-1.5729e-01,-8.1840e-01,-7.4481e-01,-4.9984e-01,-9.8116e-01,-2.2691e-01,-4.3438e-01,-5.5573e-01,-2.0774e-01,-2.7619e-01,-9.1291e-01,-9.8116e-01,-7.5474e-01,-1.7042e-01,-5.6333e-01,-3.9939e-01,-5.6732e-01,-9.1291e-01,8.7886e-02,8.7456e-02,8.7886e-02,8.4191e-02,8.8039e-02,1.0867e-01,8.8039e-02,1.0526e-01,8.8057e-02,-1.9329e+00,8.8057e-02,-1.1718e+00,9.6651e-02,-9.6651e-02,-1.0782e-02,1.0782e-02,6.2138e-01,-6.2138e-01,6.3352e-01,-6.3352e-01,8.8933e-01,-8.8933e-01,1.0838e+00,-1.0838e+00}
> Gradient: {-4.9622e-06,-9.3346e-07,-4.0159e-06,-4.0347e-06,-8.5314e-08,-1.1042e-06,-6.5303e-06,1.3192e-08,-3.2085e-06,-3.5698e-06,-1.7550e-06,-8.5314e-08,-2.0046e-06,-2.3544e-06,1.3477e-06,-1.1936e-05,1.4458e-06,-1.7550e-06,-2.3917e-06,-3.0285e-06,-4.8280e-07,-1.2137e-05,1.3376e-06,1.4458e-06,-2.5171e-06,-3.0312e-06,-4.7966e-06,-6.3781e-06,1.2911e-07,1.3376e-06,-9.9281e-07,-1.2219e-05,-2.9747e-06,-2.2932e-06,3.0943e-06,1.2911e-07,-3.9999e-06,-2.5160e-06,-3.4997e-06,-9.3861e-06,1.0510e-06,3.0943e-06,-3.9126e-06,-5.3667e-06,-1.9056e-06,-4.5064e-06,-6.1612e-07,1.0510e-06,-2.5891e-06,-5.1299e-06,-3.0571e-07,-5.8125e-06,-8.0305e-07,-6.1612e-07,-2.8457e-06,-4.5853e-06,-1.7732e-06,-4.6301e-06,-6.1906e-07,-8.0305e-07,-2.5352e-06,-5.6970e-06,-2.4923e-06,-5.2873e-06,1.4951e-06,-6.1906e-07,-1.5193e-06,-8.5725e-06,-1.2110e-06,-4.2067e-06,-1.1215e-06,1.4951e-06,1.7577e-07,1.7491e-07,1.7577e-07,1.6838e-07,1.7608e-07,2.1735e-07,1.7608e-07,2.1052e-07,1.7611e-07,-3.7528e-06,1.7611e-07,-1.0856e-05,-6.5693e-06,6.5693e-06,1.3897e-04,-1.3897e-04,-6.4234e-06,6.4234e-06,1.6282e-06,-1.6282e-06,-1.4058e-05,1.4058e-05,4.8596e-05,-4.8596e-05}
>>>> Re-trying (3/3).
After: gradient norm = 2.127414090102813E-4
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0108,0.0108}
Count Table 2:
---------------
h: {0.6214,-0.6214}
Count Table 3:
---------------
h: {0.6335,-0.6335}
Count Table 4:
---------------
h: {0.8893,-0.8893}
Count Table 5:
---------------
h: {1.0838,-1.0838}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.2399,-0.9877,-0.6036,-0.3171,-0.6027,-0.6171,0.3636,-0.4432,-0.4183,-0.4705,-1.7969,-0.6027,0.1726,0.1264,-2.4533,1.6003,-1.0776,-1.7969,-0.2737,0.5650,-3.1311,1.8073,-1.3183,-1.0776,0.0018,-0.5940,-0.2631,0.1588,-1.4136,-1.3183,-0.4702,0.6900,-1.3273,-0.0147,-0.8926,-1.4136,0.8941,-0.3804,-2.7337,0.4256,-0.7415,-0.8926,-0.5097,-0.3145,-1.0678,-0.0907,-0.7043,-0.7415,-0.5842,-0.5144,-0.8477,-0.5509,-0.2269,-0.7043,-0.1573,-0.8184,-0.7448,-0.4998,-0.9812,-0.2269,-0.4344,-0.5557,-0.2077,-0.2762,-0.9129,-0.9812,-0.7547,-0.1704,-0.5633,-0.3994,-0.5673,-0.9129}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0879,0.0875}
Activity(exp=1): {0.0879,0.0842}
Activity(exp=2): {0.0880,0.1087}
Activity(exp=3): {0.0880,0.1053}
Activity(exp=4): {0.0881,-1.9329}
Activity(exp=5): {0.0881,-1.1718}
The Likelihood DID improve.
Suggested variations:
key=12;5;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component3-2-variation2).
>> Starting new optimization: component3-2-variation2. (2021-05-21 19:48:51.407).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[84,85]},{"h":[86,87]},{"h":[88,89]},{"h":[90,91]},{"h":[92,93]},{"h":[94,95]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[72,73],[74,75],[76,77],[78,79],[80,81],[82,83]]}]}
Value and gradient before optimization:
=======================================
value = 3.652103587431399
gradient = {0.0007,0.0002,0.0005,0.0004,0.0001,0.0001,0.0007,0.0005,0.0004,0.0003,0.0000,0.0001,0.0005,0.0004,0.0000,0.0010,0.0000,0.0000,0.0003,0.0005,0.0000,0.0011,0.0000,0.0000,0.0006,0.0005,0.0003,0.0007,0.0000,0.0000,0.0004,0.0008,0.0001,0.0007,0.0000,0.0000,0.0008,0.0003,0.0000,0.0008,0.0000,0.0000,0.0004,0.0007,0.0002,0.0006,0.0000,0.0000,0.0003,0.0008,0.0002,0.0004,0.0001,0.0000,0.0007,0.0005,0.0002,0.0004,0.0000,0.0001,0.0005,0.0005,0.0006,0.0004,0.0000,0.0000,0.0003,0.0007,0.0006,0.0003,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0005,0.0000,0.0015,-0.0000,0.0000,0.0001,-0.0001,-0.0000,0.0000,0.0000,-0.0000,-0.0050,0.0050,-0.0068,0.0068}
gradient norm = 0.012625687062909023
Starting Function Value: 3.652103587431399
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.651918097866620 0.029257803293634 2.317323655168503 0.000784734074535
2 4 3.651916697583697 0.001847316755902 1.000000000000000 0.000758842805233
3 5 3.651888162424064 0.053067523346554 1.000000000000000 0.002334715946726
4 6 3.651859404730820 0.075838709235584 1.000000000000000 0.002862439475713
5 7 3.651807873299107 0.130044321879306 1.000000000000000 0.003511743688145
6 8 3.651756467615163 0.250902668330570 1.000000000000000 0.003635441211734
7 9 3.651697406072817 0.055004886078038 1.000000000000000 0.002446959454384
8 10 3.651671925297403 0.051683626121630 1.000000000000000 0.001649680256342
9 11 3.651659954561954 0.076182492053196 1.000000000000000 0.001325042188266
10 12 3.651651017944554 0.061470391597053 1.000000000000000 0.001124066883218
11 13 3.651644289266308 0.054136911399436 1.000000000000000 0.001404789764925
12 14 3.651628527045427 0.109934154541147 1.000000000000000 0.002149304744649
13 15 3.651608360896045 0.171824572116713 1.000000000000000 0.003982116892534
14 16 3.651576962883544 0.082591371327866 1.000000000000000 0.002579948603972
15 17 3.651550510809596 0.089952798675066 1.000000000000000 0.001236562491200
16 18 3.651545895021733 0.033337805629075 1.000000000000000 0.001192156453904
17 19 3.651542256146518 0.019184227035824 1.000000000000000 0.000956535639079
18 20 3.651536662589825 0.019925017901828 1.000000000000000 0.001274365086241
19 21 3.651521846509251 0.046441757968315 1.000000000000000 0.002270595282818
20 22 3.651499335504675 0.109526618820738 1.000000000000000 0.002899415501123
21 24 3.651491217855908 0.075973136474157 0.390607723800796 0.003368194622776
22 25 3.651471346390158 0.145760459104203 1.000000000000000 0.001884977208571
23 26 3.651462695648907 0.094864392321611 1.000000000000000 0.000504663050177
24 27 3.651460849022163 0.065121182392626 1.000000000000000 0.000396739570379
25 28 3.651458911644068 0.020271092782797 1.000000000000000 0.000522310252417
26 29 3.651449720841148 0.115580497872958 1.000000000000000 0.001052425109250
27 30 3.651434544278631 0.170226632107905 1.000000000000000 0.001372817602480
28 31 3.651416450298261 0.220963396054425 1.000000000000000 0.000955839172120
29 32 3.651407690421641 0.085866888187058 1.000000000000000 0.000730182301475
30 33 3.651402772609175 0.051501066410017 1.000000000000000 0.000279187194203
31 34 3.651400303772530 0.082051814085686 1.000000000000000 0.000440329545493
32 35 3.651398438080976 0.019546442670038 1.000000000000000 0.000592890152265
33 36 3.651394302057586 0.046149709263517 1.000000000000000 0.000730769791269
34 37 3.651390678987139 0.078434926157508 1.000000000000000 0.000640448202944
35 38 3.651387704747617 0.103971105920508 1.000000000000000 0.000311199750675
36 39 3.651386473554625 0.078316221419483 1.000000000000000 0.000124724300279
37 40 3.651385772336065 0.038678553449451 1.000000000000000 0.000219693861313
38 42 3.651385447152150 0.001273277632640 0.035205928896344 0.000223309647812
39 43 3.651384302090345 0.076340741666953 1.000000000000000 0.000437141260452
40 44 3.651383198105844 0.034409386504518 1.000000000000000 0.000446285508057
41 45 3.651380549695722 0.065269343119109 1.000000000000000 0.000247670016967
42 46 3.651379622984773 0.050872092155892 1.000000000000000 0.000094175995537
43 47 3.651379419156731 0.019239959615600 1.000000000000000 0.000142697237118
44 48 3.651379142921571 0.015750730772824 1.000000000000000 0.000205121264788
45 49 3.651378706400462 0.020829458705556 1.000000000000000 0.000190082800999
46 50 3.651378002749347 0.052183494035812 1.000000000000000 0.000206324962388
47 51 3.651377387779998 0.069027109351088 1.000000000000000 0.000074994556681
48 52 3.651377099751585 0.047556689443319 1.000000000000000 0.000094546897597
49 53 3.651376676979376 0.031296754823251 1.000000000000000 0.000167686126781
50 55 3.651376648215905 0.001977508542873 0.040236614006501 0.000167721177335
51 56 3.651375088447225 0.103138667148971 1.000000000000000 0.000151203754124
52 57 3.651374206092517 0.070051954051776 1.000000000000000 0.000193045039810
53 58 3.651373480353275 0.066987896085314 1.000000000000000 0.000134718000414
54 59 3.651373106528415 0.029877036042415 1.000000000000000 0.000099603733275
55 60 3.651372836351202 0.018726294222048 1.000000000000000 0.000086781871084
56 61 3.651372609003736 0.018325175500491 1.000000000000000 0.000094352018935
57 62 3.651372224935954 0.047503406302542 1.000000000000000 0.000096064050611
58 63 3.651371750038201 0.069808925379764 1.000000000000000 0.000131049501058
59 64 3.651371099239842 0.084123705377829 1.000000000000000 0.000195380846496
60 65 3.651370207675847 0.118817149053385 1.000000000000000 0.000227554457595
61 66 3.651369053803535 0.128506946787959 1.000000000000000 0.000231093583727
62 67 3.651367235825687 0.206731624112243 1.000000000000000 0.000126767178099
63 68 3.651365306347672 0.215931969652192 1.000000000000000 0.000165463109447
64 69 3.651363787491911 0.108292151263355 1.000000000000000 0.000297959888594
65 70 3.651361383396580 0.140028114367095 1.000000000000000 0.000395761515917
66 71 3.651358764644177 0.199829751529158 1.000000000000000 0.000433736845671
67 72 3.651353705954927 0.547005911892879 1.000000000000000 0.000496871522433
68 73 3.651349360102331 0.165106170348825 1.000000000000000 0.000622429160916
69 74 3.651346187475072 0.169730862853109 1.000000000000000 0.000172659332093
70 75 3.651344627770266 0.042551112037507 1.000000000000000 0.000253013344160
71 76 3.651344483023058 0.032144285487931 1.000000000000000 0.000191365364606
72 77 3.651341987805632 0.117462393588700 1.000000000000000 0.000086631365834
73 78 3.651341423100857 0.045628503172801 1.000000000000000 0.000142962341476
74 79 3.651340908298796 0.032152700179117 1.000000000000000 0.000197558993168
75 80 3.651339873987113 0.035696414446820 1.000000000000000 0.000193790538477
76 81 3.651338347547222 0.089918971608577 1.000000000000000 0.000112357418084
77 83 3.651338316162908 0.003758246345049 0.047022898698375 0.000108486137449
78 84 3.651337643817542 0.051943563230935 1.000000000000000 0.000050112164647
79 85 3.651337555138521 0.022198918173732 1.000000000000000 0.000047049368835
80 86 3.651337386094463 0.022997714055953 1.000000000000000 0.000046473704183
81 87 3.651337085107503 0.029563599781419 1.000000000000000 0.000048923057526
82 88 3.651336904805636 0.025918168853569 1.000000000000000 0.000049177214248
83 89 3.651336616458529 0.017285175823360 1.000000000000000 0.000023866342674
84 90 3.651336042736743 0.009567062455456 1.000000000000000 0.000025469596120
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-6.1846e-01,-1.0160e+00,-6.8592e-01,-8.2845e-02,-6.8536e-01,-9.0818e-01,3.3682e-01,-8.2707e-01,-3.8095e-01,-7.9399e-01,-1.6462e+00,-6.8536e-01,-7.5421e-03,-3.4395e-01,-3.4796e+00,2.5846e+00,-1.1502e+00,-1.6462e+00,-4.4245e-01,-2.7064e-01,-3.2105e+00,2.4797e+00,-1.4488e+00,-1.1502e+00,1.8765e-02,-1.4477e+00,1.9364e-01,8.2029e-03,-1.3670e+00,-1.4488e+00,-6.8351e-01,9.0596e-01,-1.1887e+00,-8.5782e-01,-8.5175e-01,-1.3670e+00,6.9622e-01,-1.1971e+00,-1.0646e+00,-5.6359e-01,-1.0620e+00,-8.5175e-01,-7.4472e-01,-5.5836e-01,-1.0898e+00,1.2619e-01,-7.1415e-01,-1.0620e+00,-7.1515e-01,-4.9693e-01,-1.0438e+00,-9.0357e-01,-1.6928e-01,-7.1415e-01,-2.7764e-02,-1.1778e+00,-9.1387e-01,-6.9706e-01,-1.0570e+00,-1.6928e-01,-6.4612e-01,-7.7720e-01,-2.1772e-01,-2.9695e-01,-1.0017e+00,-1.0570e+00,-8.8437e-01,-1.8805e-01,-7.3882e-01,-5.8934e-01,-5.9446e-01,-1.0017e+00,6.7180e-02,6.6851e-02,6.7180e-02,6.4355e-02,6.7297e-02,8.3069e-02,6.7297e-02,8.0462e-02,6.7311e-02,-2.2438e+00,6.7311e-02,-1.5516e+00,9.6666e-02,-9.6666e-02,-1.1079e-02,1.1079e-02,6.2139e-01,-6.2139e-01,6.3351e-01,-6.3351e-01,8.8653e-01,-8.8653e-01,1.0686e+00,-1.0686e+00}
> Gradient: {-4.6624e-06,-1.0986e-06,3.0945e-06,2.3903e-06,1.0642e-06,8.6503e-07,-3.9985e-06,6.1930e-06,-3.4888e-07,-3.4732e-07,-9.0950e-07,1.0642e-06,1.5666e-06,1.6310e-06,-2.2178e-06,1.9912e-06,-5.0072e-07,-9.0950e-07,1.7043e-07,-1.9054e-06,-3.7662e-07,4.3893e-06,-2.1619e-07,-5.0072e-07,9.5041e-07,6.0583e-08,-5.6027e-06,6.2447e-06,1.2402e-07,-2.1619e-07,1.7178e-06,-3.2783e-06,6.0438e-07,1.5935e-06,7.9940e-07,1.2402e-07,3.0512e-06,2.9376e-07,-1.5437e-08,-1.0664e-06,-1.5018e-06,7.9940e-07,-1.0624e-06,4.0333e-06,-2.5196e-07,1.6121e-06,-1.2685e-06,-1.5018e-06,4.9921e-06,-1.8179e-06,-6.9579e-07,-6.5047e-09,3.5732e-07,-1.2685e-06,1.8814e-06,-5.9548e-07,2.6294e-06,-4.3741e-06,1.6622e-06,3.5732e-07,-8.5526e-07,-1.8417e-06,7.8927e-07,1.8139e-06,8.4509e-08,1.6622e-06,-2.1188e-06,-7.5361e-07,1.8655e-06,-1.3147e-06,3.8900e-06,8.4509e-08,1.3436e-07,1.3370e-07,1.3436e-07,1.2871e-07,1.3459e-07,1.6614e-07,1.3459e-07,1.6092e-07,1.3462e-07,-2.2325e-06,1.3462e-07,4.2882e-06,2.8535e-06,-2.8535e-06,-1.4397e-06,1.4397e-06,-2.5506e-06,2.5506e-06,-2.0355e-06,2.0355e-06,-9.1192e-06,9.1192e-06,-6.0043e-06,6.0043e-06}
>>>> Re-trying (1/3).
Starting Function Value: 3.6513367980626743
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.651336796259395 0.000141166383142 5.545213779790268 0.000028864848712
2 4 3.651336794236396 0.000106800349103 1.000000000000000 0.000028660082889
3 6 3.651336731814859 0.006591701181540 0.372967383914085 0.000151716763228
4 7 3.651336691580157 0.005286127984219 1.000000000000000 0.000036261682157
5 8 3.651336689309108 0.000791453737933 1.000000000000000 0.000013747989994
6 9 3.651336688671258 0.000126760980045 1.000000000000000 0.000013067702144
7 10 3.651336684301887 0.000558810246114 1.000000000000000 0.000029198617082
8 13 3.651336678340434 0.000771504693238 0.660000000000000 0.000044841619273
9 14 3.651336661464081 0.003051307002249 1.000000000000000 0.000069059987821
10 16 3.651336655796071 0.001733388557229 0.344840322964541 0.000083830289113
11 17 3.651336644192511 0.002523707787279 1.000000000000000 0.000056311684315
12 18 3.651336536125365 0.003134108352448 1.000000000000000 0.000024449718542
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-6.1413e-01,-1.0152e+00,-6.8721e-01,-8.4223e-02,-6.8657e-01,-9.0927e-01,3.3992e-01,-8.3404e-01,-3.7818e-01,-7.9307e-01,-1.6447e+00,-6.8657e-01,-1.0511e-02,-3.4693e-01,-3.4759e+00,2.5848e+00,-1.1493e+00,-1.6447e+00,-4.4272e-01,-2.6770e-01,-3.2098e+00,2.4755e+00,-1.4485e+00,-1.1493e+00,1.9611e-02,-1.4473e+00,1.9646e-01,4.3429e-03,-1.3672e+00,-1.4485e+00,-6.8404e-01,9.0937e-01,-1.1887e+00,-8.5907e-01,-8.5298e-01,-1.3672e+00,6.9576e-01,-1.1980e+00,-1.0640e+00,-5.6379e-01,-1.0596e+00,-8.5298e-01,-7.4378e-01,-5.6082e-01,-1.0903e+00,1.2385e-01,-7.1194e-01,-1.0596e+00,-7.2081e-01,-4.9453e-01,-1.0425e+00,-9.0418e-01,-1.6859e-01,-7.1194e-01,-2.6478e-02,-1.1780e+00,-9.1751e-01,-6.9229e-01,-1.0597e+00,-1.6859e-01,-6.4474e-01,-7.7548e-01,-2.1612e-01,-2.9886e-01,-1.0017e+00,-1.0597e+00,-8.8129e-01,-1.8755e-01,-7.3864e-01,-5.8698e-01,-6.0040e-01,-1.0017e+00,6.6952e-02,6.6625e-02,6.6952e-02,6.4137e-02,6.7069e-02,8.2788e-02,6.7069e-02,8.0189e-02,6.7083e-02,-2.2436e+00,6.7083e-02,-1.5523e+00,9.6666e-02,-9.6666e-02,-1.1077e-02,1.1077e-02,6.2140e-01,-6.2140e-01,6.3350e-01,-6.3350e-01,8.8663e-01,-8.8663e-01,1.0686e+00,-1.0686e+00}
> Gradient: {3.1996e-06,7.1201e-07,-3.4174e-08,1.6583e-06,3.9660e-07,7.6985e-07,4.2917e-06,-1.5720e-07,2.6757e-06,3.8505e-07,-8.8963e-07,3.9660e-07,1.6414e-06,1.8697e-06,-2.1648e-06,6.6427e-06,-4.8907e-07,-8.8963e-07,5.9743e-07,-7.9123e-07,-3.7933e-07,7.8692e-06,-1.9659e-07,-4.8907e-07,3.6845e-06,3.9853e-07,2.6117e-06,4.9358e-08,6.2830e-08,-1.9659e-07,-9.8264e-08,5.8146e-06,-1.9739e-07,4.3722e-07,5.9133e-07,6.2830e-08,5.3306e-06,6.5216e-07,-3.4822e-07,1.5899e-06,-1.2054e-06,5.9133e-07,1.4883e-06,6.7103e-06,1.3616e-06,-1.2409e-06,-5.0351e-07,-1.2054e-06,-5.6893e-07,8.1807e-06,-4.1197e-07,1.2655e-07,-2.1245e-07,-5.0351e-07,5.2363e-06,1.8733e-07,-7.0806e-07,9.1621e-07,1.1910e-06,-2.1245e-07,2.6384e-07,4.1135e-08,6.5269e-06,-1.2042e-06,-1.1652e-07,1.1910e-06,-5.0953e-07,-1.2022e-06,5.7691e-06,1.0199e-07,2.6594e-06,-1.1652e-07,1.3390e-07,1.3325e-07,1.3390e-07,1.2827e-07,1.3414e-07,1.6558e-07,1.3414e-07,1.6038e-07,1.3417e-07,2.4536e-06,1.3417e-07,4.6501e-06,3.3493e-07,-3.3493e-07,-4.0097e-07,4.0097e-07,4.8617e-07,-4.8617e-07,-4.7075e-06,4.7075e-06,3.9541e-06,-3.9541e-06,1.8532e-06,-1.8532e-06}
>>>> Re-trying (2/3).
>>>> Exception caugth. Parameters reverted.
> Parameter: {-6.1413e-01,-1.0152e+00,-6.8721e-01,-8.4223e-02,-6.8657e-01,-9.0927e-01,3.3992e-01,-8.3404e-01,-3.7818e-01,-7.9307e-01,-1.6447e+00,-6.8657e-01,-1.0511e-02,-3.4693e-01,-3.4759e+00,2.5848e+00,-1.1493e+00,-1.6447e+00,-4.4272e-01,-2.6770e-01,-3.2098e+00,2.4755e+00,-1.4485e+00,-1.1493e+00,1.9611e-02,-1.4473e+00,1.9646e-01,4.3429e-03,-1.3672e+00,-1.4485e+00,-6.8404e-01,9.0937e-01,-1.1887e+00,-8.5907e-01,-8.5298e-01,-1.3672e+00,6.9576e-01,-1.1980e+00,-1.0640e+00,-5.6379e-01,-1.0596e+00,-8.5298e-01,-7.4378e-01,-5.6082e-01,-1.0903e+00,1.2385e-01,-7.1194e-01,-1.0596e+00,-7.2081e-01,-4.9453e-01,-1.0425e+00,-9.0418e-01,-1.6859e-01,-7.1194e-01,-2.6478e-02,-1.1780e+00,-9.1751e-01,-6.9229e-01,-1.0597e+00,-1.6859e-01,-6.4474e-01,-7.7548e-01,-2.1612e-01,-2.9886e-01,-1.0017e+00,-1.0597e+00,-8.8129e-01,-1.8755e-01,-7.3864e-01,-5.8698e-01,-6.0040e-01,-1.0017e+00,6.6952e-02,6.6625e-02,6.6952e-02,6.4137e-02,6.7069e-02,8.2788e-02,6.7069e-02,8.0189e-02,6.7083e-02,-2.2436e+00,6.7083e-02,-1.5523e+00,9.6666e-02,-9.6666e-02,-1.1077e-02,1.1077e-02,6.2140e-01,-6.2140e-01,6.3350e-01,-6.3350e-01,8.8663e-01,-8.8663e-01,1.0686e+00,-1.0686e+00}
> Gradient: {3.1996e-06,7.1201e-07,-3.4167e-08,1.6584e-06,3.9660e-07,7.6985e-07,4.2918e-06,-1.5715e-07,2.6757e-06,3.8506e-07,-8.8963e-07,3.9660e-07,1.6414e-06,1.8697e-06,-2.1648e-06,6.6428e-06,-4.8907e-07,-8.8963e-07,5.9743e-07,-7.9122e-07,-3.7933e-07,7.8692e-06,-1.9659e-07,-4.8907e-07,3.6845e-06,3.9853e-07,2.6118e-06,4.9376e-08,6.2830e-08,-1.9659e-07,-9.8213e-08,5.8147e-06,-1.9738e-07,4.3722e-07,5.9133e-07,6.2830e-08,5.3306e-06,6.5217e-07,-3.4822e-07,1.5899e-06,-1.2054e-06,5.9133e-07,1.4883e-06,6.7103e-06,1.3616e-06,-1.2408e-06,-5.0351e-07,-1.2054e-06,-5.6888e-07,8.1807e-06,-4.1197e-07,1.2656e-07,-2.1245e-07,-5.0351e-07,5.2363e-06,1.8737e-07,-7.0806e-07,9.1622e-07,1.1910e-06,-2.1245e-07,2.6385e-07,4.1186e-08,6.5269e-06,-1.2042e-06,-1.1652e-07,1.1910e-06,-5.0953e-07,-1.2022e-06,5.7692e-06,1.0199e-07,2.6594e-06,-1.1652e-07,1.3390e-07,1.3325e-07,1.3390e-07,1.2827e-07,1.3414e-07,1.6558e-07,1.3414e-07,1.6038e-07,1.3417e-07,2.4536e-06,1.3417e-07,4.6501e-06,3.3493e-07,-3.3493e-07,-4.0097e-07,4.0097e-07,4.8617e-07,-4.8617e-07,-4.7075e-06,4.7075e-06,3.9541e-06,-3.9541e-06,1.8531e-06,-1.8531e-06}
>>>> Re-trying (3/3).
After: gradient norm = 2.4451891120349803E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6214,-0.6214}
Count Table 3:
---------------
h: {0.6335,-0.6335}
Count Table 4:
---------------
h: {0.8866,-0.8866}
Count Table 5:
---------------
h: {1.0686,-1.0686}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.6141,-1.0152,-0.6872,-0.0842,-0.6866,-0.9093,0.3399,-0.8340,-0.3782,-0.7931,-1.6447,-0.6866,-0.0105,-0.3469,-3.4759,2.5848,-1.1493,-1.6447,-0.4427,-0.2677,-3.2098,2.4755,-1.4485,-1.1493,0.0196,-1.4473,0.1965,0.0043,-1.3672,-1.4485,-0.6840,0.9094,-1.1887,-0.8591,-0.8530,-1.3672,0.6958,-1.1980,-1.0640,-0.5638,-1.0596,-0.8530,-0.7438,-0.5608,-1.0903,0.1238,-0.7119,-1.0596,-0.7208,-0.4945,-1.0425,-0.9042,-0.1686,-0.7119,-0.0265,-1.1780,-0.9175,-0.6923,-1.0597,-0.1686,-0.6447,-0.7755,-0.2161,-0.2989,-1.0017,-1.0597,-0.8813,-0.1875,-0.7386,-0.5870,-0.6004,-1.0017}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0670,0.0666}
Activity(exp=1): {0.0670,0.0641}
Activity(exp=2): {0.0671,0.0828}
Activity(exp=3): {0.0671,0.0802}
Activity(exp=4): {0.0671,-2.2436}
Activity(exp=5): {0.0671,-1.5523}
The Likelihood DID improve.
Suggested variations:
key=12;6;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component3-2-variation3).
>> Starting new optimization: component3-2-variation3. (2021-05-21 19:55:01.936).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[84,85]},{"h":[86,87]},{"h":[88,89]},{"h":[90,91]},{"h":[92,93]},{"h":[94,95]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[72,73],[74,75],[76,77],[78,79],[80,81],[82,83]]}]}
Value and gradient before optimization:
=======================================
value = 3.6512655402305305
gradient = {0.0001,0.0000,0.0001,0.0000,0.0000,0.0000,0.0001,0.0000,0.0001,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0002,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0002,0.0000,-0.0000,0.0001,0.0000,0.0001,0.0000,0.0000,0.0000,0.0000,0.0001,0.0000,0.0000,0.0000,0.0000,0.0001,0.0000,0.0000,0.0001,0.0000,0.0000,0.0000,0.0001,0.0000,0.0001,0.0000,0.0000,0.0000,0.0001,0.0000,0.0000,0.0000,0.0000,0.0001,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0001,0.0000,0.0000,0.0000,0.0000,0.0001,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0001,0.0000,0.0001,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0009,0.0009,-0.0012,0.0012}
gradient norm = 0.002145306525814227
Starting Function Value: 3.6512655402305305
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.651259855487898 0.005234745789328 2.440092232200511 0.000190799337055
Gradient = {2.2366e-05,-1.4229e-05,-1.9980e-05,-4.7985e-05,-3.2117e-07,-2.2286e-06,-7.1771e-06,-3.0632e-05,-2.0921e-06,-2.1330e-05,-8.2499e-07,-3.2117e-07,7.0389e-06,-1.9338e-05,-2.0666e-06,-4.6781e-05,-4.9792e-07,-8.2499e-07,3.3121e-06,-4.7322e-06,-6.3966e-07,-5.9693e-05,-2.1849e-07,-4.9792e-07,-1.7268e-05,-1.3122e-05,5.0435e-06,-3.7163e-05,2.5926e-07,-2.1849e-07,-2.9552e-06,-1.9532e-05,-1.7413e-05,-2.2899e-05,7.0478e-08,2.5926e-07,-6.2576e-05,-8.4885e-06,-3.1569e-06,1.2460e-05,-7.7881e-07,7.0478e-08,-1.4482e-05,-3.0270e-05,-1.4458e-06,-1.3065e-05,-2.4280e-06,-7.7881e-07,-2.9058e-05,-2.1246e-05,-6.9603e-06,4.2717e-06,-7.0488e-06,-2.4280e-06,-3.2030e-05,-5.8072e-06,-2.0684e-05,2.4504e-06,6.5058e-07,-7.0488e-06,-1.0492e-05,-1.0314e-05,-3.5643e-05,-6.5235e-06,-5.6262e-08,6.5058e-07,-1.2065e-05,3.6767e-06,-5.3401e-05,-2.5490e-06,2.0170e-06,-5.6262e-08,1.3390e-07,1.3325e-07,1.3390e-07,1.2827e-07,1.3414e-07,1.6557e-07,1.3414e-07,1.6038e-07,1.3416e-07,-1.2733e-05,1.3416e-07,-4.9243e-05,-3.8774e-08,3.8774e-08,6.1571e-08,-6.1571e-08,-6.1672e-08,6.1672e-08,1.8148e-07,-1.8148e-07,1.3952e-05,-1.3952e-05,-5.5923e-05,5.5923e-05}
pCurr = {-5.6895e-05,3.4882e-05,4.8411e-05,1.1856e-04,6.6001e-07,5.4347e-06,1.6087e-05,7.5803e-05,3.7562e-06,5.2684e-05,2.0602e-06,6.6001e-07,-1.8005e-05,4.8010e-05,5.1507e-06,1.1282e-04,1.2435e-06,2.0602e-06,-8.5758e-06,1.1548e-05,1.5691e-06,1.4496e-04,5.4031e-07,1.2435e-06,4.1831e-05,3.2444e-05,-1.4567e-05,9.1708e-05,-6.7569e-07,5.4031e-07,6.7570e-06,4.5701e-05,4.3027e-05,5.6708e-05,-2.3707e-07,-6.7569e-07,1.5363e-04,2.0564e-05,7.5836e-06,-3.2150e-05,1.8858e-06,-2.3707e-07,3.5578e-05,7.3709e-05,3.0610e-06,3.1119e-05,5.9281e-06,1.8858e-06,7.1871e-05,5.0928e-05,1.6791e-05,-1.1442e-05,1.7205e-05,5.9281e-06,7.7982e-05,1.3713e-05,5.1040e-05,-6.9734e-06,-1.6866e-06,1.7205e-05,2.5372e-05,2.4758e-05,8.7096e-05,1.5424e-05,8.8141e-08,-1.6866e-06,2.9608e-05,-1.0958e-05,1.3176e-04,5.7084e-06,-5.1507e-06,8.8141e-08,-3.3508e-07,-3.3344e-07,-3.3508e-07,-3.2099e-07,-3.3567e-07,-4.1433e-07,-3.3567e-07,-4.0133e-07,-3.3573e-07,3.0311e-05,-3.3573e-07,1.1973e-04,9.0108e-08,-9.0108e-08,-1.4564e-07,1.4564e-07,1.4423e-07,-1.4423e-07,-3.6072e-07,3.6072e-07,-1.8250e-05,1.8250e-05,1.6255e-04,-1.6255e-04}
grad*pCur = -9.147345151959006E-8
parameters = {-6.1430e-01,-1.0153e+00,-6.8737e-01,-8.4298e-02,-6.8659e-01,-9.0928e-01,3.3970e-01,-8.3407e-01,-3.7836e-01,-7.9311e-01,-1.6447e+00,-6.8659e-01,-1.0577e-02,-3.4694e-01,-3.4759e+00,2.5844e+00,-1.1493e+00,-1.6447e+00,-4.4277e-01,-2.6772e-01,-3.2098e+00,2.4751e+00,-1.4485e+00,-1.1493e+00,1.9479e-02,-1.4474e+00,1.9620e-01,4.2708e-03,-1.3672e+00,-1.4485e+00,-6.8412e-01,9.0902e-01,-1.1887e+00,-8.5909e-01,-8.5299e-01,-1.3672e+00,6.9554e-01,-1.1980e+00,-1.0640e+00,-5.6394e-01,-1.0596e+00,-8.5299e-01,-7.4383e-01,-5.6101e-01,-1.0903e+00,1.2368e-01,-7.1195e-01,-1.0596e+00,-7.2084e-01,-4.9476e-01,-1.0426e+00,-9.0429e-01,-1.6863e-01,-7.1195e-01,-2.6675e-02,-1.1781e+00,-9.1755e-01,-6.9240e-01,-1.0597e+00,-1.6863e-01,-6.4482e-01,-7.7559e-01,-2.1629e-01,-2.9896e-01,-1.0017e+00,-1.0597e+00,-8.8134e-01,-1.8778e-01,-7.3875e-01,-5.8706e-01,-6.0042e-01,-1.0017e+00,6.6952e-02,6.6625e-02,6.6952e-02,6.4137e-02,6.7069e-02,8.2787e-02,6.7069e-02,8.0189e-02,6.7082e-02,-2.2437e+00,6.7082e-02,-1.5527e+00,9.6665e-02,-9.6665e-02,-1.1076e-02,1.1076e-02,6.2140e-01,-6.2140e-01,6.3352e-01,-6.3352e-01,8.8871e-01,-8.8871e-01,1.0716e+00,-1.0716e+00}
|grad|/|x| = 1.922513243473739E-5
>>>> Exception caugth. Parameters reverted.
> Parameter: {-6.1430e-01,-1.0153e+00,-6.8737e-01,-8.4298e-02,-6.8659e-01,-9.0928e-01,3.3970e-01,-8.3407e-01,-3.7836e-01,-7.9311e-01,-1.6447e+00,-6.8659e-01,-1.0577e-02,-3.4694e-01,-3.4759e+00,2.5844e+00,-1.1493e+00,-1.6447e+00,-4.4277e-01,-2.6772e-01,-3.2098e+00,2.4751e+00,-1.4485e+00,-1.1493e+00,1.9479e-02,-1.4474e+00,1.9620e-01,4.2705e-03,-1.3672e+00,-1.4485e+00,-6.8412e-01,9.0902e-01,-1.1887e+00,-8.5909e-01,-8.5299e-01,-1.3672e+00,6.9554e-01,-1.1980e+00,-1.0640e+00,-5.6394e-01,-1.0596e+00,-8.5299e-01,-7.4383e-01,-5.6101e-01,-1.0903e+00,1.2368e-01,-7.1195e-01,-1.0596e+00,-7.2084e-01,-4.9476e-01,-1.0426e+00,-9.0429e-01,-1.6863e-01,-7.1195e-01,-2.6675e-02,-1.1781e+00,-9.1755e-01,-6.9240e-01,-1.0597e+00,-1.6863e-01,-6.4483e-01,-7.7559e-01,-2.1629e-01,-2.9896e-01,-1.0017e+00,-1.0597e+00,-8.8134e-01,-1.8778e-01,-7.3875e-01,-5.8706e-01,-6.0042e-01,-1.0017e+00,6.6952e-02,6.6625e-02,6.6952e-02,6.4137e-02,6.7069e-02,8.2787e-02,6.7069e-02,8.0189e-02,6.7082e-02,-2.2437e+00,6.7082e-02,-1.5527e+00,9.6665e-02,-9.6665e-02,-1.1076e-02,1.1076e-02,6.2140e-01,-6.2140e-01,6.3352e-01,-6.3352e-01,8.8871e-01,-8.8871e-01,1.0716e+00,-1.0716e+00}
> Gradient: {2.2366e-05,-1.4229e-05,-1.9980e-05,-4.7985e-05,-3.2117e-07,-2.2286e-06,-7.1771e-06,-3.0632e-05,-2.0921e-06,-2.1330e-05,-8.2499e-07,-3.2117e-07,7.0389e-06,-1.9338e-05,-2.0666e-06,-4.6781e-05,-4.9792e-07,-8.2499e-07,3.3121e-06,-4.7322e-06,-6.3966e-07,-5.9693e-05,-2.1849e-07,-4.9792e-07,-1.7268e-05,-1.3122e-05,5.0435e-06,-3.7163e-05,2.5926e-07,-2.1849e-07,-2.9552e-06,-1.9532e-05,-1.7413e-05,-2.2899e-05,7.0478e-08,2.5926e-07,-6.2576e-05,-8.4885e-06,-3.1569e-06,1.2460e-05,-7.7881e-07,7.0478e-08,-1.4482e-05,-3.0270e-05,-1.4458e-06,-1.3065e-05,-2.4280e-06,-7.7881e-07,-2.9058e-05,-2.1246e-05,-6.9603e-06,4.2717e-06,-7.0488e-06,-2.4280e-06,-3.2030e-05,-5.8072e-06,-2.0684e-05,2.4504e-06,6.5058e-07,-7.0488e-06,-1.0492e-05,-1.0314e-05,-3.5643e-05,-6.5235e-06,-5.6262e-08,6.5058e-07,-1.2065e-05,3.6767e-06,-5.3401e-05,-2.5490e-06,2.0170e-06,-5.6262e-08,1.3390e-07,1.3325e-07,1.3390e-07,1.2827e-07,1.3414e-07,1.6557e-07,1.3414e-07,1.6038e-07,1.3416e-07,-1.2733e-05,1.3416e-07,-4.9243e-05,-3.8774e-08,3.8774e-08,6.1571e-08,-6.1571e-08,-6.1672e-08,6.1672e-08,1.8148e-07,-1.8148e-07,1.3952e-05,-1.3952e-05,-5.5923e-05,5.5923e-05}
>>>> Re-trying (1/3).
Starting Function Value: 3.6512598554878983
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.651259537336596 0.003271966621342 17.148731603849864 0.000345476834943
2 5 3.651259433065120 0.000646483152862 0.216352089785292 0.000301732280169
3 6 3.651259042768589 0.004887344264385 1.000000000000000 0.000119146865535
4 7 3.651258891970350 0.001514417102231 1.000000000000000 0.000142491571786
5 8 3.651258395732486 0.009814006105181 1.000000000000000 0.000323648093862
6 9 3.651251831122152 0.018613023993214 1.000000000000000 0.000453269536275
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-6.2522e-01,-1.0118e+00,-6.8437e-01,-7.3896e-02,-6.8672e-01,-9.0875e-01,3.3465e-01,-8.2463e-01,-3.8219e-01,-7.8747e-01,-1.6444e+00,-6.8672e-01,-1.3542e-02,-3.3959e-01,-3.4751e+00,2.5851e+00,-1.1491e+00,-1.6444e+00,-4.4418e-01,-2.6594e-01,-3.2096e+00,2.4806e+00,-1.4484e+00,-1.1491e+00,2.0783e-02,-1.4433e+00,1.8854e-01,1.2924e-02,-1.3672e+00,-1.4484e+00,-6.8476e-01,9.0305e-01,-1.1827e+00,-8.5208e-01,-8.5288e-01,-1.3672e+00,7.0386e-01,-1.1953e+00,-1.0629e+00,-5.7019e-01,-1.0592e+00,-8.5288e-01,-7.4055e-01,-5.5937e-01,-1.0908e+00,1.2445e-01,-7.1115e-01,-1.0592e+00,-7.1217e-01,-4.9673e-01,-1.0414e+00,-9.0802e-01,-1.6717e-01,-7.1115e-01,-2.5097e-02,-1.1777e+00,-9.1120e-01,-6.9553e-01,-1.0599e+00,-1.6717e-01,-6.4349e-01,-7.7391e-01,-2.1284e-01,-2.9878e-01,-1.0017e+00,-1.0599e+00,-8.7800e-01,-1.9383e-01,-7.2787e-01,-5.8791e-01,-6.0135e-01,-1.0017e+00,6.6902e-02,6.6575e-02,6.6902e-02,6.4090e-02,6.7019e-02,8.2726e-02,6.7019e-02,8.0129e-02,6.7033e-02,-2.2455e+00,6.7033e-02,-1.5447e+00,9.6655e-02,-9.6655e-02,-1.1052e-02,1.1052e-02,6.2138e-01,-6.2138e-01,6.3353e-01,-6.3353e-01,8.9009e-01,-8.9009e-01,1.0735e+00,-1.0735e+00}
> Gradient: {2.0754e-05,-7.5931e-06,3.3062e-06,8.2485e-06,2.5233e-06,3.7720e-07,2.6928e-05,-1.4981e-05,1.9735e-05,-5.7730e-06,-8.1663e-07,2.5233e-06,6.7205e-06,-2.2999e-05,-2.1647e-06,4.7284e-05,-5.0096e-07,-8.1663e-07,3.8878e-06,-7.1739e-06,-9.3331e-07,3.2507e-05,-2.6255e-07,-5.0096e-07,1.5651e-05,-8.9626e-06,1.4611e-05,6.3984e-06,8.9215e-08,-2.6255e-07,1.0614e-05,4.0809e-05,-1.3436e-05,-1.0047e-05,-5.0435e-07,8.9215e-08,3.8683e-05,-1.1676e-05,-5.3564e-06,7.4808e-06,-1.1031e-06,-5.0435e-07,-1.7530e-06,2.6671e-05,-1.5661e-06,6.1996e-06,-9.2459e-07,-1.1031e-06,-1.2678e-05,3.0370e-05,-2.4328e-06,8.9006e-06,4.2889e-06,-9.2459e-07,3.2598e-05,-1.2277e-06,-1.6617e-05,7.7235e-06,7.5842e-07,4.2889e-06,3.4267e-06,-4.1439e-06,2.3596e-05,3.4780e-06,5.0039e-07,7.5842e-07,-4.7479e-06,1.1840e-05,8.5361e-06,7.4021e-06,4.0850e-06,5.0039e-07,1.3380e-07,1.3315e-07,1.3380e-07,1.2818e-07,1.3404e-07,1.6545e-07,1.3404e-07,1.6026e-07,1.3407e-07,-1.3330e-05,1.3407e-07,4.1347e-05,-4.5445e-06,4.5445e-06,1.1428e-05,-1.1428e-05,-7.0161e-06,7.0161e-06,7.1016e-06,-7.1016e-06,3.0405e-04,-3.0405e-04,-2.2323e-05,2.2323e-05}
>>>> Re-trying (2/3).
Starting Function Value: 3.6512574826445974
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.651257194261008 0.001208904596842 2.684420601130152 0.000158168488152
2 4 3.651257127528956 0.000475646813605 1.000000000000000 0.000150722620915
Gradient = {2.2353e-05,-4.2994e-06,8.7267e-06,1.0360e-05,2.0171e-06,-1.6661e-07,2.9719e-05,-1.1970e-05,2.4277e-05,-4.2269e-06,-8.2654e-07,2.0171e-06,8.0134e-06,-2.1133e-05,-2.0554e-06,5.5406e-05,-5.0624e-07,-8.2654e-07,4.8068e-06,-5.1963e-06,-7.6681e-07,4.0836e-05,-2.7531e-07,-5.0624e-07,1.7834e-05,-7.4128e-06,2.0546e-05,8.1711e-06,3.5556e-08,-2.7531e-07,1.1719e-05,4.7756e-05,-1.1239e-05,-8.7788e-06,-5.9526e-07,3.5556e-08,4.1883e-05,-8.7338e-06,-2.1823e-06,9.7755e-06,-1.2487e-06,-5.9526e-07,-7.5788e-07,3.2239e-05,4.2269e-07,9.6162e-06,-1.3734e-06,-1.2487e-06,-1.0372e-05,3.7142e-05,5.9559e-07,1.0310e-05,2.5967e-06,-1.3734e-06,3.6961e-05,2.1061e-06,-1.2783e-05,9.4377e-06,5.7936e-07,2.5967e-06,5.2064e-06,-1.3770e-06,2.9104e-05,5.1220e-06,3.5477e-07,5.7936e-07,-3.4886e-06,1.6810e-05,1.3139e-05,8.4501e-06,3.7241e-06,3.5477e-07,1.3380e-07,1.3315e-07,1.3380e-07,1.2818e-07,1.3404e-07,1.6545e-07,1.3404e-07,1.6026e-07,1.3406e-07,1.2511e-05,1.3406e-07,2.6880e-05,5.0039e-07,-5.0039e-07,-1.0873e-06,1.0873e-06,7.5109e-07,-7.5109e-07,-9.2272e-07,9.2272e-07,-2.6391e-05,2.6391e-05,2.7830e-05,-2.7830e-05}
pCurr = {-8.2168e-04,2.1250e-04,-2.5142e-04,-3.0538e-04,-7.6297e-05,1.0244e-05,-1.0434e-03,5.1335e-04,-8.6373e-04,2.0548e-04,3.2538e-05,-7.6297e-05,-2.9898e-04,8.4438e-04,8.1694e-05,-1.9080e-03,1.9921e-05,3.2538e-05,-1.7862e-04,2.1737e-04,3.1094e-05,-1.3290e-03,1.0821e-05,1.9921e-05,-6.1842e-04,3.1213e-04,-6.8486e-04,-2.4666e-04,-1.4440e-06,1.0821e-05,-4.2926e-04,-1.6583e-03,4.6416e-04,3.7351e-04,2.2876e-05,-1.4440e-06,-1.4409e-03,3.7256e-04,1.0334e-04,-3.3564e-04,4.9351e-05,2.2876e-05,6.5402e-05,-1.1150e-03,1.2431e-05,-2.9673e-04,5.6139e-05,4.9351e-05,4.4925e-04,-1.2944e-03,1.3006e-05,-3.6213e-04,-9.0336e-05,5.6139e-05,-1.2971e-03,-3.7292e-05,5.4263e-04,-3.2441e-04,-2.1942e-05,-9.0336e-05,-1.5677e-04,1.0630e-04,-9.9005e-04,-1.5617e-04,-1.3422e-05,-2.1942e-05,1.6289e-04,-5.5819e-04,-3.8071e-04,-2.9826e-04,-1.4435e-04,-1.3422e-05,-5.2650e-06,-5.2393e-06,-5.2650e-06,-5.0437e-06,-5.2742e-06,-6.5103e-06,-5.2742e-06,-6.3060e-06,-5.2753e-06,-2.9909e-04,-5.2753e-06,-9.4873e-04,3.2444e-05,-3.2444e-05,-1.1039e-04,1.1039e-04,5.5611e-05,-5.5611e-05,-1.9374e-05,1.9374e-05,-5.4372e-04,5.4372e-04,-1.1544e-03,1.1544e-03}
grad*pCur = -7.228214789014602E-7
parameters = {-6.2535e-01,-1.0117e+00,-6.8441e-01,-7.3955e-02,-6.8673e-01,-9.0875e-01,3.3448e-01,-8.2455e-01,-3.8232e-01,-7.8744e-01,-1.6443e+00,-6.8673e-01,-1.3585e-02,-3.3947e-01,-3.4751e+00,2.5848e+00,-1.1491e+00,-1.6443e+00,-4.4420e-01,-2.6591e-01,-3.2096e+00,2.4804e+00,-1.4484e+00,-1.1491e+00,2.0683e-02,-1.4432e+00,1.8844e-01,1.2878e-02,-1.3672e+00,-1.4484e+00,-6.8483e-01,9.0279e-01,-1.1827e+00,-8.5203e-01,-8.5287e-01,-1.3672e+00,7.0362e-01,-1.1953e+00,-1.0628e+00,-5.7024e-01,-1.0592e+00,-8.5287e-01,-7.4055e-01,-5.5954e-01,-1.0908e+00,1.2440e-01,-7.1115e-01,-1.0592e+00,-7.1211e-01,-4.9693e-01,-1.0414e+00,-9.0808e-01,-1.6720e-01,-7.1115e-01,-2.5304e-02,-1.1777e+00,-9.1111e-01,-6.9559e-01,-1.0599e+00,-1.6720e-01,-6.4352e-01,-7.7390e-01,-2.1299e-01,-2.9881e-01,-1.0017e+00,-1.0599e+00,-8.7797e-01,-1.9392e-01,-7.2794e-01,-5.8796e-01,-6.0137e-01,-1.0017e+00,6.6901e-02,6.6575e-02,6.6901e-02,6.4089e-02,6.7018e-02,8.2725e-02,6.7018e-02,8.0128e-02,6.7032e-02,-2.2455e+00,6.7032e-02,-1.5449e+00,9.6666e-02,-9.6666e-02,-1.1078e-02,1.1078e-02,6.2140e-01,-6.2140e-01,6.3351e-01,-6.3351e-01,8.8919e-01,-8.8919e-01,1.0736e+00,-1.0736e+00}
|grad|/|x| = 1.5201443241733012E-5
>>>> Exception caugth. Parameters reverted.
> Parameter: {-6.2535e-01,-1.0117e+00,-6.8441e-01,-7.3955e-02,-6.8673e-01,-9.0875e-01,3.3448e-01,-8.2455e-01,-3.8232e-01,-7.8744e-01,-1.6443e+00,-6.8673e-01,-1.3585e-02,-3.3947e-01,-3.4751e+00,2.5848e+00,-1.1491e+00,-1.6443e+00,-4.4420e-01,-2.6591e-01,-3.2096e+00,2.4804e+00,-1.4484e+00,-1.1491e+00,2.0683e-02,-1.4432e+00,1.8844e-01,1.2878e-02,-1.3672e+00,-1.4484e+00,-6.8483e-01,9.0279e-01,-1.1827e+00,-8.5203e-01,-8.5287e-01,-1.3672e+00,7.0362e-01,-1.1953e+00,-1.0628e+00,-5.7024e-01,-1.0592e+00,-8.5287e-01,-7.4055e-01,-5.5954e-01,-1.0908e+00,1.2440e-01,-7.1115e-01,-1.0592e+00,-7.1211e-01,-4.9693e-01,-1.0414e+00,-9.0808e-01,-1.6720e-01,-7.1115e-01,-2.5304e-02,-1.1777e+00,-9.1111e-01,-6.9559e-01,-1.0599e+00,-1.6720e-01,-6.4352e-01,-7.7390e-01,-2.1299e-01,-2.9881e-01,-1.0017e+00,-1.0599e+00,-8.7797e-01,-1.9392e-01,-7.2794e-01,-5.8796e-01,-6.0137e-01,-1.0017e+00,6.6901e-02,6.6575e-02,6.6901e-02,6.4089e-02,6.7018e-02,8.2725e-02,6.7018e-02,8.0128e-02,6.7032e-02,-2.2455e+00,6.7032e-02,-1.5449e+00,9.6666e-02,-9.6666e-02,-1.1078e-02,1.1078e-02,6.2140e-01,-6.2140e-01,6.3351e-01,-6.3351e-01,8.8919e-01,-8.8919e-01,1.0736e+00,-1.0736e+00}
> Gradient: {2.2353e-05,-4.2994e-06,8.7267e-06,1.0360e-05,2.0171e-06,-1.6661e-07,2.9719e-05,-1.1970e-05,2.4277e-05,-4.2269e-06,-8.2654e-07,2.0171e-06,8.0134e-06,-2.1133e-05,-2.0554e-06,5.5406e-05,-5.0624e-07,-8.2654e-07,4.8068e-06,-5.1963e-06,-7.6681e-07,4.0836e-05,-2.7531e-07,-5.0624e-07,1.7834e-05,-7.4128e-06,2.0546e-05,8.1711e-06,3.5556e-08,-2.7531e-07,1.1719e-05,4.7756e-05,-1.1239e-05,-8.7788e-06,-5.9526e-07,3.5556e-08,4.1883e-05,-8.7338e-06,-2.1823e-06,9.7755e-06,-1.2487e-06,-5.9526e-07,-7.5788e-07,3.2239e-05,4.2269e-07,9.6162e-06,-1.3734e-06,-1.2487e-06,-1.0372e-05,3.7142e-05,5.9559e-07,1.0310e-05,2.5967e-06,-1.3734e-06,3.6961e-05,2.1061e-06,-1.2783e-05,9.4377e-06,5.7936e-07,2.5967e-06,5.2064e-06,-1.3770e-06,2.9104e-05,5.1220e-06,3.5477e-07,5.7936e-07,-3.4886e-06,1.6810e-05,1.3139e-05,8.4501e-06,3.7241e-06,3.5477e-07,1.3380e-07,1.3315e-07,1.3380e-07,1.2818e-07,1.3404e-07,1.6545e-07,1.3404e-07,1.6026e-07,1.3406e-07,1.2511e-05,1.3406e-07,2.6880e-05,5.0039e-07,-5.0039e-07,-1.0873e-06,1.0873e-06,7.5109e-07,-7.5109e-07,-9.2272e-07,9.2272e-07,-2.6391e-05,2.6391e-05,2.7830e-05,-2.7830e-05}
>>>> Re-trying (3/3).
After: gradient norm = 1.5071821472159295E-4
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6214,-0.6214}
Count Table 3:
---------------
h: {0.6335,-0.6335}
Count Table 4:
---------------
h: {0.8892,-0.8892}
Count Table 5:
---------------
h: {1.0736,-1.0736}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.6253,-1.0117,-0.6844,-0.0740,-0.6867,-0.9087,0.3345,-0.8246,-0.3823,-0.7874,-1.6443,-0.6867,-0.0136,-0.3395,-3.4751,2.5848,-1.1491,-1.6443,-0.4442,-0.2659,-3.2096,2.4804,-1.4484,-1.1491,0.0207,-1.4432,0.1884,0.0129,-1.3672,-1.4484,-0.6848,0.9028,-1.1827,-0.8520,-0.8529,-1.3672,0.7036,-1.1953,-1.0628,-0.5702,-1.0592,-0.8529,-0.7405,-0.5595,-1.0908,0.1244,-0.7111,-1.0592,-0.7121,-0.4969,-1.0414,-0.9081,-0.1672,-0.7111,-0.0253,-1.1777,-0.9111,-0.6956,-1.0599,-0.1672,-0.6435,-0.7739,-0.2130,-0.2988,-1.0017,-1.0599,-0.8780,-0.1939,-0.7279,-0.5880,-0.6014,-1.0017}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0669,0.0666}
Activity(exp=1): {0.0669,0.0641}
Activity(exp=2): {0.0670,0.0827}
Activity(exp=3): {0.0670,0.0801}
Activity(exp=4): {0.0670,-2.2455}
Activity(exp=5): {0.0670,-1.5449}
The Likelihood DID improve.
Suggested variations:
key=12;7;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component3-2-variation4).
>> Starting new optimization: component3-2-variation4. (2021-05-21 19:57:02.607).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[84,85]},{"h":[86,87]},{"h":[88,89]},{"h":[90,91]},{"h":[92,93]},{"h":[94,95]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[72,73],[74,75],[76,77],[78,79],[80,81],[82,83]]}]}
Value and gradient before optimization:
=======================================
value = 3.651134088800768
gradient = {0.0001,0.0000,0.0000,0.0001,0.0000,0.0000,0.0001,0.0000,0.0001,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0002,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0002,0.0000,-0.0000,0.0001,-0.0000,0.0001,-0.0000,0.0000,0.0000,0.0000,0.0001,0.0000,0.0000,0.0000,0.0000,0.0002,-0.0000,0.0000,0.0001,0.0000,0.0000,-0.0000,0.0001,0.0000,0.0001,0.0000,0.0000,0.0000,0.0001,-0.0000,0.0001,0.0000,0.0000,0.0001,0.0000,-0.0000,0.0001,0.0000,0.0000,0.0000,0.0000,0.0001,0.0001,0.0000,0.0000,0.0000,0.0001,0.0001,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0002,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0006,0.0006,-0.0014,0.0014}
gradient norm = 0.002200379925109879
Starting Function Value: 3.651134088800768
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.651128051638596 0.005433146734071 2.469185740184931 0.000275254521372
2 4 3.651126819739094 0.000699748680332 1.000000000000000 0.000259662887964
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-6.2548e-01,-1.0118e+00,-6.8443e-01,-7.4027e-02,-6.8678e-01,-9.0873e-01,3.3430e-01,-8.2453e-01,-3.8253e-01,-7.8736e-01,-1.6443e+00,-6.8678e-01,-1.3710e-02,-3.3943e-01,-3.4751e+00,2.5846e+00,-1.1491e+00,-1.6443e+00,-4.4430e-01,-2.6592e-01,-3.2096e+00,2.4801e+00,-1.4484e+00,-1.1491e+00,2.0396e-02,-1.4432e+00,1.8812e-01,1.3102e-02,-1.3672e+00,-1.4484e+00,-6.8496e-01,9.0276e-01,-1.1827e+00,-8.5215e-01,-8.5288e-01,-1.3672e+00,7.0325e-01,-1.1950e+00,-1.0629e+00,-5.7045e-01,-1.0592e+00,-8.5288e-01,-7.4027e-01,-5.5985e-01,-1.0908e+00,1.2418e-01,-7.1115e-01,-1.0592e+00,-7.1218e-01,-4.9723e-01,-1.0411e+00,-9.0828e-01,-1.6721e-01,-7.1115e-01,-2.5623e-02,-1.1778e+00,-9.1081e-01,-6.9578e-01,-1.0600e+00,-1.6721e-01,-6.4363e-01,-7.7394e-01,-2.1301e-01,-2.9897e-01,-1.0018e+00,-1.0600e+00,-8.7790e-01,-1.9406e-01,-7.2815e-01,-5.8799e-01,-6.0139e-01,-1.0018e+00,6.6901e-02,6.6574e-02,6.6901e-02,6.4088e-02,6.7017e-02,8.2724e-02,6.7017e-02,8.0128e-02,6.7031e-02,-2.2456e+00,6.7031e-02,-1.5452e+00,9.6665e-02,-9.6665e-02,-1.1076e-02,1.1076e-02,6.2140e-01,-6.2140e-01,6.3351e-01,-6.3351e-01,8.9061e-01,-8.9061e-01,1.0772e+00,-1.0772e+00}
> Gradient: {2.2686e-06,-5.6089e-06,-3.7816e-05,-2.8701e-05,3.9714e-06,-7.4135e-06,-1.5795e-05,-2.9477e-05,3.7848e-06,-3.4947e-05,-8.3778e-07,3.9714e-06,1.3998e-05,-1.8117e-05,-2.1494e-06,-6.5788e-05,-4.9728e-07,-8.3778e-07,1.1826e-05,-4.8732e-06,-8.4264e-08,-7.9611e-05,-1.5140e-07,-4.9728e-07,1.8348e-05,-2.2967e-05,1.2267e-05,-8.1204e-05,3.1549e-07,-1.5140e-07,9.6737e-06,-8.1865e-05,-8.5028e-06,8.0657e-06,-1.0781e-06,3.1549e-07,-3.9075e-06,-8.0438e-05,-1.8566e-06,1.5557e-05,-1.6681e-06,-1.0781e-06,-7.7728e-05,8.5789e-06,-1.7652e-06,2.6419e-06,-3.4511e-06,-1.6681e-06,-7.6276e-06,3.7631e-06,-7.7975e-05,2.1481e-05,-9.5816e-06,-3.4511e-06,6.8881e-06,-2.7339e-06,-8.5392e-05,1.7628e-05,-1.9950e-07,-9.5816e-06,-2.1713e-06,-2.0663e-05,-5.7442e-05,7.5302e-06,-3.5469e-07,-1.9950e-07,-3.4552e-05,-1.7359e-05,-7.7493e-06,-1.4830e-05,1.5446e-06,-3.5469e-07,1.3380e-07,1.3315e-07,1.3380e-07,1.2818e-07,1.3403e-07,1.6545e-07,1.3403e-07,1.6026e-07,1.3406e-07,-1.4365e-05,1.3406e-07,-5.8534e-05,-6.5396e-09,6.5396e-09,-1.2411e-08,1.2411e-08,2.3769e-09,-2.3769e-09,2.4853e-09,-2.4853e-09,-5.2650e-06,5.2650e-06,-9.8592e-06,9.8592e-06}
>>>> Re-trying (1/3).
Starting Function Value: 3.651127857561389
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 4 3.651125853890373 0.015062318025474 58.007435454229650 0.000780752881475
2 5 3.651124435671179 0.014789484451095 1.000000000000000 0.000497586711321
3 6 3.651123780842223 0.001549103429768 1.000000000000000 0.000380864236773
4 7 3.651120211451752 0.016387007848763 1.000000000000000 0.000587717164475
5 8 3.651116091740963 0.034821508958839 1.000000000000000 0.000950573059917
6 9 3.651114061735524 0.056636053255864 1.000000000000000 0.001426132998378
7 11 3.651112531074345 0.006462997985640 0.300677687860072 0.001029645095170
8 12 3.651110758596965 0.008460097770236 1.000000000000000 0.000191756616076
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-6.3395e-01,-1.0122e+00,-6.6943e-01,-6.8688e-02,-6.9037e-01,-9.0388e-01,3.2702e-01,-8.0796e-01,-3.9538e-01,-7.6807e-01,-1.6437e+00,-6.9037e-01,-2.4469e-02,-3.2597e-01,-3.4735e+00,2.5921e+00,-1.1488e+00,-1.6437e+00,-4.5326e-01,-2.6205e-01,-3.2095e+00,2.4975e+00,-1.4482e+00,-1.1488e+00,-2.9560e-03,-1.4283e+00,1.6601e-01,5.6596e-02,-1.3674e+00,-1.4482e+00,-6.9439e-01,9.2639e-01,-1.1774e+00,-8.5971e-01,-8.5183e-01,-1.3674e+00,6.7554e-01,-1.1416e+00,-1.0612e+00,-5.8709e-01,-1.0581e+00,-8.5183e-01,-6.9295e-01,-5.8147e-01,-1.0925e+00,1.0991e-01,-7.0921e-01,-1.0581e+00,-7.1320e-01,-5.1551e-01,-9.9142e-01,-9.3031e-01,-1.6468e-01,-7.0921e-01,-4.8106e-02,-1.1803e+00,-8.5611e-01,-7.1512e-01,-1.0600e+00,-1.6468e-01,-6.4795e-01,-7.6601e-01,-1.9172e-01,-3.1125e-01,-1.0016e+00,-1.0600e+00,-8.5739e-01,-1.9676e-01,-7.3605e-01,-5.8357e-01,-6.0316e-01,-1.0016e+00,6.6804e-02,6.6478e-02,6.6804e-02,6.3996e-02,6.6921e-02,8.2605e-02,6.6921e-02,8.0012e-02,6.6935e-02,-2.2474e+00,6.6935e-02,-1.5308e+00,9.6665e-02,-9.6665e-02,-1.1078e-02,1.1078e-02,6.2140e-01,-6.2140e-01,6.3351e-01,-6.3351e-01,8.9158e-01,-8.9158e-01,1.0807e+00,-1.0807e+00}
> Gradient: {-5.3240e-06,3.8837e-06,1.1688e-05,-1.3492e-05,6.1427e-06,-1.0373e-05,4.8545e-06,-9.5098e-06,5.7089e-06,-1.3806e-05,-8.6472e-07,6.1427e-06,4.5985e-06,-2.3111e-05,-2.7785e-06,1.5115e-05,-5.2477e-07,-8.6472e-07,8.3182e-06,-1.2055e-05,1.8798e-07,-3.2490e-06,-2.4296e-07,-5.2477e-07,5.0172e-06,-2.0933e-05,-4.3007e-06,1.2741e-05,1.5263e-07,-2.4296e-07,-1.0488e-05,3.2361e-05,-1.2507e-05,-1.4975e-05,-2.1099e-06,1.5263e-07,-4.9383e-06,-1.3370e-05,-5.4451e-06,1.8310e-05,-1.2298e-08,-2.1099e-06,2.2874e-06,-4.9738e-05,1.7947e-06,3.9019e-05,-9.1621e-07,-1.2298e-08,2.6706e-05,-7.1406e-05,-9.5589e-06,3.1682e-05,1.5927e-05,-9.1621e-07,-4.3501e-05,4.2145e-07,-8.1521e-06,2.7724e-05,1.4903e-08,1.5927e-05,-2.9693e-06,1.7071e-06,-3.2069e-05,2.6674e-05,-8.3221e-07,1.4903e-08,-2.3224e-07,3.1587e-05,-6.4453e-05,2.1909e-05,4.5480e-06,-8.3221e-07,1.3361e-07,1.3296e-07,1.3361e-07,1.2799e-07,1.3384e-07,1.6521e-07,1.3384e-07,1.6002e-07,1.3387e-07,-1.4035e-05,1.3387e-07,6.9614e-06,1.7956e-08,-1.7956e-08,-9.9871e-07,9.9871e-07,9.5970e-08,-9.5970e-08,-1.7614e-08,1.7614e-08,-7.1129e-05,7.1129e-05,-9.7453e-06,9.7453e-06}
>>>> Re-trying (2/3).
Starting Function Value: 3.6511107580874684
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.651110640529222 0.001810311774208 9.440674412996827 0.000313294990964
2 4 3.651110345273100 0.001587658672412 1.000000000000000 0.000296913376166
3 6 3.651109194045400 0.012877288629765 0.368013876592282 0.000701409395118
4 7 3.651108166391914 0.018078938640821 1.000000000000000 0.000169835490955
5 8 3.651108022206480 0.001765975392281 1.000000000000000 0.000131584970876
6 9 3.651107756466117 0.003798492149593 1.000000000000000 0.000222654065871
7 10 3.651107661109642 0.006304554278028 1.000000000000000 0.000339885641470
8 11 3.651107506731369 0.001489002910400 1.000000000000000 0.000136489407007
9 12 3.651107419115852 0.002746925500365 1.000000000000000 0.000124237371145
10 13 3.651107269811038 0.004749604572190 1.000000000000000 0.000205104094510
11 14 3.651106864090179 0.011904329851783 1.000000000000000 0.000369109437447
12 15 3.651106038925091 0.023723650563395 1.000000000000000 0.000545130578181
13 17 3.651105913533776 0.002698005293561 0.077557397813273 0.000546352837781
14 19 3.651105715999025 0.007186747595158 0.070650736453637 0.000665566303023
15 20 3.651104061925838 0.051220194742744 1.000000000000000 0.000297417181998
16 21 3.651103827662521 0.003135158855780 1.000000000000000 0.000138259156594
17 22 3.651103679438970 0.005346337943539 1.000000000000000 0.000126982663721
18 23 3.651102263826123 0.001570341077477 1.000000000000000 0.000164928025932
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-6.2766e-01,-1.0165e+00,-6.6857e-01,-5.7530e-02,-7.0053e-01,-8.8901e-01,3.2297e-01,-7.9660e-01,-3.9902e-01,-7.4436e-01,-1.6423e+00,-7.0053e-01,-3.1384e-02,-2.8609e-01,-3.4689e+00,2.5710e+00,-1.1478e+00,-1.6423e+00,-4.6648e-01,-2.4103e-01,-3.2096e+00,2.5072e+00,-1.4478e+00,-1.1478e+00,-8.6328e-03,-1.3930e+00,1.6468e-01,4.6773e-02,-1.3675e+00,-1.4478e+00,-6.8317e-01,8.9291e-01,-1.1579e+00,-8.4098e-01,-8.4883e-01,-1.3675e+00,6.7693e-01,-1.1134e+00,-1.0552e+00,-6.0794e-01,-1.0571e+00,-8.4883e-01,-6.8119e-01,-5.7789e-01,-1.0855e+00,1.0109e-01,-7.0492e-01,-1.0571e+00,-7.3628e-01,-4.8486e-01,-9.5595e-01,-9.5441e-01,-1.6908e-01,-7.0492e-01,-4.8320e-02,-1.1696e+00,-8.2405e-01,-7.3605e-01,-1.0584e+00,-1.6908e-01,-6.3284e-01,-7.4246e-01,-2.0003e-01,-3.2666e-01,-9.9941e-01,-1.0584e+00,-8.4471e-01,-1.9183e-01,-7.1565e-01,-6.0033e-01,-6.0789e-01,-9.9941e-01,6.6571e-02,6.6246e-02,6.6571e-02,6.3773e-02,6.6687e-02,8.2317e-02,6.6687e-02,7.9733e-02,6.6701e-02,-2.2336e+00,6.6701e-02,-1.5267e+00,9.6678e-02,-9.6678e-02,-1.0904e-02,1.0904e-02,6.2136e-01,-6.2136e-01,6.3350e-01,-6.3350e-01,8.9346e-01,-8.9346e-01,1.0821e+00,-1.0821e+00}
> Gradient: {-3.6660e-06,-7.6164e-06,-1.1002e-05,6.6563e-06,1.2288e-06,-7.3209e-06,-2.2622e-06,-7.6788e-06,-4.2861e-06,-7.9214e-06,-8.0072e-07,1.2288e-06,3.3338e-06,-2.2809e-05,-2.5952e-06,1.5946e-06,-5.3529e-07,-8.0072e-07,5.5761e-06,-1.4256e-05,-6.4931e-08,-1.2200e-05,-3.3119e-07,-5.3529e-07,-3.3401e-06,-1.6623e-05,1.1493e-05,-1.2966e-05,-4.4969e-08,-3.3119e-07,9.5102e-06,-2.4145e-05,-5.7890e-06,6.5637e-07,-1.9997e-06,-4.4969e-08,1.1931e-05,-1.1407e-05,-4.4837e-06,-1.3634e-05,-2.2192e-06,-1.9997e-06,7.7039e-06,-2.1395e-05,-5.5836e-06,4.6507e-06,-4.9683e-06,-2.2192e-06,-3.5848e-06,-1.8046e-06,-8.6649e-07,-6.3019e-06,-4.2857e-06,-4.9683e-06,-8.9318e-06,3.9335e-06,-4.2729e-06,-6.7415e-06,-1.5134e-06,-4.2857e-06,5.4385e-06,9.3717e-06,-2.8220e-05,-5.1375e-06,-1.6601e-06,-1.5134e-06,1.6710e-06,4.6837e-06,-1.6640e-05,-1.0016e-05,2.4122e-07,-1.6601e-06,1.3314e-07,1.3249e-07,1.3314e-07,1.2755e-07,1.3337e-07,1.6463e-07,1.3337e-07,1.5947e-07,1.3340e-07,-1.1274e-06,1.3340e-07,-2.0194e-05,6.0115e-06,-6.0115e-06,8.1365e-05,-8.1365e-05,-1.7968e-05,1.7968e-05,-7.1591e-06,7.1591e-06,1.5659e-05,-1.5659e-05,5.8768e-05,-5.8768e-05}
>>>> Re-trying (3/3).
After: gradient norm = 1.650683912392904E-4
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0109,0.0109}
Count Table 2:
---------------
h: {0.6214,-0.6214}
Count Table 3:
---------------
h: {0.6335,-0.6335}
Count Table 4:
---------------
h: {0.8935,-0.8935}
Count Table 5:
---------------
h: {1.0821,-1.0821}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.6277,-1.0165,-0.6686,-0.0575,-0.7005,-0.8890,0.3230,-0.7966,-0.3990,-0.7444,-1.6423,-0.7005,-0.0314,-0.2861,-3.4689,2.5710,-1.1478,-1.6423,-0.4665,-0.2410,-3.2096,2.5072,-1.4478,-1.1478,-0.0086,-1.3930,0.1647,0.0468,-1.3675,-1.4478,-0.6832,0.8929,-1.1579,-0.8410,-0.8488,-1.3675,0.6769,-1.1134,-1.0552,-0.6079,-1.0571,-0.8488,-0.6812,-0.5779,-1.0855,0.1011,-0.7049,-1.0571,-0.7363,-0.4849,-0.9560,-0.9544,-0.1691,-0.7049,-0.0483,-1.1696,-0.8241,-0.7361,-1.0584,-0.1691,-0.6328,-0.7425,-0.2000,-0.3267,-0.9994,-1.0584,-0.8447,-0.1918,-0.7157,-0.6003,-0.6079,-0.9994}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0666,0.0662}
Activity(exp=1): {0.0666,0.0638}
Activity(exp=2): {0.0667,0.0823}
Activity(exp=3): {0.0667,0.0797}
Activity(exp=4): {0.0667,-2.2336}
Activity(exp=5): {0.0667,-1.5267}
The Likelihood DID improve.
Suggested variations:
key=12;8;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component3-2-variation5).
>> Starting new optimization: component3-2-variation5. (2021-05-21 19:59:43.437).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[84,85]},{"h":[86,87]},{"h":[88,89]},{"h":[90,91]},{"h":[92,93]},{"h":[94,95]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[72,73],[74,75],[76,77],[78,79],[80,81],[82,83]]}]}
Value and gradient before optimization:
=======================================
value = 3.65094200079625
gradient = {0.0001,0.0001,0.0001,0.0001,0.0000,0.0000,0.0001,0.0001,0.0001,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0002,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0002,0.0000,-0.0000,0.0001,-0.0001,0.0001,0.0001,0.0000,0.0000,0.0001,0.0001,0.0000,0.0001,0.0000,0.0000,0.0001,0.0001,0.0000,0.0001,0.0000,0.0000,0.0001,0.0001,-0.0000,0.0001,0.0000,0.0000,0.0001,0.0001,0.0000,0.0001,0.0000,0.0000,0.0001,0.0001,0.0000,0.0001,0.0000,0.0000,0.0000,0.0001,0.0001,0.0001,0.0000,0.0000,0.0001,0.0001,0.0000,0.0001,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0002,0.0000,-0.0000,0.0001,-0.0001,-0.0000,0.0000,-0.0000,0.0000,-0.0010,0.0010,-0.0017,0.0017}
gradient norm = 0.0028855431200560068
Starting Function Value: 3.65094200079625
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.650931808521735 0.006982966842494 2.419983535840756 0.000411823349261
Gradient = {-2.1436e-05,-6.4698e-06,-6.6609e-05,-3.6206e-05,1.6747e-06,5.7289e-07,-1.3915e-05,-1.5334e-05,-4.0516e-05,-5.9582e-05,-8.0143e-07,1.6747e-06,1.6373e-05,-1.9039e-05,-2.7977e-06,-1.2182e-04,-4.7498e-07,-8.0143e-07,1.0818e-05,-2.2425e-05,7.6090e-07,-1.1692e-04,-3.2610e-07,-4.7498e-07,-1.1768e-05,-1.0731e-04,-2.1407e-05,1.1986e-05,2.5914e-07,-3.2610e-07,9.6492e-06,-1.5830e-04,-1.3910e-06,2.3183e-05,-1.9647e-06,2.5914e-07,-1.4115e-04,1.0297e-05,-5.3910e-06,1.1295e-05,-1.6482e-06,-1.9647e-06,2.9083e-05,-4.8292e-05,-9.7755e-05,-3.6630e-06,-6.2903e-06,-1.6482e-06,-2.4619e-06,-3.1261e-05,-7.6490e-05,3.9871e-06,-1.6049e-05,-6.2903e-06,-4.4458e-05,-1.0564e-05,-6.3691e-05,7.3732e-06,-1.1766e-06,-1.6049e-05,-6.5798e-05,-1.4210e-05,-4.2631e-05,-2.9762e-06,-1.6826e-06,-1.1766e-06,1.2147e-05,-3.3841e-05,-1.1537e-04,1.1258e-05,-9.8677e-07,-1.6826e-06,1.3314e-07,1.3249e-07,1.3314e-07,1.2754e-07,1.3337e-07,1.6463e-07,1.3337e-07,1.5947e-07,1.3340e-07,-6.8428e-05,1.3340e-07,-5.9647e-05,-5.9477e-07,5.9477e-07,-1.0795e-05,1.0795e-05,1.9559e-06,-1.9559e-06,2.0964e-07,-2.0964e-07,1.4924e-05,-1.4924e-05,-7.4417e-05,7.4417e-05}
pCurr = {4.9705e-05,1.3287e-05,1.5943e-04,8.3873e-05,-4.7827e-06,-2.0708e-06,2.7538e-05,3.4574e-05,9.5145e-05,1.4500e-04,1.9674e-06,-4.7827e-06,-4.2120e-05,4.5539e-05,6.8564e-06,2.8625e-04,1.1665e-06,1.9674e-06,-2.7927e-05,5.4410e-05,-2.0076e-06,2.7324e-04,7.8093e-07,1.1665e-06,2.4290e-05,2.6351e-04,4.6423e-05,-3.4587e-05,-7.5725e-07,7.8093e-07,-2.6206e-05,3.8032e-04,1.3516e-06,-5.9640e-05,4.5978e-06,-7.5725e-07,3.3961e-04,-2.9329e-05,1.2229e-05,-3.1264e-05,3.8199e-06,4.5978e-06,-7.5620e-05,1.1333e-04,2.3943e-04,3.6997e-06,1.4998e-05,3.8199e-06,3.0862e-06,7.0485e-05,1.8525e-04,-1.2290e-05,3.8137e-05,1.4998e-05,1.0337e-04,2.3313e-05,1.5318e-04,-2.1026e-05,2.6836e-06,3.8137e-05,1.5954e-04,3.1316e-05,9.7954e-05,3.9856e-06,3.9592e-06,2.6836e-06,-3.2853e-05,7.7868e-05,2.7904e-04,-3.0624e-05,2.0452e-06,3.9592e-06,-3.3013e-07,-3.2851e-07,-3.3013e-07,-3.1625e-07,-3.3070e-07,-4.0821e-07,-3.3070e-07,-3.9540e-07,-3.3077e-07,1.6558e-04,-3.3077e-07,1.3287e-04,1.2614e-06,-1.2614e-06,2.4508e-05,-2.4508e-05,-4.2516e-06,4.2516e-06,-1.6311e-07,1.6311e-07,8.0227e-06,-8.0227e-06,2.7660e-04,-2.7660e-04}
grad*pCur = -4.1380061184567553E-7
parameters = {-6.2778e-01,-1.0166e+00,-6.6869e-01,-5.7745e-02,-7.0056e-01,-8.8904e-01,3.2264e-01,-7.9673e-01,-3.9918e-01,-7.4434e-01,-1.6423e+00,-7.0056e-01,-3.1500e-02,-2.8612e-01,-3.4689e+00,2.5705e+00,-1.1478e+00,-1.6423e+00,-4.6656e-01,-2.4102e-01,-3.2096e+00,2.5067e+00,-1.4478e+00,-1.1478e+00,-8.8531e-03,-1.3929e+00,1.6439e-01,4.6492e-02,-1.3675e+00,-1.4478e+00,-6.8331e-01,8.9268e-01,-1.1580e+00,-8.4114e-01,-8.4884e-01,-1.3675e+00,6.7675e-01,-1.1136e+00,-1.0553e+00,-6.0813e-01,-1.0571e+00,-8.4884e-01,-6.8144e-01,-5.7811e-01,-1.0854e+00,1.0083e-01,-7.0493e-01,-1.0571e+00,-7.3642e-01,-4.8516e-01,-9.5597e-01,-9.5454e-01,-1.6912e-01,-7.0493e-01,-4.8572e-02,-1.1697e+00,-8.2412e-01,-7.3621e-01,-1.0584e+00,-1.6912e-01,-6.3285e-01,-7.4262e-01,-2.0033e-01,-3.2682e-01,-9.9941e-01,-1.0584e+00,-8.4488e-01,-1.9206e-01,-7.1572e-01,-6.0050e-01,-6.0790e-01,-9.9941e-01,6.6571e-02,6.6246e-02,6.6571e-02,6.3772e-02,6.6687e-02,8.2316e-02,6.6687e-02,7.9733e-02,6.6701e-02,-2.2337e+00,6.6701e-02,-1.5272e+00,9.6664e-02,-9.6664e-02,-1.1099e-02,1.1099e-02,6.2140e-01,-6.2140e-01,6.3352e-01,-6.3352e-01,8.9591e-01,-8.9591e-01,1.0862e+00,-1.0862e+00}
|grad|/|x| = 4.1468463506790366E-5
>>>> Exception caugth. Parameters reverted.
> Parameter: {-6.2778e-01,-1.0167e+00,-6.6870e-01,-5.7752e-02,-7.0056e-01,-8.8904e-01,3.2264e-01,-7.9673e-01,-3.9919e-01,-7.4435e-01,-1.6423e+00,-7.0056e-01,-3.1496e-02,-2.8612e-01,-3.4689e+00,2.5704e+00,-1.1478e+00,-1.6423e+00,-4.6656e-01,-2.4103e-01,-3.2096e+00,2.5067e+00,-1.4478e+00,-1.1478e+00,-8.8551e-03,-1.3929e+00,1.6439e-01,4.6495e-02,-1.3675e+00,-1.4478e+00,-6.8331e-01,8.9265e-01,-1.1580e+00,-8.4114e-01,-8.4884e-01,-1.3675e+00,6.7672e-01,-1.1136e+00,-1.0553e+00,-6.0813e-01,-1.0571e+00,-8.4884e-01,-6.8143e-01,-5.7812e-01,-1.0854e+00,1.0083e-01,-7.0494e-01,-1.0571e+00,-7.3642e-01,-4.8516e-01,-9.5599e-01,-9.5454e-01,-1.6912e-01,-7.0494e-01,-4.8581e-02,-1.1697e+00,-8.2413e-01,-7.3621e-01,-1.0584e+00,-1.6912e-01,-6.3286e-01,-7.4262e-01,-2.0034e-01,-3.2682e-01,-9.9941e-01,-1.0584e+00,-8.4487e-01,-1.9206e-01,-7.1574e-01,-6.0049e-01,-6.0790e-01,-9.9941e-01,6.6571e-02,6.6246e-02,6.6571e-02,6.3772e-02,6.6687e-02,8.2316e-02,6.6687e-02,7.9733e-02,6.6701e-02,-2.2337e+00,6.6701e-02,-1.5273e+00,9.6664e-02,-9.6664e-02,-1.1101e-02,1.1101e-02,6.2140e-01,-6.2140e-01,6.3352e-01,-6.3352e-01,8.9591e-01,-8.9591e-01,1.0862e+00,-1.0862e+00}
> Gradient: {-2.1436e-05,-6.4698e-06,-6.6609e-05,-3.6206e-05,1.6747e-06,5.7289e-07,-1.3915e-05,-1.5334e-05,-4.0516e-05,-5.9582e-05,-8.0143e-07,1.6747e-06,1.6373e-05,-1.9039e-05,-2.7977e-06,-1.2182e-04,-4.7498e-07,-8.0143e-07,1.0818e-05,-2.2425e-05,7.6090e-07,-1.1692e-04,-3.2610e-07,-4.7498e-07,-1.1768e-05,-1.0731e-04,-2.1407e-05,1.1986e-05,2.5914e-07,-3.2610e-07,9.6492e-06,-1.5830e-04,-1.3910e-06,2.3183e-05,-1.9647e-06,2.5914e-07,-1.4115e-04,1.0297e-05,-5.3910e-06,1.1295e-05,-1.6482e-06,-1.9647e-06,2.9083e-05,-4.8292e-05,-9.7755e-05,-3.6630e-06,-6.2903e-06,-1.6482e-06,-2.4619e-06,-3.1261e-05,-7.6490e-05,3.9871e-06,-1.6049e-05,-6.2903e-06,-4.4458e-05,-1.0564e-05,-6.3691e-05,7.3732e-06,-1.1766e-06,-1.6049e-05,-6.5798e-05,-1.4210e-05,-4.2631e-05,-2.9762e-06,-1.6826e-06,-1.1766e-06,1.2147e-05,-3.3841e-05,-1.1537e-04,1.1258e-05,-9.8677e-07,-1.6826e-06,1.3314e-07,1.3249e-07,1.3314e-07,1.2754e-07,1.3337e-07,1.6463e-07,1.3337e-07,1.5947e-07,1.3340e-07,-6.8428e-05,1.3340e-07,-5.9647e-05,-5.9477e-07,5.9477e-07,-1.0795e-05,1.0795e-05,1.9559e-06,-1.9559e-06,2.0964e-07,-2.0964e-07,1.4924e-05,-1.4924e-05,-7.4417e-05,7.4417e-05}
>>>> Re-trying (1/3).
Starting Function Value: 3.650931915236339
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.650931248659294 0.019939140725198 48.416671658248340 0.001624817903168
2 4 3.650927830734930 0.004254261077220 1.000000000000000 0.000331445748620
3 5 3.650927656663220 0.000825091651061 1.000000000000000 0.000290148524272
4 6 3.650925772651854 0.008688038247993 1.000000000000000 0.000475267832133
5 7 3.650922081787540 0.023088325362521 1.000000000000000 0.000945008758252
6 8 3.650915250955934 0.061297040948639 1.000000000000000 0.001451431394949
7 10 3.650912440106119 0.028338361524822 0.290770951439609 0.001419669197237
8 11 3.650908476735867 0.043545771160871 1.000000000000000 0.000807236647281
9 13 3.650908250805732 0.001010433450695 0.100637725010877 0.000730176570185
10 14 3.650906920886974 0.008808371816849 1.000000000000000 0.000183574791704
11 15 3.650906820316564 0.000924573373163 1.000000000000000 0.000198862433652
12 16 3.650905177141619 0.017766515876130 1.000000000000000 0.000464878382783
13 17 3.650903883726501 0.026090196468287 1.000000000000000 0.000902159930450
14 18 3.650902433949231 0.021524375923519 1.000000000000000 0.000528239452105
15 19 3.650901601799315 0.021293103128030 1.000000000000000 0.000134719127850
16 20 3.650901497697314 0.002930207674430 1.000000000000000 0.000144095922040
17 21 3.650901322426090 0.004643035601564 1.000000000000000 0.000187287242449
18 22 3.650900916968926 0.008622738565195 1.000000000000000 0.000299246048972
19 23 3.650900105086492 0.019058490478400 1.000000000000000 0.000266664886076
20 25 3.650899888042604 0.007798278520172 0.233159050776963 0.000466675337338
21 26 3.650899487164674 0.009884461279780 1.000000000000000 0.000207338391267
22 27 3.650899365221450 0.003727164664491 1.000000000000000 0.000103951888094
23 28 3.650899317615196 0.001250537897312 1.000000000000000 0.000102362794581
24 29 3.650899225662153 0.001901806273700 1.000000000000000 0.000139093723323
25 30 3.650898798483381 0.010283211383942 1.000000000000000 0.000257507718687
26 31 3.650898097486437 0.022407496300425 1.000000000000000 0.000342983722690
27 32 3.650897154203610 0.037629217633259 1.000000000000000 0.000327280445840
28 33 3.650896897506478 0.043873313037899 1.000000000000000 0.000746232864902
29 34 3.650896070603502 0.008158088171217 1.000000000000000 0.000222372977289
30 35 3.650895864549190 0.006454932195989 1.000000000000000 0.000152541383220
31 36 3.650895375401421 0.014073422423350 1.000000000000000 0.000230963551729
32 37 3.650894647950354 0.030674597403444 1.000000000000000 0.000324096575453
33 38 3.650893595327623 0.053407036864910 1.000000000000000 0.000315487721791
34 39 3.650891861300891 0.078926387595881 1.000000000000000 0.000253674074196
35 40 3.650890688507531 0.072108433318802 1.000000000000000 0.000191318759790
36 41 3.650890518379205 0.009658228575142 1.000000000000000 0.000150807164030
37 42 3.650890517854102 0.003965041824300 1.000000000000000 0.000073727996629
38 43 3.650890434781262 0.003124890994184 1.000000000000000 0.000050341610615
39 44 3.650890412878745 0.002487287167484 1.000000000000000 0.000061761073410
40 45 3.650890356960147 0.004743804166490 1.000000000000000 0.000090299480830
41 46 3.650890250087196 0.009468072876947 1.000000000000000 0.000123696078259
Gradient = {-4.6617e-06,1.5690e-06,4.2180e-06,3.6980e-07,-3.2665e-06,-5.3835e-06,-9.7829e-06,4.0877e-06,4.4756e-06,-2.0421e-06,-6.2674e-07,-3.2665e-06,-5.2450e-07,-2.0794e-06,-2.0445e-06,-1.6189e-06,-3.5017e-07,-6.2674e-07,5.9803e-06,-1.3620e-06,1.7434e-06,-1.3003e-05,-2.5323e-07,-3.5017e-07,-5.9138e-06,1.9470e-06,5.7407e-06,-8.3152e-06,-4.4974e-07,-2.5323e-07,-3.3455e-06,-3.1109e-06,4.0604e-06,-8.4228e-08,-4.3143e-06,-4.4974e-07,-3.1567e-06,-3.0990e-06,8.3955e-06,-4.2929e-06,-7.7691e-07,-4.3143e-06,3.5598e-06,-2.2465e-06,-7.2004e-07,-9.6850e-06,2.6245e-06,-7.7691e-07,1.1726e-06,-1.8371e-05,-7.4232e-07,3.6602e-06,4.4117e-06,2.6245e-06,-4.0233e-06,-2.9987e-06,-3.1594e-06,3.0627e-07,-1.7808e-06,4.4117e-06,-2.4467e-06,7.8772e-06,-1.1904e-05,1.7886e-06,-6.8943e-07,-1.7808e-06,-1.9587e-06,6.7866e-06,-1.0452e-05,-1.0009e-06,1.5908e-07,-6.8943e-07,1.3013e-07,1.2950e-07,1.3013e-07,1.2466e-07,1.3036e-07,1.6091e-07,1.3036e-07,1.5586e-07,1.3039e-07,-6.9464e-06,1.3039e-07,1.8153e-07,7.1167e-06,-7.1167e-06,5.0482e-05,-5.0482e-05,-1.9884e-05,1.9884e-05,3.0011e-05,-3.0011e-05,-3.7994e-05,3.7994e-05,-3.8008e-05,3.8008e-05}
pCurr = {1.0713e-03,5.8493e-04,-2.0871e-04,-7.6847e-04,1.3723e-03,1.2023e-03,5.2966e-04,2.2211e-03,-4.8196e-04,-8.0512e-04,4.1773e-04,1.3723e-03,-2.0185e-03,6.9967e-03,1.4122e-03,-3.7492e-03,2.4873e-04,4.1773e-04,-4.3208e-03,7.5318e-03,-8.4818e-04,5.2996e-04,1.6607e-04,2.4873e-04,2.0429e-03,2.2858e-04,-1.3268e-03,2.0068e-03,1.9003e-04,1.6607e-04,1.4074e-03,-1.4557e-03,-8.1082e-05,5.6762e-04,2.6794e-03,1.9003e-04,-1.1434e-03,-8.3072e-04,8.4637e-04,5.1009e-04,1.2458e-03,2.6794e-03,-2.0127e-03,-4.0464e-04,1.0613e-03,2.9471e-03,4.7069e-04,1.2458e-03,3.1590e-04,8.5269e-04,2.2942e-03,-4.0512e-04,-2.2079e-04,4.7069e-04,6.8737e-04,1.3775e-03,1.3802e-03,-1.2150e-03,1.2983e-03,-2.2079e-04,1.4874e-03,-2.0347e-03,4.3197e-04,1.1073e-03,9.6335e-04,1.2983e-03,8.2030e-04,1.2080e-03,-6.5468e-04,4.1946e-04,4.9719e-04,9.6335e-04,-7.8655e-05,-7.8270e-05,-7.8655e-05,-7.5348e-05,-7.8792e-05,-9.7258e-05,-7.8792e-05,-9.4205e-05,-7.8808e-05,2.7490e-03,-7.8808e-05,2.6889e-04,-2.9105e-05,2.9105e-05,2.7119e-05,-2.7119e-05,-2.3385e-05,2.3385e-05,-2.4517e-05,2.4517e-05,2.0221e-04,-2.0221e-04,6.5082e-05,-6.5082e-05}
grad*pCur = -2.4200015604122245E-7
parameters = {-5.9848e-01,-9.8140e-01,-6.2310e-01,-3.7502e-02,-7.0757e-01,-9.1137e-01,3.0021e-01,-7.8377e-01,-3.9564e-01,-6.3879e-01,-1.6339e+00,-7.0757e-01,-1.5556e-01,-8.5371e-02,-3.4396e+00,2.5529e+00,-1.1425e+00,-1.6339e+00,-5.7548e-01,1.6995e-02,-3.2226e+00,2.4640e+00,-1.4444e+00,-1.1425e+00,-2.8631e-02,-1.2080e+00,1.4673e-01,-2.8566e-03,-1.3669e+00,-1.4444e+00,-6.7012e-01,8.9713e-01,-1.1035e+00,-8.6139e-01,-7.9922e-01,-1.3669e+00,6.4470e-01,-1.1451e+00,-9.2620e-01,-6.5864e-01,-1.0196e+00,-7.9922e-01,-7.2252e-01,-5.7537e-01,-9.9903e-01,7.3953e-02,-6.6152e-01,-1.0196e+00,-7.2670e-01,-5.1640e-01,-8.8861e-01,-9.5942e-01,-1.5141e-01,-6.6152e-01,-5.8493e-02,-1.1546e+00,-7.7773e-01,-7.2801e-01,-1.0338e+00,-1.5141e-01,-5.8444e-01,-7.0650e-01,-2.0474e-01,-3.5431e-01,-9.7566e-01,-1.0338e+00,-8.7309e-01,-1.6766e-01,-6.3488e-01,-6.1331e-01,-5.9482e-01,-9.7566e-01,6.5066e-02,6.4748e-02,6.5066e-02,6.2331e-02,6.5179e-02,8.0456e-02,6.5179e-02,7.7930e-02,6.5193e-02,-2.1773e+00,6.5193e-02,-1.4871e+00,9.6681e-02,-9.6681e-02,-1.0969e-02,1.0969e-02,6.2135e-01,-6.2135e-01,6.3359e-01,-6.3359e-01,9.0370e-01,-9.0370e-01,1.0952e+00,-1.0952e+00}
|grad|/|x| = 1.2750829342885833E-5
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.9849e-01,-9.8140e-01,-6.2309e-01,-3.7494e-02,-7.0758e-01,-9.1138e-01,3.0021e-01,-7.8379e-01,-3.9564e-01,-6.3878e-01,-1.6339e+00,-7.0758e-01,-1.5554e-01,-8.5446e-02,-3.4396e+00,2.5529e+00,-1.1425e+00,-1.6339e+00,-5.7543e-01,1.6914e-02,-3.2226e+00,2.4639e+00,-1.4444e+00,-1.1425e+00,-2.8653e-02,-1.2080e+00,1.4674e-01,-2.8779e-03,-1.3669e+00,-1.4444e+00,-6.7014e-01,8.9714e-01,-1.1035e+00,-8.6140e-01,-7.9925e-01,-1.3669e+00,6.4471e-01,-1.1451e+00,-9.2621e-01,-6.5865e-01,-1.0196e+00,-7.9925e-01,-7.2250e-01,-5.7536e-01,-9.9904e-01,7.3922e-02,-6.6152e-01,-1.0196e+00,-7.2670e-01,-5.1640e-01,-8.8863e-01,-9.5942e-01,-1.5141e-01,-6.6152e-01,-5.8501e-02,-1.1547e+00,-7.7774e-01,-7.2800e-01,-1.0338e+00,-1.5141e-01,-5.8445e-01,-7.0648e-01,-2.0474e-01,-3.5432e-01,-9.7567e-01,-1.0338e+00,-8.7310e-01,-1.6768e-01,-6.3487e-01,-6.1331e-01,-5.9482e-01,-9.7567e-01,6.5067e-02,6.4749e-02,6.5067e-02,6.2331e-02,6.5180e-02,8.0457e-02,6.5180e-02,7.7931e-02,6.5194e-02,-2.1773e+00,6.5194e-02,-1.4871e+00,9.6681e-02,-9.6681e-02,-1.0970e-02,1.0970e-02,6.2135e-01,-6.2135e-01,6.3359e-01,-6.3359e-01,9.0370e-01,-9.0370e-01,1.0952e+00,-1.0952e+00}
> Gradient: {-4.6617e-06,1.5690e-06,4.2180e-06,3.6980e-07,-3.2665e-06,-5.3835e-06,-9.7829e-06,4.0877e-06,4.4756e-06,-2.0421e-06,-6.2674e-07,-3.2665e-06,-5.2450e-07,-2.0794e-06,-2.0445e-06,-1.6189e-06,-3.5017e-07,-6.2674e-07,5.9803e-06,-1.3620e-06,1.7434e-06,-1.3003e-05,-2.5323e-07,-3.5017e-07,-5.9138e-06,1.9470e-06,5.7407e-06,-8.3152e-06,-4.4974e-07,-2.5323e-07,-3.3455e-06,-3.1109e-06,4.0604e-06,-8.4228e-08,-4.3143e-06,-4.4974e-07,-3.1567e-06,-3.0990e-06,8.3955e-06,-4.2929e-06,-7.7691e-07,-4.3143e-06,3.5598e-06,-2.2465e-06,-7.2004e-07,-9.6850e-06,2.6245e-06,-7.7691e-07,1.1726e-06,-1.8371e-05,-7.4232e-07,3.6602e-06,4.4117e-06,2.6245e-06,-4.0233e-06,-2.9987e-06,-3.1594e-06,3.0627e-07,-1.7808e-06,4.4117e-06,-2.4467e-06,7.8772e-06,-1.1904e-05,1.7886e-06,-6.8943e-07,-1.7808e-06,-1.9587e-06,6.7866e-06,-1.0452e-05,-1.0009e-06,1.5908e-07,-6.8943e-07,1.3013e-07,1.2950e-07,1.3013e-07,1.2466e-07,1.3036e-07,1.6091e-07,1.3036e-07,1.5586e-07,1.3039e-07,-6.9464e-06,1.3039e-07,1.8153e-07,7.1167e-06,-7.1167e-06,5.0482e-05,-5.0482e-05,-1.9884e-05,1.9884e-05,3.0011e-05,-3.0011e-05,-3.7994e-05,3.7994e-05,-3.8008e-05,3.8008e-05}
>>>> Re-trying (2/3).
Starting Function Value: 3.6508902500871963
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.650890228745986 0.000340086915932 2.749375087062767 0.000060008491267
2 4 3.650890220701594 0.000154683377178 1.000000000000000 0.000057143458445
3 6 3.650890205832007 0.000317145826700 0.080649819898896 0.000054853713712
4 7 3.650890137145868 0.003237500611289 1.000000000000000 0.000069916388788
5 8 3.650890108821856 0.000839291592326 1.000000000000000 0.000062115913328
6 9 3.650890050278781 0.002484145727891 1.000000000000000 0.000127774340158
7 10 3.650889957733305 0.005504850226675 1.000000000000000 0.000174359992600
8 11 3.650889896056198 0.005794489031710 1.000000000000000 0.000148740562430
9 12 3.650889788284992 0.004254454949237 1.000000000000000 0.000082154314736
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.9665e-01,-9.8264e-01,-6.2592e-01,-3.9952e-02,-7.0529e-01,-9.0773e-01,3.0321e-01,-7.8612e-01,-3.9864e-01,-6.3792e-01,-1.6334e+00,-7.0529e-01,-1.5495e-01,-8.3260e-02,-3.4382e+00,2.5493e+00,-1.1423e+00,-1.6334e+00,-5.7927e-01,1.8486e-02,-3.2237e+00,2.4683e+00,-1.4442e+00,-1.1423e+00,-2.6220e-02,-1.2091e+00,1.4231e-01,1.0159e-03,-1.3666e+00,-1.4442e+00,-6.6819e-01,8.9530e-01,-1.1058e+00,-8.6135e-01,-7.9614e-01,-1.3666e+00,6.4246e-01,-1.1425e+00,-9.3143e-01,-6.5621e-01,-1.0190e+00,-7.9614e-01,-7.2476e-01,-5.7748e-01,-9.9815e-01,7.9711e-02,-6.6312e-01,-1.0190e+00,-7.2736e-01,-5.0870e-01,-8.8764e-01,-9.6205e-01,-1.5390e-01,-6.6312e-01,-5.9772e-02,-1.1528e+00,-7.7510e-01,-7.2865e-01,-1.0325e+00,-1.5390e-01,-5.8325e-01,-7.1097e-01,-2.0079e-01,-3.5552e-01,-9.7513e-01,-1.0325e+00,-8.7152e-01,-1.7173e-01,-6.3209e-01,-6.1287e-01,-5.9485e-01,-9.7513e-01,6.4977e-02,6.4659e-02,6.4977e-02,6.2245e-02,6.5090e-02,8.0345e-02,6.5090e-02,7.7823e-02,6.5104e-02,-2.1743e+00,6.5104e-02,-1.4892e+00,9.6686e-02,-9.6686e-02,-1.1103e-02,1.1103e-02,6.2132e-01,-6.2132e-01,6.3353e-01,-6.3353e-01,9.0410e-01,-9.0410e-01,1.0952e+00,-1.0952e+00}
> Gradient: {1.1965e-06,2.2862e-06,-4.1319e-06,-2.4708e-06,-2.6785e-06,-4.0086e-06,4.1241e-06,-9.5380e-07,-6.4534e-06,-3.2209e-06,-6.2465e-07,-2.6785e-06,-8.1506e-07,-2.8284e-06,-2.1075e-06,-3.1662e-06,-3.5439e-07,-6.2465e-07,4.8038e-06,-3.0084e-06,1.5865e-06,-1.2654e-05,-2.6971e-07,-3.5439e-07,-2.3294e-07,9.5369e-07,-8.2178e-06,-1.6320e-06,-4.9754e-07,-2.6971e-07,-1.5305e-06,-4.4249e-06,2.5127e-06,-2.2491e-06,-3.7068e-06,-4.9754e-07,-8.7512e-06,-1.9557e-06,6.4754e-06,-1.2147e-06,-7.4326e-07,-3.7068e-06,-3.5665e-06,2.5466e-06,-3.7566e-06,-5.0107e-06,6.3417e-07,-7.4326e-07,-3.6425e-06,3.7840e-06,-2.9557e-06,-2.7018e-06,-5.0144e-06,6.3417e-07,2.9307e-06,-1.2587e-06,-3.8897e-06,-1.0087e-06,-1.6555e-06,-5.0144e-06,-1.4186e-06,-6.4880e-06,3.2737e-06,-2.6358e-06,-8.8284e-07,-1.6555e-06,-2.9751e-06,-1.4211e-05,1.0056e-05,-1.0887e-06,-7.0544e-07,-8.8284e-07,1.2995e-07,1.2932e-07,1.2995e-07,1.2449e-07,1.3018e-07,1.6069e-07,1.3018e-07,1.5565e-07,1.3021e-07,-3.1267e-06,1.3021e-07,-6.2909e-06,9.5407e-06,-9.5407e-06,-1.2784e-05,1.2784e-05,-3.6780e-05,3.6780e-05,4.6203e-06,-4.6203e-06,2.9206e-05,-2.9206e-05,-1.6777e-05,1.6777e-05}
>>>> Re-trying (3/3).
After: gradient norm = 8.212211484841996E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6213,-0.6213}
Count Table 3:
---------------
h: {0.6335,-0.6335}
Count Table 4:
---------------
h: {0.9041,-0.9041}
Count Table 5:
---------------
h: {1.0952,-1.0952}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.5967,-0.9826,-0.6259,-0.0400,-0.7053,-0.9077,0.3032,-0.7861,-0.3986,-0.6379,-1.6334,-0.7053,-0.1549,-0.0833,-3.4382,2.5493,-1.1423,-1.6334,-0.5793,0.0185,-3.2237,2.4683,-1.4442,-1.1423,-0.0262,-1.2091,0.1423,0.0010,-1.3666,-1.4442,-0.6682,0.8953,-1.1058,-0.8614,-0.7961,-1.3666,0.6425,-1.1425,-0.9314,-0.6562,-1.0190,-0.7961,-0.7248,-0.5775,-0.9982,0.0797,-0.6631,-1.0190,-0.7274,-0.5087,-0.8876,-0.9621,-0.1539,-0.6631,-0.0598,-1.1528,-0.7751,-0.7286,-1.0325,-0.1539,-0.5833,-0.7110,-0.2008,-0.3555,-0.9751,-1.0325,-0.8715,-0.1717,-0.6321,-0.6129,-0.5948,-0.9751}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0650,0.0647}
Activity(exp=1): {0.0650,0.0622}
Activity(exp=2): {0.0651,0.0803}
Activity(exp=3): {0.0651,0.0778}
Activity(exp=4): {0.0651,-2.1743}
Activity(exp=5): {0.0651,-1.4892}
The Likelihood DID improve.
Suggested variations:
key=12;9;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component3-2-variation6).
>> Starting new optimization: component3-2-variation6. (2021-05-21 20:04:20.894).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[84,85]},{"h":[86,87]},{"h":[88,89]},{"h":[90,91]},{"h":[92,93]},{"h":[94,95]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[72,73],[74,75],[76,77],[78,79],[80,81],[82,83]]}]}
Value and gradient before optimization:
=======================================
value = 3.6508784083525825
gradient = {0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0002,0.0002,-0.0003,0.0003}
gradient norm = 5.486836987608372E-4
Starting Function Value: 3.6508784083525825
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.650877924410059 0.001304569756406 2.377635346834594 0.000078220034700
2 4 3.650877910496654 0.000190175910840 1.000000000000000 0.000072422878149
3 5 3.650877744596529 0.002949857048217 1.000000000000000 0.000063743872033
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.9668e-01,-9.8254e-01,-6.2564e-01,-3.9547e-02,-7.0516e-01,-9.0755e-01,3.0326e-01,-7.8584e-01,-3.9823e-01,-6.3776e-01,-1.6334e+00,-7.0516e-01,-1.5497e-01,-8.3230e-02,-3.4381e+00,2.5503e+00,-1.1423e+00,-1.6334e+00,-5.7953e-01,1.9091e-02,-3.2238e+00,2.4690e+00,-1.4442e+00,-1.1423e+00,-2.6110e-02,-1.2088e+00,1.4284e-01,1.1111e-03,-1.3665e+00,-1.4442e+00,-6.6788e-01,8.9598e-01,-1.1060e+00,-8.6128e-01,-7.9597e-01,-1.3665e+00,6.4309e-01,-1.1424e+00,-9.3148e-01,-6.5597e-01,-1.0189e+00,-7.9597e-01,-7.2458e-01,-5.7747e-01,-9.9762e-01,8.0038e-02,-6.6314e-01,-1.0189e+00,-7.2720e-01,-5.0871e-01,-8.8715e-01,-9.6192e-01,-1.5358e-01,-6.6314e-01,-5.9267e-02,-1.1528e+00,-7.7487e-01,-7.2873e-01,-1.0324e+00,-1.5358e-01,-5.8331e-01,-7.1039e-01,-2.0061e-01,-3.5527e-01,-9.7509e-01,-1.0324e+00,-8.7124e-01,-1.7064e-01,-6.3253e-01,-6.1279e-01,-5.9484e-01,-9.7509e-01,6.4971e-02,6.4653e-02,6.4971e-02,6.2239e-02,6.5084e-02,8.0338e-02,6.5084e-02,7.7816e-02,6.5098e-02,-2.1741e+00,6.5098e-02,-1.4883e+00,9.6661e-02,-9.6661e-02,-1.1067e-02,1.1067e-02,6.2142e-01,-6.2142e-01,6.3351e-01,-6.3351e-01,9.0481e-01,-9.0481e-01,1.0967e+00,-1.0967e+00}
> Gradient: {4.2020e-06,-1.0470e-06,-1.5375e-06,4.5509e-07,-2.8864e-06,-3.9146e-06,8.4799e-06,-5.2687e-06,-4.0216e-06,-3.9999e-07,-6.3167e-07,-2.8864e-06,1.8899e-07,-2.0263e-06,-2.0804e-06,9.2557e-08,-3.6075e-07,-6.3167e-07,5.2015e-06,-1.4353e-05,1.5352e-06,3.4466e-06,-2.8683e-07,-3.6075e-07,2.5718e-06,-5.8139e-06,-4.0310e-06,3.2959e-06,-5.5357e-07,-2.8683e-07,-5.1830e-06,1.8461e-06,3.7934e-06,-4.3727e-07,-4.2833e-06,-5.5357e-07,4.5240e-06,-1.3690e-06,1.6320e-07,-3.0670e-06,-7.8554e-07,-4.2833e-06,-1.1244e-06,8.1937e-06,-1.0044e-05,-1.4497e-06,3.9185e-07,-7.8554e-07,-1.1385e-06,8.8601e-06,-8.2234e-06,4.6365e-07,-5.1713e-06,3.9185e-07,-1.0612e-06,1.2879e-06,-3.1767e-06,4.7399e-06,-1.4362e-06,-5.1713e-06,4.2219e-06,-8.6217e-06,4.5679e-06,-2.5827e-06,-8.7763e-07,-1.4362e-06,-5.2108e-06,-1.4708e-05,1.6007e-05,9.5849e-08,-3.4526e-08,-8.7763e-07,1.2994e-07,1.2931e-07,1.2994e-07,1.2448e-07,1.3017e-07,1.6068e-07,1.3017e-07,1.5563e-07,1.3020e-07,3.4877e-06,1.3020e-07,-7.8266e-06,-1.8892e-06,1.8892e-06,4.4442e-06,-4.4442e-06,8.6733e-06,-8.6733e-06,-3.1887e-07,3.1887e-07,6.8838e-06,-6.8838e-06,3.2058e-05,-3.2058e-05}
>>>> Re-trying (1/3).
Starting Function Value: 3.6508777966274204
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.650877787443043 0.000277409511619 4.351932291306158 0.000056849312337
2 4 3.650877779145744 0.000203956677799 1.000000000000000 0.000056337670522
3 6 3.650877775937922 0.000079724866769 0.011654810469887 0.000055995247771
4 7 3.650877672382546 0.006349046603486 1.000000000000000 0.000082418241255
Gradient = {-4.6159e-06,-6.0540e-06,-8.4346e-06,-1.2086e-05,-2.5680e-06,-4.1321e-06,-1.1344e-05,-8.4874e-06,-9.8271e-06,-5.0397e-06,-6.2347e-07,-2.5680e-06,-9.8041e-07,-2.8084e-06,-2.1272e-06,-3.1090e-05,-3.4991e-07,-6.2347e-07,4.6366e-06,-1.5321e-05,1.5379e-06,-2.8216e-05,-2.6748e-07,-3.4991e-07,-7.6603e-06,-8.9140e-06,-1.3525e-05,-7.1629e-06,-4.4983e-07,-2.6748e-07,-7.5566e-06,-2.4799e-05,1.8482e-06,-2.8585e-06,-4.1637e-06,-4.4983e-07,-2.1806e-05,-3.7364e-06,-1.7125e-06,-5.9388e-06,-6.2188e-07,-4.1637e-06,-2.9237e-06,-1.9532e-05,-1.0644e-05,-4.9238e-06,6.6559e-07,-6.2188e-07,-3.2345e-06,-2.2501e-05,-8.8383e-06,-1.9234e-06,-2.1476e-06,6.6559e-07,-2.4965e-05,-4.1389e-06,-5.8802e-06,4.1648e-07,-1.2636e-06,-2.1476e-06,-2.2776e-06,-6.8127e-06,-2.2438e-05,-4.3421e-06,-7.5581e-07,-1.2636e-06,-5.8761e-06,-1.2993e-05,-1.6054e-05,-2.4103e-06,1.9889e-07,-7.5581e-07,1.2988e-07,1.2924e-07,1.2988e-07,1.2442e-07,1.3010e-07,1.6060e-07,1.3010e-07,1.5556e-07,1.3013e-07,-2.1681e-05,1.3013e-07,-1.5820e-05,1.5531e-05,-1.5531e-05,-1.1440e-04,1.1440e-04,-1.0723e-04,1.0723e-04,-1.3775e-06,1.3775e-06,1.1135e-04,-1.1135e-04,-1.4012e-06,1.4012e-06}
pCurr = {-2.4204e-04,8.0255e-05,8.0162e-05,6.9251e-05,2.0235e-04,2.9068e-04,-4.3519e-04,3.5306e-04,2.6963e-04,4.3326e-05,4.7488e-05,2.0235e-04,-3.4323e-05,9.9332e-05,1.5646e-04,1.9150e-04,2.6996e-05,4.7488e-05,-4.1676e-04,1.0472e-03,-1.2118e-04,-6.9542e-05,2.0785e-05,2.6996e-05,-1.2066e-04,3.9728e-04,3.1647e-04,-1.6387e-04,3.7451e-05,2.0785e-05,3.8236e-04,4.7576e-05,-3.2209e-04,2.6425e-05,3.1572e-04,3.7451e-05,-8.2132e-05,3.5881e-05,-3.5752e-05,2.0340e-04,5.0323e-05,3.1572e-04,3.6099e-05,-2.5937e-04,6.6787e-04,4.0022e-05,-4.7492e-05,5.0323e-05,4.5856e-05,-2.6416e-04,4.8627e-04,-4.7298e-05,3.1427e-04,-4.7492e-05,3.7733e-04,-9.1410e-05,1.3659e-04,-3.5070e-04,1.0137e-04,3.1427e-04,-3.1019e-04,5.1313e-04,-2.8772e-05,1.4522e-04,5.9910e-05,1.0137e-04,3.3854e-04,9.2861e-04,-8.1279e-04,-2.4363e-05,-9.2563e-06,5.9910e-05,-9.8962e-06,-9.8479e-06,-9.8962e-06,-9.4802e-06,-9.9135e-06,-1.2237e-05,-9.9135e-06,-1.1853e-05,-9.9156e-06,-5.3967e-05,-9.9156e-06,5.0496e-04,4.3854e-05,-4.3854e-05,-2.8696e-04,2.8696e-04,-2.8867e-04,2.8867e-04,-3.3741e-06,3.3741e-06,3.2189e-04,-3.2189e-04,1.5839e-04,-1.5839e-04}
grad*pCur = 1.3756353154946325E-7
parameters = {-5.9773e-01,-9.8239e-01,-6.2552e-01,-3.9715e-02,-7.0450e-01,-9.0663e-01,3.0124e-01,-7.8475e-01,-3.9748e-01,-6.3775e-01,-1.6332e+00,-7.0450e-01,-1.5509e-01,-8.2886e-02,-3.4376e+00,2.5500e+00,-1.1422e+00,-1.6332e+00,-5.8088e-01,2.2503e-02,-3.2242e+00,2.4679e+00,-1.4441e+00,-1.1422e+00,-2.6805e-02,-1.2076e+00,1.4363e-01,2.5895e-04,-1.3664e+00,-1.4441e+00,-6.6671e-01,8.9537e-01,-1.1071e+00,-8.6126e-01,-7.9494e-01,-1.3664e+00,6.4199e-01,-1.1423e+00,-9.3160e-01,-6.5537e-01,-1.0188e+00,-7.9494e-01,-7.2450e-01,-5.7915e-01,-9.9542e-01,8.0098e-02,-6.6329e-01,-1.0188e+00,-7.2709e-01,-5.1050e-01,-8.8552e-01,-9.6214e-01,-1.5249e-01,-6.6329e-01,-5.8785e-02,-1.1532e+00,-7.7444e-01,-7.2998e-01,-1.0321e+00,-1.5249e-01,-5.8449e-01,-7.0862e-01,-2.0151e-01,-3.5485e-01,-9.7489e-01,-1.0321e+00,-8.7014e-01,-1.6750e-01,-6.3613e-01,-6.1294e-01,-5.9487e-01,-9.7489e-01,6.4939e-02,6.4621e-02,6.4939e-02,6.2209e-02,6.5052e-02,8.0298e-02,6.5052e-02,7.7778e-02,6.5065e-02,-2.1746e+00,6.5065e-02,-1.4872e+00,9.6699e-02,-9.6699e-02,-1.1318e-02,1.1318e-02,6.2116e-01,-6.2116e-01,6.3351e-01,-6.3351e-01,9.0488e-01,-9.0488e-01,1.0964e+00,-1.0964e+00}
|grad|/|x| = 2.95607823083296E-5
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.9748e-01,-9.8247e-01,-6.2560e-01,-3.9784e-02,-7.0470e-01,-9.0692e-01,3.0168e-01,-7.8510e-01,-3.9775e-01,-6.3780e-01,-1.6333e+00,-7.0470e-01,-1.5506e-01,-8.2986e-02,-3.4377e+00,2.5498e+00,-1.1422e+00,-1.6333e+00,-5.8046e-01,2.1456e-02,-3.2241e+00,2.4679e+00,-1.4441e+00,-1.1422e+00,-2.6684e-02,-1.2080e+00,1.4331e-01,4.2283e-04,-1.3665e+00,-1.4441e+00,-6.6709e-01,8.9532e-01,-1.1068e+00,-8.6128e-01,-7.9526e-01,-1.3665e+00,6.4207e-01,-1.1424e+00,-9.3156e-01,-6.5558e-01,-1.0188e+00,-7.9526e-01,-7.2454e-01,-5.7889e-01,-9.9609e-01,8.0058e-02,-6.6324e-01,-1.0188e+00,-7.2714e-01,-5.1024e-01,-8.8600e-01,-9.6209e-01,-1.5281e-01,-6.6324e-01,-5.9162e-02,-1.1531e+00,-7.7457e-01,-7.2963e-01,-1.0322e+00,-1.5281e-01,-5.8418e-01,-7.0913e-01,-2.0149e-01,-3.5499e-01,-9.7495e-01,-1.0322e+00,-8.7048e-01,-1.6843e-01,-6.3532e-01,-6.1291e-01,-5.9486e-01,-9.7495e-01,6.4948e-02,6.4631e-02,6.4948e-02,6.2218e-02,6.5062e-02,8.0310e-02,6.5062e-02,7.7789e-02,6.5075e-02,-2.1746e+00,6.5075e-02,-1.4877e+00,9.6655e-02,-9.6655e-02,-1.1031e-02,1.1031e-02,6.2145e-01,-6.2145e-01,6.3351e-01,-6.3351e-01,9.0456e-01,-9.0456e-01,1.0963e+00,-1.0963e+00}
> Gradient: {-4.6159e-06,-6.0540e-06,-8.4346e-06,-1.2086e-05,-2.5680e-06,-4.1321e-06,-1.1344e-05,-8.4874e-06,-9.8271e-06,-5.0397e-06,-6.2347e-07,-2.5680e-06,-9.8041e-07,-2.8084e-06,-2.1272e-06,-3.1090e-05,-3.4991e-07,-6.2347e-07,4.6366e-06,-1.5321e-05,1.5379e-06,-2.8216e-05,-2.6748e-07,-3.4991e-07,-7.6603e-06,-8.9140e-06,-1.3525e-05,-7.1629e-06,-4.4983e-07,-2.6748e-07,-7.5566e-06,-2.4799e-05,1.8482e-06,-2.8585e-06,-4.1637e-06,-4.4983e-07,-2.1806e-05,-3.7364e-06,-1.7125e-06,-5.9388e-06,-6.2188e-07,-4.1637e-06,-2.9237e-06,-1.9532e-05,-1.0644e-05,-4.9238e-06,6.6559e-07,-6.2188e-07,-3.2345e-06,-2.2501e-05,-8.8383e-06,-1.9234e-06,-2.1476e-06,6.6559e-07,-2.4965e-05,-4.1389e-06,-5.8802e-06,4.1648e-07,-1.2636e-06,-2.1476e-06,-2.2776e-06,-6.8127e-06,-2.2438e-05,-4.3421e-06,-7.5581e-07,-1.2636e-06,-5.8761e-06,-1.2993e-05,-1.6054e-05,-2.4103e-06,1.9889e-07,-7.5581e-07,1.2988e-07,1.2924e-07,1.2988e-07,1.2442e-07,1.3010e-07,1.6060e-07,1.3010e-07,1.5556e-07,1.3013e-07,-2.1681e-05,1.3013e-07,-1.5820e-05,1.5531e-05,-1.5531e-05,-1.1440e-04,1.1440e-04,-1.0723e-04,1.0723e-04,-1.3775e-06,1.3775e-06,1.1135e-04,-1.1135e-04,-1.4012e-06,1.4012e-06}
>>>> Re-trying (2/3).
Starting Function Value: 3.6508776531713405
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.650877635015299 0.000430969606496 5.229130125304360 0.000090105236445
2 4 3.650877186624770 0.000335944994693 1.000000000000000 0.000077136351631
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.9747e-01,-9.8243e-01,-6.2556e-01,-3.9693e-02,-7.0467e-01,-9.0687e-01,3.0174e-01,-7.8504e-01,-3.9768e-01,-6.3776e-01,-1.6333e+00,-7.0467e-01,-1.5506e-01,-8.2974e-02,-3.4377e+00,2.5500e+00,-1.1422e+00,-1.6333e+00,-5.8052e-01,2.1602e-02,-3.2241e+00,2.4681e+00,-1.4441e+00,-1.1422e+00,-2.6639e-02,-1.2079e+00,1.4341e-01,4.6454e-04,-1.3665e+00,-1.4441e+00,-6.6702e-01,8.9549e-01,-1.1068e+00,-8.6126e-01,-7.9521e-01,-1.3665e+00,6.4223e-01,-1.1424e+00,-9.3157e-01,-6.5553e-01,-1.0188e+00,-7.9521e-01,-7.2452e-01,-5.7876e-01,-9.9600e-01,8.0084e-02,-6.6325e-01,-1.0188e+00,-7.2712e-01,-5.1009e-01,-8.8594e-01,-9.6208e-01,-1.5278e-01,-6.6325e-01,-5.8962e-02,-1.1531e+00,-7.7455e-01,-7.2966e-01,-1.0322e+00,-1.5278e-01,-5.8418e-01,-7.0907e-01,-2.0133e-01,-3.5496e-01,-9.7495e-01,-1.0322e+00,-8.7043e-01,-1.6831e-01,-6.3525e-01,-6.1290e-01,-5.9486e-01,-9.7495e-01,6.4947e-02,6.4630e-02,6.4947e-02,6.2217e-02,6.5060e-02,8.0309e-02,6.5060e-02,7.7788e-02,6.5074e-02,-2.1745e+00,6.5074e-02,-1.4875e+00,9.6677e-02,-9.6677e-02,-1.1131e-02,1.1131e-02,6.2133e-01,-6.2133e-01,6.3351e-01,-6.3351e-01,9.0460e-01,-9.0460e-01,1.0964e+00,-1.0964e+00}
> Gradient: {-6.1964e-07,-2.6940e-06,-2.9264e-06,-5.9907e-06,-2.6255e-06,-4.0638e-06,-2.8994e-06,-5.4519e-06,-4.9894e-06,-2.3300e-06,-6.2386e-07,-2.6255e-06,8.4429e-08,-1.2883e-06,-2.0571e-06,-1.4773e-05,-3.5156e-07,-6.2386e-07,5.3269e-06,-1.3708e-05,1.6166e-06,-1.1624e-05,-2.6951e-07,-3.5156e-07,-2.7350e-06,-6.0584e-06,-7.0890e-06,-2.3926e-06,-4.6474e-07,-2.6951e-07,-5.8899e-06,-1.0904e-05,3.6751e-06,-1.2683e-06,-4.1573e-06,-4.6474e-07,-9.9619e-06,-9.8365e-07,2.4233e-07,-3.5082e-06,-6.4063e-07,-4.1573e-06,-8.9683e-07,-8.5981e-06,-8.2324e-06,-1.2699e-06,6.2852e-07,-6.4063e-07,-1.0753e-06,-1.0106e-05,-5.4671e-06,-8.9368e-08,-2.8997e-06,6.2852e-07,-1.5192e-05,-5.3159e-07,-2.0490e-06,2.9561e-06,-1.2935e-06,-2.8997e-06,1.5357e-06,-4.6526e-06,-1.1318e-05,-2.4193e-06,-7.7214e-07,-1.2935e-06,-4.4563e-06,-9.3118e-06,-3.8331e-06,-7.0251e-07,1.5571e-07,-7.7214e-07,1.2989e-07,1.2926e-07,1.2989e-07,1.2443e-07,1.3012e-07,1.6062e-07,1.3012e-07,1.5558e-07,1.3015e-07,-4.7092e-06,1.3015e-07,-1.3822e-05,5.5821e-06,-5.5821e-06,-2.5911e-05,2.5911e-05,-3.2092e-05,3.2092e-05,-7.3450e-08,7.3450e-08,-1.2587e-05,1.2587e-05,1.8172e-07,-1.8172e-07}
>>>> Re-trying (3/3).
After: gradient norm = 7.72389958245117E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6213,-0.6213}
Count Table 3:
---------------
h: {0.6335,-0.6335}
Count Table 4:
---------------
h: {0.9046,-0.9046}
Count Table 5:
---------------
h: {1.0964,-1.0964}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.5975,-0.9824,-0.6256,-0.0397,-0.7047,-0.9069,0.3017,-0.7850,-0.3977,-0.6378,-1.6333,-0.7047,-0.1551,-0.0830,-3.4377,2.5500,-1.1422,-1.6333,-0.5805,0.0216,-3.2241,2.4681,-1.4441,-1.1422,-0.0266,-1.2079,0.1434,0.0005,-1.3665,-1.4441,-0.6670,0.8955,-1.1068,-0.8613,-0.7952,-1.3665,0.6422,-1.1424,-0.9316,-0.6555,-1.0188,-0.7952,-0.7245,-0.5788,-0.9960,0.0801,-0.6632,-1.0188,-0.7271,-0.5101,-0.8859,-0.9621,-0.1528,-0.6632,-0.0590,-1.1531,-0.7745,-0.7297,-1.0322,-0.1528,-0.5842,-0.7091,-0.2013,-0.3550,-0.9749,-1.0322,-0.8704,-0.1683,-0.6352,-0.6129,-0.5949,-0.9749}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0649,0.0646}
Activity(exp=1): {0.0649,0.0622}
Activity(exp=2): {0.0651,0.0803}
Activity(exp=3): {0.0651,0.0778}
Activity(exp=4): {0.0651,-2.1745}
Activity(exp=5): {0.0651,-1.4875}
The Likelihood DID improve.
Suggested variations:
key=12;10;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component3-2-variation7).
>> Starting new optimization: component3-2-variation7. (2021-05-21 20:05:53.286).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[84,85]},{"h":[86,87]},{"h":[88,89]},{"h":[90,91]},{"h":[92,93]},{"h":[94,95]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[72,73],[74,75],[76,77],[78,79],[80,81],[82,83]]}]}
Value and gradient before optimization:
=======================================
value = 3.6508652303388702
gradient = {0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0001,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0001,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0003,0.0003,-0.0004,0.0004}
gradient norm = 7.566674864909979E-4
Starting Function Value: 3.6508652303388702
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 4 3.650865130699362 0.000205859473516 0.272060683445653 0.000671026187331
2 5 3.650864554481839 0.001685881089334 1.000000000000000 0.000117681725853
3 6 3.650864521529198 0.000309976958292 1.000000000000000 0.000114653457431
4 7 3.650864296820854 0.003803769034993 1.000000000000000 0.000084302426734
5 9 3.650864274504667 0.000891244881839 0.411504304123673 0.000131470528827
6 10 3.650864235340606 0.000950927852866 1.000000000000000 0.000111427270424
7 11 3.650864060090755 0.005476692638537 1.000000000000000 0.000178181807412
8 12 3.650863836954621 0.008604730539334 1.000000000000000 0.000280236976867
9 13 3.650863562735293 0.016257459973351 1.000000000000000 0.000348051167260
10 14 3.650863428010585 0.013086722042613 1.000000000000000 0.000295084526510
11 15 3.650863310101447 0.004283089298610 1.000000000000000 0.000094034947975
12 16 3.650863285825653 0.000990663605754 1.000000000000000 0.000058317698454
13 17 3.650863267772548 0.000497363008503 1.000000000000000 0.000080923606325
14 18 3.650863208629130 0.002341181107446 1.000000000000000 0.000158128641464
15 19 3.650863099390272 0.005378813352414 1.000000000000000 0.000235235305319
16 20 3.650862935008397 0.010313800586841 1.000000000000000 0.000265456515598
17 22 3.650862859876431 0.005706435019795 0.285194192691972 0.000249979303360
18 23 3.650862785828628 0.005368165171698 1.000000000000000 0.000118454184580
19 24 3.650862762030422 0.001664722147382 1.000000000000000 0.000046996672142
20 25 3.650862741160976 0.000405649851293 1.000000000000000 0.000063821408513
21 26 3.650862711559147 0.001097725370392 1.000000000000000 0.000113979572327
22 27 3.650862644281804 0.003205358575058 1.000000000000000 0.000188619412172
23 28 3.650862504266006 0.008651339401823 1.000000000000000 0.000269183900659
24 29 3.650862382584194 0.017651476624621 1.000000000000000 0.000398154862099
25 30 3.650862197252853 0.010431539003831 1.000000000000000 0.000213501200640
26 31 3.650862120505497 0.003648555552382 1.000000000000000 0.000088450528138
27 34 3.650862106894990 0.000048421113318 0.018905610245958 0.000086929083619
28 35 3.650862104459558 0.003218434875344 1.000000000000000 0.000048198904039
29 36 3.650862086371659 0.000749805630938 1.000000000000000 0.000058978969710
30 39 3.650862029936304 0.004991168723640 0.660000000000000 0.000120989927953
31 40 3.650861892877445 0.013825358223154 1.000000000000000 0.000237848236894
32 41 3.650861728255932 0.016633281514262 1.000000000000000 0.000285116359623
33 42 3.650861500577029 0.022055861801570 1.000000000000000 0.000217066487610
34 43 3.650861392933922 0.009939773672635 1.000000000000000 0.000081788823268
35 44 3.650861355779872 0.002794066421839 1.000000000000000 0.000055786276162
36 45 3.650861343439263 0.002184527103945 1.000000000000000 0.000080729728294
37 46 3.650861325902409 0.002127906282439 1.000000000000000 0.000104667779254
38 47 3.650861260144579 0.004515696722058 1.000000000000000 0.000149375076827
39 48 3.650861103368737 0.008979206787243 1.000000000000000 0.000156393758614
40 50 3.650860844326060 0.007381384755912 0.244656094346421 0.000192444598064
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.8682e-01,-9.7424e-01,-6.2608e-01,-4.3894e-02,-6.9690e-01,-8.8935e-01,2.9410e-01,-7.5881e-01,-3.9778e-01,-6.2900e-01,-1.6289e+00,-6.9690e-01,-1.6774e-01,-1.2874e-02,-3.4234e+00,2.5115e+00,-1.1398e+00,-1.6289e+00,-6.1896e-01,1.0977e-01,-3.2365e+00,2.4664e+00,-1.4421e+00,-1.1398e+00,-2.8873e-02,-1.1620e+00,1.3552e-01,-3.5006e-04,-1.3634e+00,-1.4421e+00,-6.5097e-01,8.9243e-01,-1.1275e+00,-8.5051e-01,-7.6120e-01,-1.3634e+00,6.2813e-01,-1.1144e+00,-9.2600e-01,-6.7408e-01,-1.0137e+00,-7.6120e-01,-7.1993e-01,-5.7566e-01,-9.8892e-01,9.6527e-02,-6.5954e-01,-1.0137e+00,-7.2756e-01,-4.9216e-01,-8.7461e-01,-9.6185e-01,-1.4544e-01,-6.5954e-01,-4.8361e-02,-1.1441e+00,-7.6170e-01,-7.3789e-01,-1.0237e+00,-1.4544e-01,-5.7781e-01,-7.0667e-01,-1.8950e-01,-3.4764e-01,-9.7197e-01,-1.0237e+00,-8.5792e-01,-1.4980e-01,-6.4270e-01,-6.0007e-01,-5.9482e-01,-9.7197e-01,6.3969e-02,6.3656e-02,6.3969e-02,6.1279e-02,6.4080e-02,7.9099e-02,6.4080e-02,7.6616e-02,6.4094e-02,-2.1600e+00,6.4094e-02,-1.4655e+00,9.6667e-02,-9.6667e-02,-1.1115e-02,1.1115e-02,6.2130e-01,-6.2130e-01,6.3328e-01,-6.3328e-01,9.0803e-01,-9.0803e-01,1.1021e+00,-1.1021e+00}
> Gradient: {3.4558e-06,2.5397e-06,6.6095e-06,8.4139e-06,1.0125e-06,9.4695e-07,1.1014e-05,1.8985e-06,5.6191e-06,3.9313e-06,-4.9735e-07,1.0125e-06,3.4184e-06,1.2112e-06,-1.5805e-06,2.0601e-05,-2.6249e-07,-4.9735e-07,4.5608e-06,-3.5783e-06,1.7535e-06,2.0678e-05,-2.6090e-07,-2.6249e-07,8.8830e-06,4.8269e-06,1.3172e-06,8.5225e-06,-3.9816e-07,-2.6090e-07,5.0387e-06,2.0417e-05,-5.0350e-07,1.7031e-06,-3.3668e-06,-3.9816e-07,1.4551e-05,9.2286e-06,2.7661e-06,-2.6943e-09,-2.8586e-07,-3.3668e-06,6.7246e-06,5.1583e-06,3.2129e-06,9.0137e-06,-9.3307e-07,-2.8586e-07,4.3458e-06,8.6729e-06,5.5952e-06,2.6162e-06,2.5937e-06,-9.3307e-07,8.9639e-06,1.9928e-06,8.9317e-06,1.0694e-06,-6.6084e-07,2.5937e-06,4.3487e-06,2.2715e-06,8.6422e-06,8.5019e-06,-1.2501e-07,-6.6084e-07,5.2610e-06,6.5737e-06,5.5492e-06,5.7925e-06,-7.2919e-08,-1.2501e-07,1.2794e-07,1.2731e-07,1.2794e-07,1.2256e-07,1.2816e-07,1.5820e-07,1.2816e-07,1.5323e-07,1.2819e-07,3.6905e-06,1.2819e-07,1.9671e-05,7.3560e-07,-7.3560e-07,-1.8350e-05,1.8350e-05,-4.5323e-05,4.5323e-05,-1.0150e-04,1.0150e-04,-3.9240e-05,3.9240e-05,-5.1126e-05,5.1126e-05}
>>>> Re-trying (1/3).
Starting Function Value: 3.650861708220826
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.650861080498250 0.000446975301032 2.323132432086159 0.000025740428692
2 4 3.650861078999871 0.000061588104419 1.000000000000000 0.000024439393534
3 5 3.650861061355624 0.001178905618943 1.000000000000000 0.000038319406211
Gradient = {-2.1734e-06,-1.2258e-06,-1.3910e-06,-2.0268e-06,4.1144e-07,2.5759e-07,-1.1955e-06,-2.3867e-06,-1.8163e-06,-6.5158e-07,-5.0927e-07,4.1144e-07,1.9894e-06,-6.9172e-07,-1.6424e-06,-5.1120e-06,-2.6977e-07,-5.0927e-07,3.6326e-06,-5.1053e-06,1.6718e-06,-5.8894e-06,-2.7560e-07,-2.6977e-07,9.1427e-07,2.7002e-07,-7.2703e-06,5.8719e-07,-4.6127e-07,-2.7560e-07,1.8825e-06,-7.7701e-07,-2.4893e-06,-9.0733e-07,-3.4832e-06,-4.6127e-07,-4.6481e-06,4.7503e-06,1.6430e-06,-3.9983e-06,-4.9933e-07,-3.4832e-06,1.7017e-06,-5.1696e-06,-1.4449e-06,6.9972e-07,-1.5233e-06,-4.9933e-07,7.2629e-08,-2.5860e-06,-1.2960e-06,-1.1925e-06,2.8938e-07,-1.5233e-06,-2.6122e-06,-1.9678e-06,1.9162e-06,-2.9735e-06,-8.8783e-07,2.8938e-07,-1.4761e-06,-3.0572e-06,-3.6810e-06,3.2601e-06,-3.0594e-07,-8.8783e-07,1.8125e-06,-2.9237e-06,-6.0285e-06,1.8194e-06,-5.2165e-07,-3.0594e-07,1.2792e-07,1.2730e-07,1.2792e-07,1.2255e-07,1.2815e-07,1.5818e-07,1.2815e-07,1.5322e-07,1.2817e-07,-4.5270e-06,1.2817e-07,-1.2375e-06,6.9327e-08,-6.9327e-08,-2.5341e-06,2.5341e-06,-5.8798e-06,5.8798e-06,1.9154e-05,-1.9154e-05,-2.8252e-06,2.8252e-06,9.4707e-06,-9.4707e-06}
pCurr = {2.7424e-05,1.7820e-05,-2.9247e-05,-5.8903e-05,-2.4703e-05,-1.9356e-05,-1.2571e-04,7.4919e-05,-4.4637e-06,-3.0188e-05,2.3180e-05,-2.4703e-05,-1.0223e-04,2.8088e-05,7.4714e-05,-1.1899e-04,1.2267e-05,2.3180e-05,-1.7199e-04,2.2921e-04,-7.6149e-05,-8.8873e-05,1.2570e-05,1.2267e-05,-1.5502e-04,-5.7861e-05,2.3865e-04,-1.4232e-04,2.1010e-05,1.2570e-05,-1.2391e-04,-2.5438e-04,1.0177e-04,1.2347e-05,1.6020e-04,2.1010e-05,-7.0248e-05,-2.5830e-04,-7.5589e-05,1.3957e-04,2.1400e-05,1.6020e-04,-1.4488e-04,1.0110e-04,1.6869e-05,-1.4110e-04,6.3647e-05,2.1400e-05,-5.6932e-05,-2.8172e-05,-1.6031e-05,9.0323e-07,-4.6385e-05,6.3647e-05,-3.8958e-05,4.5802e-05,-1.6430e-04,8.2730e-05,3.8146e-05,-4.6385e-05,-4.9371e-06,7.9088e-05,7.3982e-06,-2.1923e-04,1.2568e-05,3.8146e-05,-1.2273e-04,1.2645e-05,1.2827e-04,-1.3636e-04,1.8653e-05,1.2568e-05,-5.8230e-06,-5.7946e-06,-5.8230e-06,-5.5782e-06,-5.8332e-06,-7.2003e-06,-5.8332e-06,-6.9743e-06,-5.8344e-06,1.2637e-04,-5.8344e-06,-2.3080e-04,-4.5904e-07,4.5904e-07,4.1323e-07,-4.1323e-07,2.2788e-05,-2.2788e-05,-2.0439e-05,2.0439e-05,2.9392e-05,-2.9392e-05,-1.1318e-04,1.1318e-04}
grad*pCur = -1.371009634435682E-8
parameters = {-5.8683e-01,-9.7424e-01,-6.2616e-01,-4.4051e-02,-6.9693e-01,-8.8938e-01,2.9385e-01,-7.5874e-01,-3.9783e-01,-6.2907e-01,-1.6289e+00,-6.9693e-01,-1.6787e-01,-1.2841e-02,-3.4233e+00,2.5111e+00,-1.1397e+00,-1.6289e+00,-6.1916e-01,1.1003e-01,-3.2366e+00,2.4661e+00,-1.4420e+00,-1.1397e+00,-2.9119e-02,-1.1621e+00,1.3574e-01,-5.8315e-04,-1.3634e+00,-1.4420e+00,-6.5114e-01,8.9196e-01,-1.1274e+00,-8.5051e-01,-7.6101e-01,-1.3634e+00,6.2788e-01,-1.1147e+00,-9.2609e-01,-6.7394e-01,-1.0136e+00,-7.6101e-01,-7.2014e-01,-5.7562e-01,-9.8893e-01,9.6300e-02,-6.5947e-01,-1.0136e+00,-7.2766e-01,-4.9228e-01,-8.7467e-01,-9.6188e-01,-1.4552e-01,-6.5947e-01,-4.8498e-02,-1.1440e+00,-7.6193e-01,-7.3783e-01,-1.0237e+00,-1.4552e-01,-5.7786e-01,-7.0661e-01,-1.8958e-01,-3.4794e-01,-9.7195e-01,-1.0237e+00,-8.5809e-01,-1.4986e-01,-6.4264e-01,-6.0026e-01,-5.9480e-01,-9.7195e-01,6.3962e-02,6.3649e-02,6.3962e-02,6.1273e-02,6.4073e-02,7.9090e-02,6.4073e-02,7.6608e-02,6.4087e-02,-2.1599e+00,6.4087e-02,-1.4660e+00,9.6665e-02,-9.6665e-02,-1.1081e-02,1.1081e-02,6.2138e-01,-6.2138e-01,6.3356e-01,-6.3356e-01,9.0803e-01,-9.0803e-01,1.1020e+00,-1.1020e+00}
|grad|/|x| = 3.9844473002814466E-6
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.8683e-01,-9.7424e-01,-6.2616e-01,-4.4051e-02,-6.9693e-01,-8.8938e-01,2.9385e-01,-7.5874e-01,-3.9783e-01,-6.2907e-01,-1.6289e+00,-6.9693e-01,-1.6787e-01,-1.2841e-02,-3.4233e+00,2.5111e+00,-1.1397e+00,-1.6289e+00,-6.1916e-01,1.1003e-01,-3.2366e+00,2.4661e+00,-1.4420e+00,-1.1397e+00,-2.9119e-02,-1.1621e+00,1.3574e-01,-5.8290e-04,-1.3634e+00,-1.4420e+00,-6.5114e-01,8.9197e-01,-1.1274e+00,-8.5051e-01,-7.6101e-01,-1.3634e+00,6.2788e-01,-1.1147e+00,-9.2609e-01,-6.7394e-01,-1.0136e+00,-7.6101e-01,-7.2014e-01,-5.7562e-01,-9.8893e-01,9.6300e-02,-6.5947e-01,-1.0136e+00,-7.2766e-01,-4.9228e-01,-8.7467e-01,-9.6188e-01,-1.4552e-01,-6.5947e-01,-4.8498e-02,-1.1440e+00,-7.6193e-01,-7.3783e-01,-1.0237e+00,-1.4552e-01,-5.7786e-01,-7.0661e-01,-1.8958e-01,-3.4794e-01,-9.7195e-01,-1.0237e+00,-8.5809e-01,-1.4986e-01,-6.4264e-01,-6.0026e-01,-5.9480e-01,-9.7195e-01,6.3962e-02,6.3649e-02,6.3962e-02,6.1273e-02,6.4073e-02,7.9090e-02,6.4073e-02,7.6608e-02,6.4087e-02,-2.1599e+00,6.4087e-02,-1.4660e+00,9.6665e-02,-9.6665e-02,-1.1081e-02,1.1081e-02,6.2138e-01,-6.2138e-01,6.3356e-01,-6.3356e-01,9.0803e-01,-9.0803e-01,1.1020e+00,-1.1020e+00}
> Gradient: {-2.1734e-06,-1.2258e-06,-1.3910e-06,-2.0268e-06,4.1144e-07,2.5759e-07,-1.1955e-06,-2.3867e-06,-1.8163e-06,-6.5158e-07,-5.0927e-07,4.1144e-07,1.9894e-06,-6.9172e-07,-1.6424e-06,-5.1120e-06,-2.6977e-07,-5.0927e-07,3.6326e-06,-5.1053e-06,1.6718e-06,-5.8894e-06,-2.7560e-07,-2.6977e-07,9.1427e-07,2.7002e-07,-7.2703e-06,5.8719e-07,-4.6127e-07,-2.7560e-07,1.8825e-06,-7.7701e-07,-2.4893e-06,-9.0733e-07,-3.4832e-06,-4.6127e-07,-4.6481e-06,4.7503e-06,1.6430e-06,-3.9983e-06,-4.9933e-07,-3.4832e-06,1.7017e-06,-5.1696e-06,-1.4449e-06,6.9972e-07,-1.5233e-06,-4.9933e-07,7.2629e-08,-2.5860e-06,-1.2960e-06,-1.1925e-06,2.8938e-07,-1.5233e-06,-2.6122e-06,-1.9678e-06,1.9162e-06,-2.9735e-06,-8.8783e-07,2.8938e-07,-1.4761e-06,-3.0572e-06,-3.6810e-06,3.2601e-06,-3.0594e-07,-8.8783e-07,1.8125e-06,-2.9237e-06,-6.0285e-06,1.8194e-06,-5.2165e-07,-3.0594e-07,1.2792e-07,1.2730e-07,1.2792e-07,1.2255e-07,1.2815e-07,1.5818e-07,1.2815e-07,1.5322e-07,1.2817e-07,-4.5270e-06,1.2817e-07,-1.2375e-06,6.9327e-08,-6.9327e-08,-2.5341e-06,2.5341e-06,-5.8798e-06,5.8798e-06,1.9154e-05,-1.9154e-05,-2.8252e-06,2.8252e-06,9.4707e-06,-9.4707e-06}
>>>> Re-trying (2/3).
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.8683e-01,-9.7424e-01,-6.2616e-01,-4.4051e-02,-6.9693e-01,-8.8938e-01,2.9385e-01,-7.5874e-01,-3.9783e-01,-6.2907e-01,-1.6289e+00,-6.9693e-01,-1.6787e-01,-1.2841e-02,-3.4233e+00,2.5111e+00,-1.1397e+00,-1.6289e+00,-6.1916e-01,1.1003e-01,-3.2366e+00,2.4661e+00,-1.4420e+00,-1.1397e+00,-2.9119e-02,-1.1621e+00,1.3574e-01,-5.8290e-04,-1.3634e+00,-1.4420e+00,-6.5114e-01,8.9197e-01,-1.1274e+00,-8.5051e-01,-7.6101e-01,-1.3634e+00,6.2788e-01,-1.1147e+00,-9.2609e-01,-6.7394e-01,-1.0136e+00,-7.6101e-01,-7.2014e-01,-5.7562e-01,-9.8893e-01,9.6300e-02,-6.5947e-01,-1.0136e+00,-7.2766e-01,-4.9228e-01,-8.7467e-01,-9.6188e-01,-1.4552e-01,-6.5947e-01,-4.8498e-02,-1.1440e+00,-7.6193e-01,-7.3783e-01,-1.0237e+00,-1.4552e-01,-5.7786e-01,-7.0661e-01,-1.8958e-01,-3.4794e-01,-9.7195e-01,-1.0237e+00,-8.5809e-01,-1.4986e-01,-6.4264e-01,-6.0026e-01,-5.9480e-01,-9.7195e-01,6.3962e-02,6.3649e-02,6.3962e-02,6.1273e-02,6.4073e-02,7.9090e-02,6.4073e-02,7.6608e-02,6.4087e-02,-2.1599e+00,6.4087e-02,-1.4660e+00,9.6665e-02,-9.6665e-02,-1.1081e-02,1.1081e-02,6.2138e-01,-6.2138e-01,6.3356e-01,-6.3356e-01,9.0803e-01,-9.0803e-01,1.1020e+00,-1.1020e+00}
> Gradient: {-2.1720e-06,-1.2249e-06,-1.3888e-06,-2.0235e-06,4.1137e-07,2.5753e-07,-1.1914e-06,-2.3863e-06,-1.8144e-06,-6.5036e-07,-5.0928e-07,4.1137e-07,1.9895e-06,-6.9179e-07,-1.6424e-06,-5.1044e-06,-2.6977e-07,-5.0928e-07,3.6327e-06,-5.1052e-06,1.6718e-06,-5.8819e-06,-2.7561e-07,-2.6977e-07,9.1698e-07,2.7110e-07,-7.2690e-06,5.8983e-07,-4.6132e-07,-2.7561e-07,1.8832e-06,-7.7036e-07,-2.4892e-06,-9.0692e-07,-3.4834e-06,-4.6132e-07,-4.6422e-06,4.7513e-06,1.6433e-06,-3.9977e-06,-4.9939e-07,-3.4834e-06,1.7033e-06,-5.1671e-06,-1.4437e-06,7.0231e-07,-1.5234e-06,-4.9939e-07,7.3902e-08,-2.5831e-06,-1.2939e-06,-1.1912e-06,2.8970e-07,-1.5234e-06,-2.6092e-06,-1.9665e-06,1.9183e-06,-2.9725e-06,-8.8786e-07,2.8970e-07,-1.4745e-06,-3.0557e-06,-3.6780e-06,3.2617e-06,-3.0598e-07,-8.8786e-07,1.8134e-06,-2.9206e-06,-6.0260e-06,1.8206e-06,-5.2167e-07,-3.0598e-07,1.2792e-07,1.2730e-07,1.2792e-07,1.2255e-07,1.2815e-07,1.5818e-07,1.2815e-07,1.5322e-07,1.2817e-07,-4.5208e-06,1.2817e-07,-1.2360e-06,7.3530e-08,-7.3530e-08,-2.5432e-06,2.5432e-06,-5.8984e-06,5.8984e-06,1.8982e-05,-1.8982e-05,-2.8617e-06,2.8617e-06,9.4935e-06,-9.4935e-06}
>>>> Re-trying (3/3).
After: gradient norm = 3.8320571749960174E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6214,-0.6214}
Count Table 3:
---------------
h: {0.6336,-0.6336}
Count Table 4:
---------------
h: {0.9080,-0.9080}
Count Table 5:
---------------
h: {1.1020,-1.1020}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.5868,-0.9742,-0.6262,-0.0441,-0.6969,-0.8894,0.2939,-0.7587,-0.3978,-0.6291,-1.6289,-0.6969,-0.1679,-0.0128,-3.4233,2.5111,-1.1397,-1.6289,-0.6192,0.1100,-3.2366,2.4661,-1.4420,-1.1397,-0.0291,-1.1621,0.1357,-0.0006,-1.3634,-1.4420,-0.6511,0.8920,-1.1274,-0.8505,-0.7610,-1.3634,0.6279,-1.1147,-0.9261,-0.6739,-1.0136,-0.7610,-0.7201,-0.5756,-0.9889,0.0963,-0.6595,-1.0136,-0.7277,-0.4923,-0.8747,-0.9619,-0.1455,-0.6595,-0.0485,-1.1440,-0.7619,-0.7378,-1.0237,-0.1455,-0.5779,-0.7066,-0.1896,-0.3479,-0.9720,-1.0237,-0.8581,-0.1499,-0.6426,-0.6003,-0.5948,-0.9720}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0640,0.0636}
Activity(exp=1): {0.0640,0.0613}
Activity(exp=2): {0.0641,0.0791}
Activity(exp=3): {0.0641,0.0766}
Activity(exp=4): {0.0641,-2.1599}
Activity(exp=5): {0.0641,-1.4660}
The Likelihood DID improve.
Suggested variations:
key=12;11;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component3-2-variation8).
>> Starting new optimization: component3-2-variation8. (2021-05-21 20:09:30.766).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[84,85]},{"h":[86,87]},{"h":[88,89]},{"h":[90,91]},{"h":[92,93]},{"h":[94,95]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[72,73],[74,75],[76,77],[78,79],[80,81],[82,83]]}]}
Value and gradient before optimization:
=======================================
value = 3.6508589087637273
gradient = {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0001,0.0001,-0.0002,0.0002}
gradient norm = 3.413682005785421E-4
Starting Function Value: 3.6508589087637273
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.650858771889364 0.000793622665889 2.324828922388398 0.000044708128435
2 7 3.650858769306272 0.000059625536101 0.560755837094259 0.000043022137352
3 8 3.650858751227013 0.002009003655420 1.000000000000000 0.000114589205243
4 9 3.650858737514390 0.000488235225237 1.000000000000000 0.000070799632239
5 10 3.650858730482380 0.000377356882705 1.000000000000000 0.000020908977643
6 11 3.650858690435751 0.000084783492460 1.000000000000000 0.000018779490854
7 13 3.650857951227020 0.000319383541209 0.166108323100042 0.000019566156906
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.8673e-01,-9.7401e-01,-6.2609e-01,-4.3894e-02,-6.9697e-01,-8.8940e-01,2.9411e-01,-7.5863e-01,-3.9770e-01,-6.2909e-01,-1.6288e+00,-6.9697e-01,-1.6807e-01,-1.2701e-02,-3.4232e+00,2.5115e+00,-1.1397e+00,-1.6288e+00,-6.1946e-01,1.1054e-01,-3.2368e+00,2.4664e+00,-1.4420e+00,-1.1397e+00,-2.9216e-02,-1.1622e+00,1.3637e-01,-5.5173e-04,-1.3634e+00,-1.4420e+00,-6.5134e-01,8.9217e-01,-1.1272e+00,-8.5049e-01,-7.6072e-01,-1.3634e+00,6.2827e-01,-1.1150e+00,-9.2622e-01,-6.7369e-01,-1.0136e+00,-7.6072e-01,-7.2031e-01,-5.7517e-01,-9.8888e-01,9.6320e-02,-6.5934e-01,-1.0136e+00,-7.2772e-01,-4.9213e-01,-8.7464e-01,-9.6167e-01,-1.4549e-01,-6.5934e-01,-4.8293e-02,-1.1440e+00,-7.6204e-01,-7.3762e-01,-1.0236e+00,-1.4549e-01,-5.7777e-01,-7.0639e-01,-1.8925e-01,-3.4818e-01,-9.7193e-01,-1.0236e+00,-8.5813e-01,-1.4963e-01,-6.4199e-01,-6.0062e-01,-5.9481e-01,-9.7193e-01,6.3951e-02,6.3639e-02,6.3951e-02,6.1263e-02,6.4063e-02,7.9077e-02,6.4063e-02,7.6595e-02,6.4076e-02,-2.1595e+00,6.4076e-02,-1.4659e+00,9.6665e-02,-9.6665e-02,-1.1074e-02,1.1074e-02,6.2140e-01,-6.2140e-01,6.3352e-01,-6.3352e-01,9.0859e-01,-9.0859e-01,1.1027e+00,-1.1027e+00}
> Gradient: {3.6388e-07,-2.0651e-06,6.6361e-07,1.3139e-06,4.6300e-07,4.4783e-07,5.9930e-07,-7.7696e-07,-1.8039e-09,1.4047e-06,-5.0115e-07,4.6300e-07,2.5459e-06,-1.9702e-06,-1.6191e-06,2.9113e-06,-2.6742e-07,-5.0115e-07,3.6423e-06,-6.3772e-06,1.6970e-06,2.6734e-06,-2.6880e-07,-2.6742e-07,2.7336e-06,1.6878e-06,-4.0994e-06,1.4687e-06,-4.2250e-07,-2.6880e-07,3.0917e-06,3.5278e-06,-1.8872e-06,4.0589e-07,-3.6163e-06,-4.2250e-07,1.8537e-06,3.8263e-06,1.4615e-06,-2.0049e-06,-4.2097e-07,-3.6163e-06,2.8030e-06,-8.6196e-07,-1.3995e-07,1.1898e-06,-1.4706e-06,-4.2097e-07,1.2945e-06,2.9779e-06,-1.3533e-07,-1.6611e-06,9.3957e-08,-1.4706e-06,2.2465e-06,-4.3309e-07,1.5389e-06,-1.5132e-06,-8.3375e-07,9.3957e-08,-9.7430e-09,-1.7824e-06,5.2901e-07,3.5781e-06,-2.9408e-07,-8.3375e-07,7.6319e-07,-6.5813e-07,-3.4949e-06,4.7432e-06,1.2782e-07,-2.9408e-07,1.2790e-07,1.2728e-07,1.2790e-07,1.2253e-07,1.2813e-07,1.5815e-07,1.2813e-07,1.5319e-07,1.2815e-07,-2.4258e-06,1.2815e-07,3.9963e-06,-1.3513e-08,1.3513e-08,8.2084e-07,-8.2084e-07,1.3221e-06,-1.3221e-06,9.3514e-07,-9.3514e-07,4.8055e-06,-4.8055e-06,-2.2413e-06,2.2413e-06}
>>>> Re-trying (1/3).
Starting Function Value: 3.650858723258416
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.650858720853137 0.000250523211335 12.876852965635424 0.000038580783765
2 4 3.650858717148604 0.000217373529672 1.000000000000000 0.000036012023041
3 5 3.650858716791960 0.005805363054952 1.000000000000000 0.000172528938436
4 6 3.650858666350694 0.001004268367010 1.000000000000000 0.000059840494941
Gradient = {-3.4986e-06,-2.8095e-06,-4.5710e-06,-7.9261e-06,1.7456e-07,9.0204e-08,-9.0384e-06,-1.5403e-06,-4.8716e-06,-2.7769e-06,-4.8777e-07,1.7456e-07,2.2565e-06,-9.8688e-07,-1.5797e-06,-1.7568e-05,-2.6194e-07,-4.8777e-07,3.3736e-06,-5.5364e-06,1.7304e-06,-1.7680e-05,-2.5350e-07,-2.6194e-07,-5.8625e-06,-1.0850e-06,-4.8859e-06,-6.1660e-06,-3.7519e-07,-2.5350e-07,3.3144e-07,-1.2361e-05,-1.7895e-06,-1.0686e-06,-3.3649e-06,-3.7519e-07,-1.4293e-05,1.2376e-06,1.6420e-06,-3.3957e-06,-4.5400e-07,-3.3649e-06,-2.2481e-06,-7.2405e-06,-2.6054e-06,-4.4397e-06,-1.6404e-06,-4.5400e-07,-2.2808e-06,-5.0270e-06,-4.2827e-06,-3.8717e-06,-1.5255e-06,-1.6404e-06,-6.9912e-06,-2.4639e-06,-2.6815e-06,-4.0454e-06,-9.2051e-07,-1.5255e-06,-3.8884e-06,-4.0687e-06,-7.8898e-06,-1.4625e-06,-3.1054e-07,-9.2051e-07,-1.5520e-06,-6.3816e-06,-1.0003e-05,-1.6127e-07,-1.3152e-07,-3.1054e-07,1.2779e-07,1.2717e-07,1.2779e-07,1.2242e-07,1.2802e-07,1.5802e-07,1.2802e-07,1.5306e-07,1.2804e-07,-6.3968e-06,1.2804e-07,-1.1761e-05,-1.4446e-07,1.4446e-07,1.6903e-05,-1.6903e-05,1.8847e-05,-1.8847e-05,3.3048e-06,-3.3048e-06,-1.5966e-06,1.5966e-06,-1.0729e-05,1.0729e-05}
pCurr = {1.6749e-05,-5.5840e-05,2.8495e-05,5.3527e-05,1.2583e-05,1.2258e-05,3.4284e-05,-2.1008e-05,9.2976e-06,4.6531e-05,-1.3916e-05,1.2583e-05,7.0495e-05,-5.7231e-05,-4.4874e-05,1.1829e-04,-7.4233e-06,-1.3916e-05,1.0089e-04,-1.7820e-04,4.6842e-05,1.1074e-04,-7.5027e-06,-7.4233e-06,9.1842e-05,5.1465e-05,-1.1307e-04,5.4544e-05,-1.1932e-05,-7.5027e-06,9.0222e-05,1.2766e-04,-5.2990e-05,1.3351e-05,-1.0097e-04,-1.1932e-05,8.1073e-05,1.1008e-04,4.0890e-05,-5.3790e-05,-1.1942e-05,-1.0097e-04,8.6586e-05,-1.1054e-05,2.8850e-07,4.2617e-05,-4.1151e-05,-1.1942e-05,4.2298e-05,9.8923e-05,3.7458e-06,-4.2207e-05,3.7367e-06,-4.1151e-05,8.0014e-05,-7.5539e-06,4.9887e-05,-3.7548e-05,-2.3191e-05,3.7367e-06,6.3732e-06,-4.5054e-05,3.0422e-05,1.0761e-04,-8.3910e-06,-2.3191e-05,2.4619e-05,-6.7189e-06,-8.5239e-05,1.3999e-04,3.5132e-06,-8.3910e-06,3.5376e-06,3.5203e-06,3.5376e-06,3.3888e-06,3.5437e-06,4.3743e-06,3.5437e-06,4.2370e-06,3.5445e-06,-4.3670e-05,3.5445e-06,1.2205e-04,1.6056e-07,-1.6056e-07,-2.1211e-05,2.1211e-05,-2.1803e-05,2.1803e-05,-1.1497e-06,1.1497e-06,2.3193e-05,-2.3193e-05,6.6432e-05,-6.6432e-05}
grad*pCur = -9.846176529746443E-9
parameters = {-5.8680e-01,-9.7311e-01,-6.2628e-01,-4.4264e-02,-6.9715e-01,-8.8958e-01,2.9405e-01,-7.5827e-01,-3.9760e-01,-6.2961e-01,-1.6286e+00,-6.9715e-01,-1.6914e-01,-1.1869e-02,-3.4225e+00,2.5107e+00,-1.1396e+00,-1.6286e+00,-6.2100e-01,1.1324e-01,-3.2375e+00,2.4657e+00,-1.4419e+00,-1.1396e+00,-3.0218e-02,-1.1629e+00,1.3817e-01,-1.0223e-03,-1.3632e+00,-1.4419e+00,-6.5260e-01,8.9099e-01,-1.1264e+00,-8.5063e-01,-7.5918e-01,-1.3632e+00,6.2782e-01,-1.1166e+00,-9.2686e-01,-6.7279e-01,-1.0134e+00,-7.5918e-01,-7.2141e-01,-5.7467e-01,-9.8877e-01,9.5937e-02,-6.5870e-01,-1.0134e+00,-7.2820e-01,-4.9325e-01,-8.7450e-01,-9.6091e-01,-1.4547e-01,-6.5870e-01,-4.9063e-02,-1.1437e+00,-7.6261e-01,-7.3692e-01,-1.0232e+00,-1.4547e-01,-5.7768e-01,-7.0558e-01,-1.8930e-01,-3.4960e-01,-9.7180e-01,-1.0232e+00,-8.5840e-01,-1.4924e-01,-6.4034e-01,-6.0254e-01,-5.9485e-01,-9.7180e-01,6.3897e-02,6.3585e-02,6.3897e-02,6.1211e-02,6.4008e-02,7.9010e-02,6.4008e-02,7.6530e-02,6.4022e-02,-2.1586e+00,6.4022e-02,-1.4671e+00,9.6665e-02,-9.6665e-02,-1.1040e-02,1.1040e-02,6.2144e-01,-6.2144e-01,6.3352e-01,-6.3352e-01,9.0849e-01,-9.0849e-01,1.1023e+00,-1.1023e+00}
|grad|/|x| = 6.204759015027985E-6
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.8680e-01,-9.7311e-01,-6.2628e-01,-4.4264e-02,-6.9715e-01,-8.8958e-01,2.9405e-01,-7.5827e-01,-3.9760e-01,-6.2961e-01,-1.6286e+00,-6.9715e-01,-1.6914e-01,-1.1869e-02,-3.4225e+00,2.5107e+00,-1.1396e+00,-1.6286e+00,-6.2100e-01,1.1324e-01,-3.2375e+00,2.4657e+00,-1.4419e+00,-1.1396e+00,-3.0218e-02,-1.1629e+00,1.3817e-01,-1.0223e-03,-1.3632e+00,-1.4419e+00,-6.5260e-01,8.9099e-01,-1.1264e+00,-8.5063e-01,-7.5918e-01,-1.3632e+00,6.2782e-01,-1.1166e+00,-9.2686e-01,-6.7279e-01,-1.0134e+00,-7.5918e-01,-7.2141e-01,-5.7467e-01,-9.8877e-01,9.5937e-02,-6.5870e-01,-1.0134e+00,-7.2820e-01,-4.9325e-01,-8.7450e-01,-9.6091e-01,-1.4547e-01,-6.5870e-01,-4.9063e-02,-1.1437e+00,-7.6261e-01,-7.3692e-01,-1.0232e+00,-1.4547e-01,-5.7768e-01,-7.0558e-01,-1.8930e-01,-3.4960e-01,-9.7180e-01,-1.0232e+00,-8.5840e-01,-1.4924e-01,-6.4034e-01,-6.0254e-01,-5.9485e-01,-9.7180e-01,6.3897e-02,6.3585e-02,6.3897e-02,6.1211e-02,6.4008e-02,7.9010e-02,6.4008e-02,7.6530e-02,6.4022e-02,-2.1586e+00,6.4022e-02,-1.4671e+00,9.6665e-02,-9.6665e-02,-1.1040e-02,1.1040e-02,6.2144e-01,-6.2144e-01,6.3352e-01,-6.3352e-01,9.0849e-01,-9.0849e-01,1.1023e+00,-1.1023e+00}
> Gradient: {-3.4986e-06,-2.8095e-06,-4.5710e-06,-7.9261e-06,1.7456e-07,9.0204e-08,-9.0384e-06,-1.5403e-06,-4.8716e-06,-2.7769e-06,-4.8777e-07,1.7456e-07,2.2565e-06,-9.8688e-07,-1.5797e-06,-1.7568e-05,-2.6194e-07,-4.8777e-07,3.3736e-06,-5.5364e-06,1.7304e-06,-1.7680e-05,-2.5350e-07,-2.6194e-07,-5.8625e-06,-1.0850e-06,-4.8859e-06,-6.1660e-06,-3.7519e-07,-2.5350e-07,3.3144e-07,-1.2361e-05,-1.7895e-06,-1.0686e-06,-3.3649e-06,-3.7519e-07,-1.4293e-05,1.2376e-06,1.6420e-06,-3.3957e-06,-4.5400e-07,-3.3649e-06,-2.2481e-06,-7.2405e-06,-2.6054e-06,-4.4397e-06,-1.6404e-06,-4.5400e-07,-2.2808e-06,-5.0270e-06,-4.2827e-06,-3.8717e-06,-1.5255e-06,-1.6404e-06,-6.9912e-06,-2.4639e-06,-2.6815e-06,-4.0454e-06,-9.2051e-07,-1.5255e-06,-3.8884e-06,-4.0687e-06,-7.8898e-06,-1.4625e-06,-3.1054e-07,-9.2051e-07,-1.5520e-06,-6.3816e-06,-1.0003e-05,-1.6127e-07,-1.3152e-07,-3.1054e-07,1.2779e-07,1.2717e-07,1.2779e-07,1.2242e-07,1.2802e-07,1.5802e-07,1.2802e-07,1.5306e-07,1.2804e-07,-6.3968e-06,1.2804e-07,-1.1761e-05,-1.4446e-07,1.4446e-07,1.6903e-05,-1.6903e-05,1.8847e-05,-1.8847e-05,3.3048e-06,-3.3048e-06,-1.5966e-06,1.5966e-06,-1.0729e-05,1.0729e-05}
>>>> Re-trying (2/3).
Starting Function Value: 3.650858666350694
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.650858655861283 0.000295611364225 4.939988623377404 0.000062182763247
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.8679e-01,-9.7310e-01,-6.2626e-01,-4.4225e-02,-6.9715e-01,-8.8958e-01,2.9410e-01,-7.5826e-01,-3.9758e-01,-6.2960e-01,-1.6286e+00,-6.9715e-01,-1.6915e-01,-1.1864e-02,-3.4225e+00,2.5108e+00,-1.1396e+00,-1.6286e+00,-6.2102e-01,1.1327e-01,-3.2375e+00,2.4658e+00,-1.4419e+00,-1.1396e+00,-3.0189e-02,-1.1629e+00,1.3819e-01,-9.9179e-04,-1.3632e+00,-1.4419e+00,-6.5260e-01,8.9105e-01,-1.1264e+00,-8.5062e-01,-7.5916e-01,-1.3632e+00,6.2789e-01,-1.1166e+00,-9.2687e-01,-6.7278e-01,-1.0134e+00,-7.5916e-01,-7.2140e-01,-5.7463e-01,-9.8876e-01,9.5959e-02,-6.5869e-01,-1.0134e+00,-7.2819e-01,-4.9322e-01,-8.7448e-01,-9.6089e-01,-1.4547e-01,-6.5869e-01,-4.9028e-02,-1.1437e+00,-7.6259e-01,-7.3690e-01,-1.0232e+00,-1.4547e-01,-5.7766e-01,-7.0556e-01,-1.8926e-01,-3.4960e-01,-9.7180e-01,-1.0232e+00,-8.5839e-01,-1.4921e-01,-6.4029e-01,-6.0254e-01,-5.9485e-01,-9.7180e-01,6.3896e-02,6.3584e-02,6.3896e-02,6.1210e-02,6.4008e-02,7.9009e-02,6.4008e-02,7.6529e-02,6.4021e-02,-2.1586e+00,6.4021e-02,-1.4670e+00,9.6666e-02,-9.6666e-02,-1.1124e-02,1.1124e-02,6.2134e-01,-6.2134e-01,6.3351e-01,-6.3351e-01,9.0850e-01,-9.0850e-01,1.1024e+00,-1.1024e+00}
> Gradient: {-2.7633e-06,-2.3675e-06,-3.5815e-06,-6.4402e-06,1.8772e-07,1.2033e-07,-7.3378e-06,-1.1090e-06,-3.9028e-06,-2.1938e-06,-4.8873e-07,1.8772e-07,2.3677e-06,-9.1776e-07,-1.5763e-06,-1.4054e-05,-2.6263e-07,-4.8873e-07,3.4242e-06,-5.4413e-06,1.7315e-06,-1.4128e-05,-2.5547e-07,-2.6263e-07,-4.8846e-06,-6.7726e-07,-3.5719e-06,-5.1603e-06,-3.8249e-07,-2.5547e-07,6.8255e-07,-9.4279e-06,-1.6357e-06,-7.6939e-07,-3.3991e-06,-3.8249e-07,-1.1440e-05,1.5465e-06,1.7404e-06,-2.9165e-06,-4.6324e-07,-3.3991e-06,-1.7304e-06,-5.4770e-06,-2.1457e-06,-3.4903e-06,-1.6253e-06,-4.6324e-07,-1.8178e-06,-3.1245e-06,-3.6367e-06,-3.3719e-06,-1.3559e-06,-1.6253e-06,-5.1204e-06,-1.9504e-06,-2.0668e-06,-3.5215e-06,-9.1700e-07,-1.3559e-06,-3.2107e-06,-3.4211e-06,-6.0252e-06,-9.5758e-07,-3.1273e-07,-9.1700e-07,-1.2673e-06,-5.0953e-06,-8.2660e-06,2.1174e-07,-1.1485e-07,-3.1273e-07,1.2779e-07,1.2717e-07,1.2779e-07,1.2242e-07,1.2802e-07,1.5802e-07,1.2802e-07,1.5306e-07,1.2804e-07,-4.3030e-06,1.2804e-07,-1.0158e-05,1.9187e-07,-1.9187e-07,-2.2590e-05,2.2590e-05,-2.4165e-05,2.4165e-05,-2.8820e-06,2.8820e-06,-9.5809e-06,9.5809e-06,-8.2763e-06,8.2763e-06}
>>>> Re-trying (3/3).
After: gradient norm = 6.218233802008635E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0967,-0.0967}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6213,-0.6213}
Count Table 3:
---------------
h: {0.6335,-0.6335}
Count Table 4:
---------------
h: {0.9085,-0.9085}
Count Table 5:
---------------
h: {1.1024,-1.1024}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
Dinucleotide(d=1): {-0.2691,-0.4414,0.0083,-0.5357,0.6828,0.0000,-0.0065,-0.6207,-0.1889,-0.0277,-0.2994,0.0000,0.1556,0.4969,-0.1001,-0.1425,-0.7618,0.0000,0.0167,0.0648,-0.4358,-0.2617,-0.1663,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.2346,-0.4457,-0.0192,-0.0415,-0.3410,0.0000,-0.2142,-0.3762,-1.1626,0.6660,0.7491,0.0000,-0.3285,-0.2563,-0.5722,0.7152,-0.5043,0.0000,-0.3024,-0.2619,-0.2408,0.0080,0.0612,0.0000,0.8011,0.3815,0.2612,-1.3362,-1.1166,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-0.5578,-0.4918,0.1102,-0.1741,0.2727,0.0000,0.0540,0.3612,-1.5595,-0.2546,0.7970,0.0000,0.0466,0.3059,-0.8104,-0.0548,-0.4921,0.0000,0.3128,-0.3675,-1.6489,0.2050,-0.1056,0.0000,-0.8487,-0.6514,2.7568,-0.2381,-1.1397,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-0.1132,-0.3349,-0.8469,-0.1574,0.5667,0.0000,-1.7122,0.8435,-0.2304,0.4697,0.0810,0.0000,-0.8517,-0.1959,0.4216,-0.1629,0.1022,0.0000,1.4044,-1.2829,-0.1450,-1.1201,-0.9652,0.0000,-0.4556,-0.2176,0.1009,0.3979,-0.3255,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,1.8914,-0.7372,-1.2781,-0.2541,-0.1600,0.0000,-2.4074,0.9497,-0.6445,0.9941,1.3844,0.0000,1.0259,-0.7580,-0.2168,-0.2905,-1.3506,0.0000,0.2774,-0.3075,-0.5910,-0.3275,-0.1825,0.0000,1.1630,-1.1210,0.1901,-0.4242,-0.4773,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.3036,0.7750,-0.2660,-0.6482,0.0692,0.0000,-0.8169,0.0900,-2.2963,1.4876,-0.0058,0.0000,0.3758,-0.8472,2.3317,-2.2963,-0.5160,0.0000,0.1713,-0.4736,-0.8472,0.0900,-0.0894,0.0000,0.0286,0.1713,0.3758,-0.8169,-0.6525,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3659,-0.6525,-0.0894,-0.5160,-0.0058,-0.0061,0.0000,-0.4242,-0.3275,-0.2905,0.9941,-0.6482,0.0000,0.1901,-0.5910,-0.2168,-0.6445,-0.2660,0.0000,-1.1210,-0.3075,-0.7580,0.9497,0.7750,0.0000,1.1630,0.2774,1.0259,-2.4074,-0.3036,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2676,-0.4773,-0.1825,-1.3506,1.3844,0.0692,0.0000,0.3979,-1.1201,-0.1629,0.4697,-0.2541,0.0000,0.1009,-0.1450,0.4216,-0.2304,-1.2781,0.0000,-0.2176,-1.2829,-0.1959,0.8435,-0.7372,0.0000,-0.4556,1.4044,-0.8517,-1.7122,1.8914,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3736,-0.3255,-0.9652,0.1022,0.0810,-0.1600,0.0000,-0.2381,0.2050,-0.0548,-0.2546,-0.1574,0.0000,2.7568,-1.6489,-0.8104,-1.5595,-0.8469,0.0000,-0.6514,-0.3675,0.3059,0.3612,-0.3349,0.0000,-0.8487,0.3128,0.0466,0.0540,-0.1132,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5380,-1.1397,-0.1056,-0.4921,0.7970,0.5667,0.0000,-1.3362,0.0080,0.7152,0.6660,-0.1741,0.0000,0.2612,-0.2408,-0.5722,-1.1626,0.1102,0.0000,0.3815,-0.2619,-0.2563,-0.3762,-0.4918,0.0000,0.8011,-0.3024,-0.3285,-0.2142,-0.5578,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8856,-1.1166,0.0612,-0.5043,0.7491,0.2727,0.0000,-0.2617,-0.1425,-0.0277,-0.5357,-0.0415,0.0000,-0.4358,-0.1001,-0.1889,0.0083,-0.0192,0.0000,0.0648,0.4969,-0.6207,-0.4414,-0.4457,0.0000,0.0167,0.1556,-0.0065,-0.2691,-0.2346,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8408,-0.1663,-0.7618,-0.2994,0.6828,-0.3410,0.0000}
Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.5868,-0.9731,-0.6263,-0.0442,-0.6972,-0.8896,0.2941,-0.7583,-0.3976,-0.6296,-1.6286,-0.6972,-0.1692,-0.0119,-3.4225,2.5108,-1.1396,-1.6286,-0.6210,0.1133,-3.2375,2.4658,-1.4419,-1.1396,-0.0302,-1.1629,0.1382,-0.0010,-1.3632,-1.4419,-0.6526,0.8910,-1.1264,-0.8506,-0.7592,-1.3632,0.6279,-1.1166,-0.9269,-0.6728,-1.0134,-0.7592,-0.7214,-0.5746,-0.9888,0.0960,-0.6587,-1.0134,-0.7282,-0.4932,-0.8745,-0.9609,-0.1455,-0.6587,-0.0490,-1.1437,-0.7626,-0.7369,-1.0232,-0.1455,-0.5777,-0.7056,-0.1893,-0.3496,-0.9718,-1.0232,-0.8584,-0.1492,-0.6403,-0.6025,-0.5949,-0.9718}
Dinucleotide(d=1): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Activity(exp=0): {0.0639,0.0636}
Activity(exp=1): {0.0639,0.0612}
Activity(exp=2): {0.0640,0.0790}
Activity(exp=3): {0.0640,0.0765}
Activity(exp=4): {0.0640,-2.1586}
Activity(exp=5): {0.0640,-1.4670}
The Likelihood DID improve.
> No varitions possible for Binding mode 3.
> Unfreezing component (component3-3-f0).
>> Starting new optimization: component3-3-f0. (2021-05-21 20:11:23.065).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{},{},{},{},{}],"countTable":[{"h":[480,481]},{"h":[482,483]},{"h":[484,485]},{"h":[486,487]},{"h":[488,489]},{"h":[490,491]}],"bindingModeInteractions":[],"bindingModes":[{},{},{},{"mononucleotide":[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71],"activity":[[468,469],[470,471],[472,473],[474,475],[476,477],[478,479]],"dinucleotide":[[72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467]]}]}
Value and gradient before optimization:
=======================================
value = 3.650858657081483
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gradient norm = 0.001237056679387447
Starting Function Value: 3.650858657081483
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
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10 12 3.649245598088608 0.083787588962272 1.000000000000000 0.004112030182435
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186 197 3.644695977025840 0.032814818984971 1.000000000000000 0.000159651412499
187 199 3.644695901700281 0.001852554698562 0.061609126949583 0.000158178882219
188 200 3.644692844183378 0.101628146462847 1.000000000000000 0.000115812468389
189 201 3.644691338500867 0.050856025953321 1.000000000000000 0.000174380958539
190 202 3.644689427360334 0.101085721084040 1.000000000000000 0.000256161964952
191 203 3.644688504547627 0.040112012574588 1.000000000000000 0.000103378644508
192 204 3.644687810358481 0.021928339122150 1.000000000000000 0.000097990727738
193 205 3.644686833617537 0.037299833862798 1.000000000000000 0.000191087417179
194 206 3.644685760982070 0.047852842870551 1.000000000000000 0.000224229494581
195 207 3.644684503945870 0.070736079773559 1.000000000000000 0.000233025255589
196 209 3.644684042746690 0.041085013545570 0.247668403877886 0.000134864995647
197 210 3.644682589044987 0.127908819905043 1.000000000000000 0.000217012612116
198 211 3.644681789189540 0.020552741266382 1.000000000000000 0.000173386080932
199 212 3.644680465547785 0.036931693296607 1.000000000000000 0.000180662388043
200 213 3.644679467374917 0.069330010505293 1.000000000000000 0.000103755550611
201 214 3.644679098191050 0.064133914614068 1.000000000000000 0.000135806247953
202 215 3.644678069666866 0.057858909642108 1.000000000000000 0.000159397829775
203 216 3.644677409244397 0.061078796623988 1.000000000000000 0.000220928232022
204 217 3.644676440513263 0.061823111184574 1.000000000000000 0.000173062183479
205 218 3.644674899918714 0.109623050619804 1.000000000000000 0.000345646092166
206 219 3.644674469275323 0.074610886798679 1.000000000000000 0.000616994404066
207 220 3.644673610726241 0.038877825291288 1.000000000000000 0.000248324989097
208 221 3.644673322618186 0.012113315817488 1.000000000000000 0.000144676208161
209 222 3.644673105070057 0.012084313596504 1.000000000000000 0.000121009529322
210 223 3.644672521801442 0.034568300634482 1.000000000000000 0.000115958204694
211 224 3.644671148294995 0.082953161009621 1.000000000000000 0.000240726949452
212 226 3.644671039942529 0.004633825291002 0.069430027051285 0.000235513149555
213 227 3.644669128887429 0.135803167276072 1.000000000000000 0.000345361012305
214 229 3.644668851578381 0.022324936241797 0.210740593544555 0.000304869200628
215 230 3.644668270947177 0.046684440609063 1.000000000000000 0.000274531518383
216 231 3.644667474471827 0.034957082059763 1.000000000000000 0.000198970988036
217 232 3.644666916667992 0.027386567676320 1.000000000000000 0.000252423523230
218 233 3.644666221225335 0.075631054337139 1.000000000000000 0.000372301954157
219 234 3.644665681091147 0.019929145457289 1.000000000000000 0.000197489018677
220 235 3.644665468154121 0.010505676548677 1.000000000000000 0.000159764596682
221 236 3.644665004270972 0.024671176382592 1.000000000000000 0.000261867803523
222 237 3.644663512814546 0.023876552101724 1.000000000000000 0.000232050148980
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: 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> Gradient: {1.1209e-05,6.6763e-06,1.4157e-05,3.1808e-06,-1.3107e-06,-8.2685e-06,1.6225e-05,-7.9673e-06,1.9750e-06,1.1084e-05,5.6371e-06,-1.3107e-06,5.9124e-06,-6.8049e-06,5.4159e-06,1.5640e-05,-2.1862e-07,5.6371e-06,-4.4117e-06,1.4573e-05,9.1963e-06,6.6858e-06,-2.4315e-07,-2.1862e-07,-7.5640e-06,2.0029e-05,7.3360e-06,6.6326e-06,-6.0853e-07,-2.4315e-07,9.0520e-06,6.2399e-06,4.1839e-06,5.9060e-06,8.0866e-07,-6.0853e-07,1.7367e-05,9.0329e-06,3.8036e-08,-3.2962e-06,1.6317e-06,8.0866e-07,9.0585e-07,1.9125e-05,1.2655e-06,1.1932e-05,-9.2791e-06,1.6317e-06,1.2775e-05,1.7617e-05,2.8624e-06,-6.0506e-06,7.6575e-06,-9.2791e-06,-1.5526e-06,6.3075e-06,1.3122e-05,-9.1151e-08,1.3861e-07,7.6575e-06,6.4961e-06,9.1093e-06,8.2964e-06,3.2289e-06,-1.6257e-06,1.3861e-07,1.3472e-06,-5.1515e-07,1.2289e-05,1.1142e-05,3.0066e-06,-1.6257e-06,-6.9281e-06,-1.2536e-06,9.6166e-06,1.4677e-06,9.1324e-06,0.0000e+00,1.3095e-05,9.6370e-08,7.0545e-06,8.2514e-07,-1.3025e-05,0.0000e+00,1.1331e-05,-1.7571e-06,6.7973e-07,6.6125e-07,4.1230e-06,0.0000e+00,-1.1157e-06,-2.0000e-06,-1.2278e-05,6.9846e-06,1.1652e-05,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-3.2945e-07,-5.7085e-07,-1.9857e-06,-2.5380e-06,2.0318e-06,-3.9536e-06,0.0000e+00,-7.4787e-07,-9.7958e-06,5.2119e-06,1.9988e-05,1.1551e-06,0.0000e+00,-2.5410e-06,-1.3218e-06,5.9480e-06,-7.8764e-06,-1.1088e-06,0.0000e+00,1.3729e-05,-6.7563e-06,1.0695e-06,-7.0032e-06,1.4955e-06,0.0000e+00,-7.1012e-07,6.8406e-06,-1.4926e-06,7.0607e-06,2.7182e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,7.9294e-06,-3.5795e-06,4.2452e-06,-5.0372e-07,-6.3154e-08,-4.2818e-07,0.0000e+00,-3.0262e-06,5.1660e-06,2.9885e-06,-1.1256e-07,1.1347e-06,0.0000e+00,-4.1823e-07,-5.5814e-06,2.7401e-06,-3.3980e-06,-1.3062e-07,0.0000e+00,3.8120e-06,4.3304e-06,4.9839e-07,1.2229e-06,3.6945e-07,0.0000e+00,-3.9402e-06,1.1167e-05,6.7641e-06,-2.0463e-06,1.6140e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.3854e-06,3.5179e-08,-6.6828e-07,7.6198e-07,7.5490e-06,2.5146e-07,0.0000e+00,-8.1031e-07,5.5813e-06,1.1864e-06,-9.2231e-06,-2.7182e-07,0.0000e+00,1.0199e-06,1.6149e-05,-1.5351e-06,-4.2867e-07,-7.9157e-07,0.0000e+00,9.0245e-07,-4.3567e-06,3.7792e-06,1.2810e-05,6.1806e-07,0.0000e+00,-9.0322e-06,3.3751e-06,3.4346e-06,3.6974e-06,1.7401e-06,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.7864e-06,3.9854e-07,9.1668e-07,2.7650e-07,-2.2170e-07,1.5391e-08,0.0000e+00,-6.8352e-08,-7.9336e-06,4.2110e-07,1.0408e-06,-9.8149e-07,0.0000e+00,9.0882e-06,3.9847e-06,1.7291e-06,5.6871e-06,1.1766e-06,0.0000e+00,9.1988e-08,2.0063e-06,5.0922e-06,-8.5509e-07,8.0616e-07,0.0000e+00,1.0938e-06,5.4406e-06,-1.0895e-06,7.6528e-07,4.2393e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.3102e-06,-2.3509e-07,1.4878e-06,-3.8351e-07,4.6520e-07,4.5202e-07,0.0000e+00,7.7581e-06,-4.4553e-07,-2.5102e-06,4.9657e-06,2.0252e-07,0.0000e+00,1.0603e-06,3.1264e-06,3.4354e-06,-3.7036e-06,1.0672e-06,0.0000e+00,1.7868e-06,3.0989e-06,-2.4817e-06,1.9718e-06,1.3935e-06,0.0000e+00,6.3309e-06,4.2867e-06,2.9088e-06,-6.3048e-06,-1.1824e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.8772e-06,-4.5308e-07,5.3809e-07,-9.6157e-09,7.2162e-07,5.1318e-07,0.0000e+00,-1.0465e-06,1.2336e-05,-1.3033e-06,1.1078e-05,-4.5812e-06,0.0000e+00,2.1918e-06,6.2346e-06,5.5993e-07,1.0609e-06,5.5727e-07,0.0000e+00,-4.2258e-07,-7.4413e-07,1.6016e-06,1.0195e-06,-1.1175e-07,0.0000e+00,-1.0051e-06,1.5514e-06,9.1900e-07,-1.3113e-06,-2.5033e-06,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,3.0581e-06,2.2036e-06,5.5614e-07,8.7997e-07,-4.9537e-08,-1.7130e-06,0.0000e+00,2.7407e-06,-1.5811e-06,3.7635e-06,-2.3035e-06,-6.9831e-07,0.0000e+00,8.7745e-06,8.8565e-06,1.1341e-06,2.4812e-06,-1.3120e-06,0.0000e+00,-6.6958e-06,3.1005e-06,1.9606e-06,-3.6403e-06,7.9323e-06,0.0000e+00,8.1546e-06,7.5882e-06,-4.8129e-06,-1.2273e-06,2.0948e-06,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-8.3520e-06,8.2590e-07,3.4679e-07,2.0481e-06,-8.0901e-09,-1.5452e-07,0.0000e+00,2.4882e-06,1.3002e-06,3.9922e-06,4.8858e-06,1.1336e-06,0.0000e+00,9.7442e-06,5.2543e-06,1.0778e-06,1.9151e-06,3.1960e-07,0.0000e+00,-1.2216e-05,3.5568e-06,8.9517e-06,2.1017e-06,1.6994e-06,0.0000e+00,-1.0662e-06,-2.3537e-06,1.7196e-06,-2.8679e-06,-1.2998e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,7.8623e-06,-4.3349e-07,1.5980e-07,-1.5460e-06,-5.0886e-06,-1.4438e-06,0.0000e+00,4.4063e-06,1.7130e-06,1.6677e-07,-6.7760e-06,-9.9360e-07,0.0000e+00,2.6304e-06,6.0422e-06,-2.4500e-06,1.4764e-06,2.1829e-07,0.0000e+00,3.0029e-06,1.9269e-06,3.9457e-06,4.9053e-06,4.1456e-07,0.0000e+00,-1.6257e-06,4.8537e-07,4.3804e-06,-1.7026e-06,-5.9135e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.5788e-06,-1.1048e-06,-6.4969e-08,2.5199e-06,5.8178e-06,6.9425e-07,0.0000e+00,2.1143e-06,-1.2761e-06,5.6908e-06,3.0357e-06,-2.2556e-06,0.0000e+00,-6.2160e-07,9.3262e-08,8.1117e-07,7.2060e-06,2.6136e-06,0.0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>>>> Re-trying (1/3).
Starting Function Value: 3.6446648174404723
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.644664623137278 0.000564591358513 2.430928290715172 0.000114679344420
Gradient = 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pCurr = {-1.3537e-05,-2.8887e-06,-1.5433e-05,1.5909e-05,6.8656e-06,2.3823e-05,-1.1029e-05,3.2452e-05,1.7876e-05,-1.8270e-05,-1.3156e-05,6.8656e-06,-4.8651e-06,3.1456e-05,-5.5693e-06,6.4070e-06,6.1990e-07,-1.3156e-05,1.5125e-05,2.6227e-06,-1.7286e-05,1.3075e-05,7.3676e-07,6.1990e-07,2.5579e-05,-4.8302e-06,-5.1859e-06,-3.0801e-06,1.6728e-06,7.3676e-07,8.5244e-06,1.4805e-05,-7.3108e-06,-3.2035e-06,4.0464e-07,1.6728e-06,-1.6879e-05,-1.4107e-05,3.2346e-05,1.6424e-05,-3.2959e-06,4.0464e-07,5.0214e-06,-3.4584e-05,3.7691e-05,-1.4871e-05,2.4931e-05,-3.2959e-06,-2.4276e-05,-2.8608e-05,3.5489e-05,2.0396e-05,-1.3040e-05,2.4931e-05,4.1368e-05,-1.1526e-05,-1.5645e-05,1.3412e-05,3.2328e-07,-1.3040e-05,-4.1483e-06,-1.3576e-05,2.3871e-05,3.6243e-06,4.6435e-06,3.2328e-07,3.2676e-06,2.3222e-05,9.6746e-06,-1.9817e-05,-6.2531e-06,4.6435e-06,2.2322e-05,5.7292e-06,-1.8720e-05,-2.2568e-06,-2.2678e-05,-0.0000e+00,-2.6093e-05,3.1366e-06,-1.7075e-05,8.7731e-07,3.2838e-05,-0.0000e+00,-2.0872e-05,6.0880e-06,7.3461e-06,-4.9348e-08,-1.0152e-05,-0.0000e+00,1.1737e-05,9.3952e-06,3.7736e-05,-1.4272e-05,-2.8843e-05,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,4.4097e-06,2.9136e-06,5.4322e-06,7.1879e-06,-4.7871e-06,9.9423e-06,-0.0000e+00,4.9268e-06,2.9313e-05,-9.9365e-06,-3.1429e-05,-2.8665e-06,-0.0000e+00,7.5943e-06,6.9946e-06,-1.4683e-05,2.7082e-05,2.7931e-06,-0.0000e+00,-3.1138e-05,1.8820e-05,1.1129e-06,3.1406e-05,-3.7256e-06,-0.0000e+00,3.4427e-06,-1.3329e-05,4.1178e-06,-1.4049e-05,-6.7103e-07,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-1.8893e-05,9.7130e-06,-1.0384e-05,1.7635e-06,2.2417e-06,1.0755e-06,-0.0000e+00,8.5973e-06,-5.3101e-06,-6.6672e-06,7.4643e-07,-2.8274e-06,-0.0000e+00,1.2014e-06,2.6478e-05,-6.8402e-06,1.0239e-05,3.3635e-07,-0.0000e+00,-8.5696e-06,-4.4310e-06,-7.6481e-07,-2.9417e-06,-9.1858e-07,-0.0000e+00,1.1758e-05,-1.6230e-05,-1.2536e-05,3.2565e-05,-3.0453e-07,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-3.3946e-06,-5.0197e-08,2.5152e-06,-1.8824e-06,-1.8847e-05,-6.2847e-07,-0.0000e+00,2.1930e-06,-1.1676e-05,-2.8988e-06,2.4630e-05,6.8865e-07,-0.0000e+00,-2.4005e-06,-3.6555e-06,3.8540e-06,3.2307e-06,1.9930e-06,-0.0000e+00,-2.1910e-06,1.2166e-05,-8.3476e-06,-2.8779e-05,-1.5398e-06,-0.0000e+00,2.8864e-05,-3.4960e-06,3.3781e-06,-2.7526e-06,-4.2329e-06,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-4.3426e-06,-9.9299e-07,-2.2656e-06,-6.8487e-07,5.8713e-07,-3.8276e-08,-0.0000e+00,7.5781e-07,2.4187e-05,-5.4637e-07,-1.8540e-06,2.9281e-06,-0.0000e+00,4.5637e-06,8.5733e-07,-4.1764e-06,-7.3201e-06,-2.8511e-06,-0.0000e+00,8.9234e-07,3.7385e-06,-1.1358e-05,2.5000e-06,-4.7173e-07,-0.0000e+00,-5.9877e-07,-7.1881e-06,3.8311e-06,1.6215e-06,-7.4922e-07,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-3.1293e-06,6.1042e-07,-3.6511e-06,9.7104e-07,-1.1473e-06,-1.1257e-06,-0.0000e+00,-1.7457e-05,2.0211e-06,3.2985e-05,-1.0999e-05,-3.2435e-07,-0.0000e+00,1.9750e-05,-3.7101e-06,-7.9577e-06,1.2237e-05,-2.3750e-06,-0.0000e+00,-3.5899e-06,-7.0224e-06,6.9809e-06,-4.1899e-06,-3.4575e-06,-0.0000e+00,-1.4564e-05,-8.0054e-06,-2.9889e-06,1.8786e-05,5.7271e-07,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-2.2697e-06,1.1937e-06,-1.3238e-06,6.1994e-08,-1.7795e-06,-1.2818e-06,-0.0000e+00,4.6631e-06,-2.4638e-05,1.2944e-05,-1.9867e-05,1.2230e-05,-0.0000e+00,-2.7179e-06,-1.2065e-05,-1.3479e-06,-6.7867e-07,-1.2315e-06,-0.0000e+00,1.2436e-06,1.9661e-06,2.5340e-05,1.2834e-07,4.0313e-07,-0.0000e+00,4.5412e-06,-8.3233e-07,-8.1244e-07,4.5453e-06,6.6123e-06,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-6.8659e-06,-5.2499e-06,-1.0396e-06,-1.9158e-06,1.3394e-06,4.5963e-06,-0.0000e+00,-5.4194e-06,4.5467e-06,-6.2041e-06,7.0571e-06,2.4998e-06,-0.0000e+00,-1.8852e-05,-1.4348e-05,-2.6775e-06,-4.7195e-06,3.9892e-06,-0.0000e+00,1.7874e-05,-6.8541e-06,3.1748e-05,1.0093e-05,-1.8653e-05,-0.0000e+00,-1.8440e-05,-1.2918e-05,1.4293e-05,4.3984e-06,-1.8658e-06,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,2.2610e-05,-2.0032e-06,-7.7182e-07,-4.7502e-06,1.8211e-07,4.7725e-07,-0.0000e+00,-5.8521e-06,-1.9218e-06,-6.4260e-06,-9.9836e-06,-2.6574e-06,-0.0000e+00,-1.0651e-05,-1.2562e-05,-2.5331e-06,-3.8265e-06,-7.7339e-07,-0.0000e+00,5.1303e-05,-7.6086e-06,-1.0430e-05,3.1676e-06,-4.0230e-06,-0.0000e+00,5.0006e-06,6.5810e-06,-3.1267e-06,8.0830e-06,4.7301e-07,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-1.3552e-05,1.3939e-06,-4.3353e-08,4.1847e-06,1.3376e-05,3.6996e-06,-0.0000e+00,-9.3429e-06,-1.9192e-06,2.9443e-05,2.0402e-05,2.6115e-06,-0.0000e+00,-5.4860e-06,-1.3203e-05,6.2710e-06,-2.6469e-06,-4.8958e-07,-0.0000e+00,-4.9262e-07,-3.3449e-06,-4.6724e-06,-8.8885e-06,-9.3320e-07,-0.0000e+00,5.6740e-06,5.5114e-07,-2.7861e-06,5.7977e-06,1.5794e-06,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-0.0000e+00,-3.2812e-06,3.4643e-06,1.8547e-06,-5.0512e-06,-1.2272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grad*pCur = -2.6705323172008533E-8
parameters = {-5.5268e-01,-6.7606e-01,-5.6600e-01,-1.0396e-01,-4.4113e-01,-6.7143e-01,1.4680e-01,-4.7993e-01,-1.7980e-01,-1.0232e+00,-1.0340e+00,-4.4113e-01,-2.4003e-01,-6.5465e-01,-1.5047e+00,1.4517e+00,-1.0604e+00,-1.0340e+00,-6.2262e-01,1.3041e-01,-1.2205e+00,7.8092e-01,-1.0499e+00,-1.0604e+00,-8.4328e-01,1.0729e-01,-7.4002e-01,6.7529e-01,-1.1915e+00,-1.0499e+00,-4.3296e-01,6.0610e-01,-1.1252e+00,-5.4467e-01,-3.5389e-01,-1.1915e+00,1.6290e-01,-8.3432e-01,-8.0939e-01,-4.0859e-01,-7.9881e-01,-3.5389e-01,-6.3031e-01,-9.0857e-01,-7.9844e-01,3.6126e-01,-2.6724e-01,-7.9881e-01,-5.7000e-01,-1.3843e+00,-2.2521e-01,-6.5549e-01,6.0080e-02,-2.6724e-01,-1.3476e-01,-1.0734e+00,-5.6964e-01,-5.0492e-01,-8.1948e-01,6.0080e-02,-5.1846e-01,-5.4021e-01,-1.5376e-01,-1.5591e-01,-8.2342e-01,-8.1948e-01,-6.9313e-01,-2.3985e-02,-4.7964e-01,-4.2294e-01,-5.6814e-01,-8.2342e-01,-6.1786e-02,1.1074e-01,1.9898e-01,-1.9202e-01,-1.9564e-01,0.0000e+00,-2.8387e-01,-3.1569e-02,8.2098e-02,-8.8719e-02,3.3084e-01,0.0000e+00,1.7498e-01,-3.4471e-01,1.4957e-01,-1.5829e-01,5.3186e-02,0.0000e+00,-3.6755e-02,1.8813e-01,-2.4120e-01,2.0372e-01,-1.8674e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,4.9496e-02,1.4726e-01,1.3110e-01,-8.9454e-02,-3.4479e-01,1.1051e-01,0.0000e+00,-1.4477e-01,-2.9972e-01,2.7551e-01,2.8646e-01,-1.7765e-01,0.0000e+00,-7.5597e-01,2.9758e-01,7.0483e-01,-3.1211e-01,1.1937e-01,0.0000e+00,1.2765e-01,-3.3240e-01,4.1810e-01,1.0022e-01,-2.1358e-01,0.0000e+00,2.5725e-01,4.3582e-01,-9.2559e-01,-3.1462e-01,-3.2958e-02,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.1214e-01,3.9484e-01,-7.4757e-01,4.3106e-01,-7.5254e-02,4.6424e-02,0.0000e+00,5.2585e-01,-1.6211e-01,6.3988e-01,-9.5538e-01,-1.6923e-01,0.0000e+00,-1.1439e+00,5.0512e-01,-5.1452e-01,4.8362e-01,2.3387e-02,0.0000e+00,1.1467e+00,8.1813e-01,6.9023e-01,-1.7320e+00,-1.9220e-02,0.0000e+00,-7.3705e-01,-1.7248e+00,2.6170e-01,1.7458e+00,1.3906e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-2.5840e-01,2.2807e-02,6.1438e-01,-1.9368e-02,-4.9653e-01,-9.1483e-03,0.0000e+00,-5.2420e-02,7.3991e-01,-1.3662e+00,4.6293e-01,3.0201e-02,0.0000e+00,-8.0780e-01,1.7331e+00,-1.1373e+00,7.0609e-02,1.9209e-01,0.0000e+00,-7.7856e-01,2.2219e-01,5.6641e-01,1.1424e+00,-9.4534e-02,0.0000e+00,8.9638e-01,-1.6947e+00,1.1559e+00,-9.5397e-01,-3.5809e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-3.5153e-02,-7.9636e-02,-7.4838e-02,-5.6124e-02,-4.5997e-02,-1.8049e-03,0.0000e+00,-6.5479e-01,1.7065e-01,-4.2087e-01,-3.2552e-01,4.0850e-01,0.0000e+00,7.9084e-01,-6.6341e-01,7.8950e-01,1.2968e+00,-1.2880e+00,0.0000e+00,-5.9940e-01,4.3242e-01,-3.4920e-01,-1.8083e+00,1.4872e+00,0.0000e+00,3.8649e-01,1.0412e-01,-4.0869e-01,9.6110e-01,-3.6704e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-2.3214e-01,1.0317e-01,-6.4766e-02,5.6788e-02,-7.0103e-02,-6.0241e-02,0.0000e+00,-1.8290e-01,-3.5533e-01,3.1239e-01,-3.0288e-02,2.8243e-01,0.0000e+00,9.1299e-01,-7.4221e-01,7.2417e-01,-5.7660e-01,-3.3934e-01,0.0000e+00,-1.8509e-01,5.2649e-01,-4.4643e-01,2.6107e-01,-4.8851e-01,0.0000e+00,-9.5233e-01,5.7632e-01,-7.5922e-01,6.2159e-01,5.6761e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.8038e-01,1.2833e-01,-5.3775e-02,1.1992e-02,-2.1088e-01,-1.0780e-01,0.0000e+00,-1.3456e-01,2.4750e-01,-3.9417e-01,1.7127e-01,-1.6901e-01,0.0000e+00,2.0487e-01,4.8040e-01,-2.3107e-01,-1.0043e-01,-4.0227e-01,0.0000e+00,-6.2487e-01,-1.5129e+00,1.1446e+00,8.3546e-01,5.5635e-04,0.0000e+00,8.0103e-01,5.8922e-01,-2.3876e-01,-9.0677e-01,-1.7983e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-8.5611e-02,-3.6908e-01,-3.0843e-01,-3.8320e-01,2.9420e-01,9.4688e-01,0.0000e+00,4.6255e-01,-6.0921e-01,-1.1738e-01,3.9372e-01,-2.5229e-01,0.0000e+00,3.8037e-01,-3.7422e-01,-4.5110e-01,2.2353e-01,-2.8275e-01,0.0000e+00,-1.2725e-01,-5.7326e-01,6.7074e-01,-3.2057e-01,2.4775e-01,0.0000e+00,-1.8456e-01,1.0218e+00,-6.3753e-01,-5.7870e-01,6.7271e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.9632e-01,-5.8864e-01,-5.0227e-01,9.2550e-01,3.0276e-01,-2.2296e-01,0.0000e+00,-1.3577e+00,4.0286e-01,2.9136e-01,4.2006e-01,1.8591e-01,0.0000e+00,1.7989e+00,-1.0929e+00,-7.8300e-02,-8.7216e-02,-1.5776e+00,0.0000e+00,-2.2801e-02,4.6323e-02,2.9380e-01,-2.9606e-01,3.6896e-01,0.0000e+00,3.6771e-01,-2.9933e-02,-2.7094e-01,-2.7487e-01,2.2877e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.6245e-01,-8.8632e-01,4.0514e-01,-2.6888e-01,2.5177e-01,6.9460e-01,0.0000e+00,-2.9971e-01,-1.9607e-01,5.1772e-01,2.4936e-01,-3.7155e-01,0.0000e+00,-7.5360e-02,8.7570e-02,1.4176e-02,-3.5713e-02,-2.5915e-01,0.0000e+00,3.9715e-01,-7.4971e-02,-1.3604e-02,-4.5259e-01,1.1107e-01,0.0000e+00,4.2563e-01,1.7145e-02,-3.1086e-01,-1.9974e-02,-9.8258e-02,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-9.9381e-02,-5.5964e-01,1.2267e-01,-2.2799e-01,3.4904e-01,4.7838e-01,0.0000e+00,-6.2621e-02,5.8726e-02,2.9417e-01,-2.5989e-01,-1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|grad|/|x| = 9.777470020442758E-6
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.5268e-01,-6.7606e-01,-5.6600e-01,-1.0396e-01,-4.4113e-01,-6.7143e-01,1.4680e-01,-4.7993e-01,-1.7980e-01,-1.0232e+00,-1.0340e+00,-4.4113e-01,-2.4003e-01,-6.5465e-01,-1.5047e+00,1.4517e+00,-1.0604e+00,-1.0340e+00,-6.2262e-01,1.3041e-01,-1.2205e+00,7.8092e-01,-1.0499e+00,-1.0604e+00,-8.4328e-01,1.0729e-01,-7.4002e-01,6.7529e-01,-1.1915e+00,-1.0499e+00,-4.3296e-01,6.0610e-01,-1.1252e+00,-5.4467e-01,-3.5389e-01,-1.1915e+00,1.6290e-01,-8.3432e-01,-8.0939e-01,-4.0859e-01,-7.9881e-01,-3.5389e-01,-6.3031e-01,-9.0857e-01,-7.9844e-01,3.6126e-01,-2.6724e-01,-7.9881e-01,-5.7000e-01,-1.3843e+00,-2.2521e-01,-6.5549e-01,6.0080e-02,-2.6724e-01,-1.3476e-01,-1.0734e+00,-5.6964e-01,-5.0492e-01,-8.1948e-01,6.0080e-02,-5.1846e-01,-5.4021e-01,-1.5376e-01,-1.5591e-01,-8.2342e-01,-8.1948e-01,-6.9313e-01,-2.3985e-02,-4.7964e-01,-4.2294e-01,-5.6814e-01,-8.2342e-01,-6.1786e-02,1.1074e-01,1.9898e-01,-1.9202e-01,-1.9564e-01,0.0000e+00,-2.8387e-01,-3.1569e-02,8.2098e-02,-8.8719e-02,3.3084e-01,0.0000e+00,1.7498e-01,-3.4471e-01,1.4957e-01,-1.5829e-01,5.3186e-02,0.0000e+00,-3.6755e-02,1.8813e-01,-2.4120e-01,2.0372e-01,-1.8674e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,4.9496e-02,1.4726e-01,1.3110e-01,-8.9454e-02,-3.4479e-01,1.1051e-01,0.0000e+00,-1.4477e-01,-2.9972e-01,2.7551e-01,2.8646e-01,-1.7765e-01,0.0000e+00,-7.5597e-01,2.9758e-01,7.0483e-01,-3.1211e-01,1.1937e-01,0.0000e+00,1.2765e-01,-3.3240e-01,4.1810e-01,1.0022e-01,-2.1358e-01,0.0000e+00,2.5725e-01,4.3582e-01,-9.2559e-01,-3.1462e-01,-3.2958e-02,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.1214e-01,3.9484e-01,-7.4757e-01,4.3106e-01,-7.5254e-02,4.6424e-02,0.0000e+00,5.2585e-01,-1.6211e-01,6.3988e-01,-9.5538e-01,-1.6923e-01,0.0000e+00,-1.1439e+00,5.0512e-01,-5.1452e-01,4.8362e-01,2.3387e-02,0.0000e+00,1.1467e+00,8.1813e-01,6.9023e-01,-1.7320e+00,-1.9220e-02,0.0000e+00,-7.3705e-01,-1.7248e+00,2.6170e-01,1.7458e+00,1.3906e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-2.5840e-01,2.2807e-02,6.1438e-01,-1.9368e-02,-4.9653e-01,-9.1483e-03,0.0000e+00,-5.2420e-02,7.3991e-01,-1.3662e+00,4.6293e-01,3.0201e-02,0.0000e+00,-8.0780e-01,1.7331e+00,-1.1373e+00,7.0609e-02,1.9209e-01,0.0000e+00,-7.7856e-01,2.2219e-01,5.6641e-01,1.1424e+00,-9.4534e-02,0.0000e+00,8.9638e-01,-1.6947e+00,1.1559e+00,-9.5397e-01,-3.5809e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-3.5153e-02,-7.9636e-02,-7.4838e-02,-5.6124e-02,-4.5997e-02,-1.8049e-03,0.0000e+00,-6.5479e-01,1.7065e-01,-4.2087e-01,-3.2552e-01,4.0850e-01,0.0000e+00,7.9084e-01,-6.6341e-01,7.8950e-01,1.2968e+00,-1.2880e+00,0.0000e+00,-5.9940e-01,4.3242e-01,-3.4920e-01,-1.8083e+00,1.4872e+00,0.0000e+00,3.8649e-01,1.0412e-01,-4.0869e-01,9.6110e-01,-3.6704e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-2.3214e-01,1.0317e-01,-6.4766e-02,5.6788e-02,-7.0103e-02,-6.0241e-02,0.0000e+00,-1.8290e-01,-3.5533e-01,3.1239e-01,-3.0288e-02,2.8243e-01,0.0000e+00,9.1299e-01,-7.4221e-01,7.2417e-01,-5.7660e-01,-3.3934e-01,0.0000e+00,-1.8509e-01,5.2649e-01,-4.4643e-01,2.6107e-01,-4.8851e-01,0.0000e+00,-9.5233e-01,5.7632e-01,-7.5922e-01,6.2159e-01,5.6761e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.8038e-01,1.2833e-01,-5.3775e-02,1.1992e-02,-2.1088e-01,-1.0780e-01,0.0000e+00,-1.3456e-01,2.4750e-01,-3.9417e-01,1.7127e-01,-1.6901e-01,0.0000e+00,2.0487e-01,4.8040e-01,-2.3107e-01,-1.0043e-01,-4.0227e-01,0.0000e+00,-6.2487e-01,-1.5129e+00,1.1446e+00,8.3546e-01,5.5635e-04,0.0000e+00,8.0103e-01,5.8922e-01,-2.3876e-01,-9.0677e-01,-1.7983e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-8.5611e-02,-3.6908e-01,-3.0843e-01,-3.8320e-01,2.9420e-01,9.4688e-01,0.0000e+00,4.6255e-01,-6.0921e-01,-1.1738e-01,3.9372e-01,-2.5229e-01,0.0000e+00,3.8037e-01,-3.7422e-01,-4.5110e-01,2.2353e-01,-2.8275e-01,0.0000e+00,-1.2725e-01,-5.7326e-01,6.7074e-01,-3.2057e-01,2.4775e-01,0.0000e+00,-1.8456e-01,1.0218e+00,-6.3753e-01,-5.7870e-01,6.7271e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.9632e-01,-5.8864e-01,-5.0227e-01,9.2550e-01,3.0276e-01,-2.2296e-01,0.0000e+00,-1.3577e+00,4.0286e-01,2.9136e-01,4.2006e-01,1.8591e-01,0.0000e+00,1.7989e+00,-1.0929e+00,-7.8300e-02,-8.7216e-02,-1.5776e+00,0.0000e+00,-2.2801e-02,4.6323e-02,2.9380e-01,-2.9606e-01,3.6896e-01,0.0000e+00,3.6771e-01,-2.9933e-02,-2.7094e-01,-2.7487e-01,2.2877e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.6245e-01,-8.8632e-01,4.0514e-01,-2.6888e-01,2.5177e-01,6.9460e-01,0.0000e+00,-2.9971e-01,-1.9607e-01,5.1772e-01,2.4936e-01,-3.7155e-01,0.0000e+00,-7.5360e-02,8.7570e-02,1.4176e-02,-3.5713e-02,-2.5915e-01,0.0000e+00,3.9715e-01,-7.4971e-02,-1.3604e-02,-4.5259e-01,1.1107e-01,0.0000e+00,4.2563e-01,1.7145e-02,-3.1086e-01,-1.9974e-02,-9.8258e-02,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-9.9381e-02,-5.5964e-01,1.2267e-01,-2.2799e-01,3.4904e-01,4.7838e-01,0.0000e+00,-6.2621e-02,5.8726e-02,2.9417e-01,-2.5989e-01,-1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> Gradient: {3.9583e-06,-2.2626e-07,4.1688e-06,-8.7411e-06,-3.1016e-06,-9.8312e-06,1.4507e-06,-1.4216e-05,-9.4212e-06,6.3537e-06,5.1614e-06,-3.1016e-06,9.5163e-07,-1.4009e-05,1.4280e-06,-7.1114e-06,-2.5496e-07,5.1614e-06,-6.4512e-06,-4.9532e-06,6.3344e-06,-8.2026e-06,-3.0720e-07,-2.5496e-07,-1.0884e-05,-2.5948e-06,7.5552e-07,-1.2035e-07,-6.8334e-07,-3.0720e-07,-6.5208e-06,-8.9549e-06,2.6054e-06,1.2331e-07,-4.0446e-07,-6.8334e-07,4.0876e-06,4.7875e-06,-1.6164e-05,-7.3790e-06,1.2382e-06,-4.0446e-07,-2.7345e-06,1.2491e-05,-1.9141e-05,4.4434e-06,-1.0132e-05,1.2382e-06,8.9306e-06,9.8835e-06,-1.8440e-05,-8.6740e-06,4.5975e-06,-1.0132e-05,-2.0273e-05,4.1798e-06,4.5334e-06,-6.6763e-06,-1.9616e-07,4.5975e-06,4.4774e-07,4.5031e-06,-1.3997e-05,-2.6178e-06,-1.9128e-06,-1.9616e-07,-1.9689e-06,-1.1470e-05,-7.9044e-06,7.1116e-06,2.3714e-06,-1.9128e-06,-9.4167e-06,-2.5480e-06,6.9454e-06,7.6015e-07,9.0434e-06,0.0000e+00,9.7582e-06,-1.5906e-06,6.7649e-06,-6.4446e-07,-1.3145e-05,0.0000e+00,7.5911e-06,-2.6013e-06,-3.8387e-06,-1.4068e-07,4.0398e-06,0.0000e+00,-5.5832e-06,-4.1922e-06,-1.5778e-05,5.3819e-06,1.1492e-05,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-2.1203e-06,-1.3126e-06,-2.2167e-06,-2.9555e-06,1.8830e-06,-3.9773e-06,0.0000e+00,-2.2738e-06,-1.2191e-05,3.6597e-06,1.0699e-05,1.1429e-06,0.0000e+00,-3.1578e-06,-3.1629e-06,5.8468e-06,-1.1557e-05,-1.1178e-06,0.0000e+00,1.2119e-05,-7.7104e-06,-8.2292e-07,-1.3935e-05,1.4869e-06,0.0000e+00,-1.5419e-06,4.9468e-06,-1.6835e-06,5.2514e-06,2.6719e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,7.4538e-06,-3.9563e-06,4.1250e-06,-7.5486e-07,-1.1040e-06,-4.3013e-07,0.0000e+00,-3.5373e-06,1.3605e-06,2.5828e-06,-3.4468e-07,1.1285e-06,0.0000e+00,-4.9547e-07,-1.1829e-05,2.7313e-06,-4.2644e-06,-1.3533e-07,0.0000e+00,3.3271e-06,1.1308e-06,2.5740e-07,1.1635e-06,3.6642e-07,0.0000e+00,-4.8876e-06,5.3142e-06,4.5701e-06,-1.5754e-05,1.1174e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.3491e-06,1.6274e-08,-1.0892e-06,7.4966e-07,7.5260e-06,2.5102e-07,0.0000e+00,-8.9269e-07,4.4363e-06,1.1512e-06,-9.9959e-06,-2.7599e-07,0.0000e+00,9.4394e-07,-2.2115e-06,-1.5411e-06,-1.5064e-06,-7.9748e-07,0.0000e+00,8.6866e-07,-4.9873e-06,3.2244e-06,1.1171e-05,6.1452e-07,0.0000e+00,-1.2158e-05,9.0215e-07,-2.5464e-06,4.5013e-07,1.6791e-06,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.7223e-06,3.9631e-07,9.0237e-07,2.7293e-07,-2.3782e-07,1.5269e-08,0.0000e+00,-3.6141e-07,-1.0097e-05,1.6760e-07,6.6578e-07,-1.2171e-06,0.0000e+00,-4.5515e-06,-1.4244e-06,1.6538e-06,2.2343e-06,1.1298e-06,0.0000e+00,-4.6871e-07,-2.3691e-06,4.3997e-06,-1.0348e-06,3.3924e-08,0.0000e+00,2.5539e-08,2.2297e-06,-1.6410e-06,-1.0013e-06,2.6819e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.2354e-06,-2.4610e-07,1.4516e-06,-3.8911e-07,4.5672e-07,4.4923e-07,0.0000e+00,6.7794e-06,-8.9803e-07,-1.5847e-05,4.2519e-06,1.1135e-07,0.0000e+00,-1.0130e-05,1.0713e-06,3.1161e-06,-5.1856e-06,9.1935e-07,0.0000e+00,1.3463e-06,2.7326e-06,-2.8661e-06,1.5997e-06,1.3785e-06,0.0000e+00,5.6913e-06,2.9266e-06,7.6565e-07,-7.8064e-06,-2.5650e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,6.6408e-07,-4.8294e-07,5.2662e-07,-2.8562e-08,7.0837e-07,5.1188e-07,0.0000e+00,-2.0674e-06,9.2209e-06,-6.1392e-06,7.1526e-06,-4.9631e-06,0.0000e+00,8.0941e-07,4.4670e-06,5.3329e-07,7.3662e-08,4.7576e-07,0.0000e+00,-5.1543e-07,-7.9591e-07,-1.3056e-05,-3.1879e-07,-1.7341e-07,0.0000e+00,-2.0169e-06,2.7827e-08,1.7602e-07,-1.9423e-06,-2.6767e-06,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,2.6646e-06,2.0711e-06,3.8018e-07,7.3681e-07,-6.5671e-07,-1.8673e-06,0.0000e+00,2.0215e-06,-1.8756e-06,2.1577e-06,-2.9488e-06,-1.0740e-06,0.0000e+00,7.2221e-06,4.9517e-06,1.0538e-06,1.7368e-06,-1.6645e-06,0.0000e+00,-7.2533e-06,2.6482e-06,-1.6346e-05,-4.1307e-06,7.3328e-06,0.0000e+00,7.1712e-06,4.5547e-06,-5.9352e-06,-1.8899e-06,4.0771e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-9.2048e-06,7.9404e-07,2.9878e-07,1.8604e-06,-8.8945e-08,-1.9974e-07,0.0000e+00,2.3008e-06,6.3480e-07,2.2114e-06,3.7648e-06,1.0438e-06,0.0000e+00,2.8828e-06,4.9604e-06,9.9575e-07,1.4324e-06,3.0637e-07,0.0000e+00,-2.2569e-05,2.9111e-06,2.9714e-06,-2.1079e-06,1.5844e-06,0.0000e+00,-2.2310e-06,-2.6984e-06,1.1317e-06,-3.3201e-06,-2.0376e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,4.8023e-06,-5.8780e-07,-1.8317e-08,-1.7036e-06,-5.4083e-06,-1.4868e-06,0.0000e+00,3.5647e-06,5.3031e-07,-1.4747e-05,-8.4960e-06,-1.0559e-06,0.0000e+00,2.0824e-06,5.0838e-06,-2.5194e-06,9.5289e-07,1.8994e-07,0.0000e+00,-5.0467e-07,1.1890e-06,1.3471e-06,3.2129e-06,3.6244e-07,0.0000e+00,-2.4274e-06,-3.9663e-07,2.9592e-07,-2.4700e-06,-6.4101e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.2440e-06,-1.4541e-06,-9.1032e-07,1.8927e-06,4.6745e-06,5.9956e-07,0.0000e+00,1.6762e-06,-2.5375e-06,1.9876e-06,2.5016e-06,-2.3671e-06,0.0000e+00,-1.2668e-06,-2.6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>>>> Re-trying (2/3).
Starting Function Value: 3.6446646231372775
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.644664603025750 0.000300967568158 2.624427002785188 0.000122250265361
2 4 3.644664577446253 0.000331374850695 1.000000000000000 0.000140857584793
3 5 3.644664183823900 0.007140827640517 1.000000000000000 0.000374126193630
4 6 3.644663924657832 0.006578008314790 1.000000000000000 0.000383418418979
5 8 3.644663773927796 0.005905650813011 0.482654641649748 0.000311637238730
6 9 3.644663645787660 0.002988060608237 1.000000000000000 0.000125771018209
7 10 3.644663553606807 0.001469917098327 1.000000000000000 0.000138248591601
8 11 3.644663485080455 0.001615297140536 1.000000000000000 0.000183295402086
9 13 3.644663458499835 0.000570654717039 0.140797584106024 0.000186422591886
10 14 3.644662983158001 0.014372061346431 1.000000000000000 0.000277055437606
11 16 3.644662917274031 0.003337544876181 0.260621974331777 0.000303760327564
12 17 3.644662342783295 0.007098947216493 1.000000000000000 0.000185749603277
stepAlphaMin = 1.0E-20
>>>> Exception caugth. Parameters reverted.
> Parameter: {-5.5681e-01,-6.7587e-01,-5.6864e-01,-1.0711e-01,-4.4019e-01,-6.6536e-01,1.4966e-01,-4.7670e-01,-1.8153e-01,-1.0275e+00,-1.0377e+00,-4.4019e-01,-2.4172e-01,-6.5066e-01,-1.5067e+00,1.4522e+00,-1.0602e+00,-1.0377e+00,-6.1813e-01,1.2720e-01,-1.2231e+00,7.7918e-01,-1.0497e+00,-1.0602e+00,-8.4243e-01,1.0358e-01,-7.4181e-01,6.7657e-01,-1.1910e+00,-1.0497e+00,-4.3485e-01,6.0757e-01,-1.1273e+00,-5.4463e-01,-3.5461e-01,-1.1910e+00,1.6060e-01,-8.3746e-01,-8.0802e-01,-4.0540e-01,-7.9991e-01,-3.5461e-01,-6.3082e-01,-9.1608e-01,-7.9710e-01,3.6137e-01,-2.6226e-01,-7.9991e-01,-5.7528e-01,-1.3884e+00,-2.2558e-01,-6.5227e-01,5.8945e-02,-2.6226e-01,-1.2960e-01,-1.0773e+00,-5.7383e-01,-5.0337e-01,-8.1961e-01,5.8945e-02,-5.1987e-01,-5.4408e-01,-1.5283e-01,-1.5546e-01,-8.2214e-01,-8.1961e-01,-6.9263e-01,-2.1449e-02,-4.8050e-01,-4.2730e-01,-5.6996e-01,-8.2214e-01,-5.4710e-02,1.1129e-01,1.9355e-01,-1.9224e-01,-2.0236e-01,0.0000e+00,-2.8937e-01,-3.1492e-02,7.6687e-02,-8.8566e-02,3.4068e-01,0.0000e+00,1.7329e-01,-3.4355e-01,1.4937e-01,-1.5786e-01,5.0179e-02,0.0000e+00,-3.4093e-02,1.8750e-01,-2.3397e-01,1.9978e-01,-1.9525e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,4.9704e-02,1.4787e-01,1.3238e-01,-8.7780e-02,-3.4620e-01,1.1347e-01,0.0000e+00,-1.4386e-01,-2.9310e-01,2.7269e-01,2.8578e-01,-1.7851e-01,0.0000e+00,-7.5365e-01,2.9714e-01,7.0022e-01,-3.0777e-01,1.2020e-01,0.0000e+00,1.1893e-01,-3.2743e-01,4.1831e-01,1.0273e-01,-2.1470e-01,0.0000e+00,2.5825e-01,4.3174e-01,-9.2426e-01,-3.1766e-01,-3.3159e-02,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.0671e-01,3.9747e-01,-7.5067e-01,4.3136e-01,-7.5205e-02,4.6744e-02,0.0000e+00,5.2848e-01,-1.6422e-01,6.3798e-01,-9.5502e-01,-1.7008e-01,0.0000e+00,-1.1436e+00,5.0816e-01,-5.1657e-01,4.8617e-01,2.3485e-02,0.0000e+00,1.1441e+00,8.1656e-01,6.8998e-01,-1.7328e+00,-1.9494e-02,0.0000e+00,-7.3354e-01,-1.7282e+00,2.6044e-01,1.7503e+00,1.3897e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-2.5942e-01,2.2779e-02,6.1534e-01,-1.9933e-02,-5.0214e-01,-9.3356e-03,0.0000e+00,-5.1782e-02,7.3639e-01,-1.3671e+00,4.7032e-01,3.0405e-02,0.0000e+00,-8.0852e-01,1.7282e+00,-1.1362e+00,7.1389e-02,1.9268e-01,0.0000e+00,-7.7921e-01,2.2609e-01,5.6409e-01,1.1359e+00,-9.4992e-02,0.0000e+00,8.9823e-01,-1.6944e+00,1.1565e+00,-9.5453e-01,-3.5937e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-3.6455e-02,-7.9933e-02,-7.5513e-02,-5.6328e-02,-4.5829e-02,-1.8165e-03,0.0000e+00,-6.5475e-01,1.7201e-01,-4.2111e-01,-3.2631e-01,4.0893e-01,0.0000e+00,7.8791e-01,-6.6164e-01,7.8823e-01,1.2951e+00,-1.2889e+00,0.0000e+00,-5.9908e-01,4.3330e-01,-3.5223e-01,-1.8076e+00,1.4867e+00,0.0000e+00,3.8631e-01,1.0359e-01,-4.0770e-01,9.6239e-01,-3.6732e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-2.3309e-01,1.0335e-01,-6.5851e-02,5.7075e-02,-7.0446e-02,-6.0579e-02,0.0000e+00,-1.8682e-01,-3.5486e-01,3.1641e-01,-3.3327e-02,2.8234e-01,0.0000e+00,9.1936e-01,-7.4302e-01,7.2000e-01,-5.7477e-01,-3.4014e-01,0.0000e+00,-1.8580e-01,5.2447e-01,-4.4463e-01,2.5977e-01,-4.8954e-01,0.0000e+00,-9.5603e-01,5.7477e-01,-7.6050e-01,6.2711e-01,5.6776e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.7886e-01,1.2868e-01,-5.4175e-02,1.2013e-02,-2.1142e-01,-1.0819e-01,0.0000e+00,-1.3439e-01,2.4271e-01,-3.9168e-01,1.6948e-01,-1.6674e-01,0.0000e+00,2.0412e-01,4.7736e-01,-2.3154e-01,-1.0004e-01,-4.0272e-01,0.0000e+00,-6.2461e-01,-1.5123e+00,1.1442e+00,8.3539e-01,6.2567e-04,0.0000e+00,8.0168e-01,5.8863e-01,-2.3929e-01,-9.0553e-01,-1.7812e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-8.7772e-02,-3.7069e-01,-3.0870e-01,-3.8395e-01,2.9464e-01,9.4757e-01,0.0000e+00,4.6097e-01,-6.0813e-01,-1.2004e-01,3.9492e-01,-2.5161e-01,0.0000e+00,3.7615e-01,-3.7697e-01,-4.5194e-01,2.2171e-01,-2.8123e-01,0.0000e+00,-1.2227e-01,-5.7561e-01,6.7158e-01,-3.1827e-01,2.4228e-01,0.0000e+00,-1.8919e-01,1.0215e+00,-6.3465e-01,-5.7820e-01,6.7453e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,2.0061e-01,-5.8924e-01,-5.0250e-01,9.2398e-01,3.0279e-01,-2.2281e-01,0.0000e+00,-1.3596e+00,4.0259e-01,2.9049e-01,4.1779e-01,1.8513e-01,0.0000e+00,1.7998e+00,-1.0964e+00,-7.8869e-02,-8.8369e-02,-1.5779e+00,0.0000e+00,-1.6008e-02,4.3548e-02,2.9036e-01,-2.9665e-01,3.6767e-01,0.0000e+00,3.6709e-01,-2.8129e-02,-2.7200e-01,-2.7289e-01,2.2888e-01,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.6116e-01,-8.8641e-01,4.0479e-01,-2.6792e-01,2.5457e-01,6.9559e-01,0.0000e+00,-3.0257e-01,-1.9714e-01,5.2074e-01,2.5463e-01,-3.7081e-01,0.0000e+00,-7.6956e-02,8.3538e-02,1.5810e-02,-3.6738e-02,-2.5929e-01,0.0000e+00,3.9749e-01,-7.5930e-02,-1.4784e-02,-4.5551e-01,1.1079e-01,0.0000e+00,4.2654e-01,1.6984e-02,-3.1241e-01,-1.8805e-02,-9.7851e-02,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-1.0058e-01,-5.5845e-01,1.2427e-01,-2.2919e-01,3.4662e-01,4.7791e-01,0.0000e+00,-6.4169e-02,5.9547e-02,2.9278e-01,-2.6151e-01,-1.4059e-01,0.0000e+00,-4.2340e-01,3.2980e-02,-5.2391e-01,3.9532e-01,4.7073e-01,0.0000e+00,3.3333e-01,2.3263e-02,-1.0204e-01,-1.9078e-01,-8.3609e-02,0.0000e+00,-2.1187e-01,-6.0907e-02,1.3056e-01,2.5311e-01,-2.0687e-02,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,-1.3925e-01,2.7668e-01,2.8520e-02,1.7205e-01,-2.0002e-01,-3.7781e-01,0.0000e+00,4.4901e-02,4.4681e-02,4.4901e-02,4.3013e-02,4.4979e-02,5.5520e-02,4.4979e-02,5.3778e-02,4.4988e-02,-1.8416e+00,4.4988e-02,-1.0378e+00,9.6755e-02,-9.6755e-02,-1.1130e-02,1.1130e-02,6.2148e-01,-6.2148e-01,6.3336e-01,-6.3336e-01,1.0466e+00,-1.0466e+00,1.3621e+00,-1.3621e+00}
> Gradient: {-3.0958e-06,-7.6107e-06,-2.2312e-06,3.0261e-06,1.5588e-06,-1.7327e-06,1.6388e-05,5.0023e-06,-2.5166e-05,-1.0761e-05,2.8919e-06,1.5588e-06,-1.0485e-05,-5.9494e-06,-1.0126e-05,1.3821e-05,-2.9995e-07,2.8919e-06,-3.7494e-06,-3.2161e-05,-2.6694e-07,2.6593e-05,-2.6270e-07,-2.9995e-07,1.1884e-05,-3.2155e-05,4.2557e-06,6.7035e-06,-5.7203e-07,-2.6270e-07,-2.0522e-05,1.7009e-05,-5.9212e-07,-6.2595e-06,7.8968e-07,-5.7203e-07,1.8573e-05,-1.0554e-05,-2.0219e-05,7.5267e-08,1.1884e-06,7.8968e-07,-3.5914e-07,-5.6290e-06,-2.0600e-05,1.0811e-05,4.4421e-06,1.1884e-06,-1.3318e-05,1.4115e-05,-1.8328e-05,2.9793e-06,-3.7598e-08,4.4421e-06,1.4438e-05,-1.3418e-06,-1.9381e-05,-4.5471e-06,7.2189e-07,-3.7598e-08,-2.2327e-06,-1.5743e-06,-1.2441e-05,6.4060e-06,-9.6559e-07,7.2189e-07,-1.6715e-06,6.4628e-06,-1.2678e-05,-3.2593e-06,2.0262e-06,-9.6559e-07,-5.1372e-07,1.2413e-06,-1.0694e-05,-7.3658e-07,8.4317e-06,0.0000e+00,4.3866e-06,2.7028e-06,3.0679e-06,-3.1038e-06,-1.3297e-05,0.0000e+00,4.9781e-06,5.8806e-07,-6.3771e-06,-4.1342e-06,3.5941e-06,0.0000e+00,3.9657e-06,2.0231e-06,-9.6899e-06,-3.6071e-06,1.0396e-05,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,2.5385e-06,3.1584e-06,-4.8738e-07,-9.1410e-07,1.7055e-06,-3.9449e-06,0.0000e+00,-1.8186e-06,-3.6309e-06,7.1568e-08,2.0223e-05,1.1304e-06,0.0000e+00,-3.7912e-06,2.0348e-06,4.8764e-06,4.0794e-06,-1.1315e-06,0.0000e+00,1.6781e-06,-7.4905e-06,-7.5126e-06,-1.2759e-05,1.4768e-06,0.0000e+00,-3.4861e-06,-7.9496e-07,-2.5186e-06,-3.3393e-06,2.6284e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,5.1808e-06,-2.8294e-06,3.9489e-06,-2.3289e-07,2.0889e-06,-4.3690e-07,0.0000e+00,-3.4922e-06,-8.7577e-06,1.8438e-06,-9.5342e-07,1.1123e-06,0.0000e+00,-3.3703e-07,-5.9754e-06,2.7293e-06,-2.2135e-06,-1.3604e-07,0.0000e+00,3.2583e-06,-1.0035e-05,4.5375e-08,1.0544e-06,3.6075e-07,0.0000e+00,-2.3774e-06,-4.3245e-06,-1.0832e-06,1.7898e-05,1.7972e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.3017e-06,7.1611e-08,-3.2271e-06,7.4785e-07,7.3414e-06,2.4704e-07,0.0000e+00,-9.3355e-07,3.6317e-06,1.2208e-06,-6.5180e-06,-2.7754e-07,0.0000e+00,8.0563e-07,-2.9687e-05,-1.5770e-06,-1.0785e-06,-7.8335e-07,0.0000e+00,8.7643e-07,-5.4728e-06,3.8670e-06,4.4093e-06,6.0323e-07,0.0000e+00,1.0776e-05,1.3668e-07,2.8839e-07,1.0140e-05,1.7859e-06,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.7638e-06,4.0188e-07,8.6993e-07,2.6238e-07,-2.4810e-07,1.5599e-08,0.0000e+00,6.7582e-08,9.5388e-06,5.0746e-08,2.1770e-06,9.2026e-08,0.0000e+00,-1.9458e-05,-9.3581e-06,1.3678e-06,-4.2258e-06,1.1534e-06,0.0000e+00,-5.3549e-07,4.2935e-06,1.3792e-06,-5.3144e-07,-5.4427e-07,0.0000e+00,5.4387e-07,9.8389e-06,-1.4240e-06,-2.9568e-06,7.0293e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.3438e-06,-2.2223e-07,1.4432e-06,-3.8287e-07,4.7310e-07,4.5254e-07,0.0000e+00,5.2389e-07,-1.0186e-06,-2.2027e-05,3.0529e-06,-1.3558e-07,0.0000e+00,1.5167e-05,-8.4410e-06,5.7922e-06,2.1172e-06,1.1214e-06,0.0000e+00,-2.3421e-07,1.2388e-06,-2.1983e-06,8.1882e-07,1.3659e-06,0.0000e+00,2.6232e-06,-1.3094e-06,-4.3072e-07,-5.6895e-06,-2.5760e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.8566e-06,-3.8943e-07,5.4568e-07,-5.2324e-08,7.2132e-07,5.1857e-07,0.0000e+00,4.2097e-06,-1.7805e-06,-2.3872e-06,1.3557e-05,4.0910e-06,0.0000e+00,-4.9100e-06,-4.2422e-06,5.8804e-07,-1.2695e-06,8.4901e-07,0.0000e+00,-3.8125e-07,-7.9228e-07,-1.8197e-05,4.8876e-07,-3.4772e-08,0.0000e+00,1.3328e-07,2.2731e-06,-5.7420e-08,-2.5549e-07,-1.0727e-06,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,2.6127e-06,1.6030e-06,-2.7954e-07,8.4283e-07,-1.8450e-06,1.5353e-06,0.0000e+00,-5.0557e-07,-7.3889e-08,-9.2561e-07,2.3620e-06,-2.0215e-07,0.0000e+00,-6.0939e-06,2.7425e-06,2.4939e-07,1.7113e-06,-3.4308e-06,0.0000e+00,-6.5539e-06,4.0415e-06,-2.0525e-05,-2.1310e-06,5.9580e-06,0.0000e+00,8.1013e-08,7.7473e-06,2.2182e-06,2.4599e-06,-1.8304e-06,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,5.3678e-06,7.7826e-07,3.5076e-07,1.8840e-06,-7.2452e-08,-3.2783e-07,0.0000e+00,2.5343e-06,-4.0274e-06,-1.0263e-05,-1.2830e-06,7.4486e-07,0.0000e+00,9.3257e-06,3.3995e-06,1.7952e-07,1.5615e-06,3.4194e-07,0.0000e+00,-7.5005e-06,1.5949e-06,-8.7571e-06,-4.2367e-06,1.8001e-06,0.0000e+00,7.5122e-06,-2.2981e-06,6.6157e-07,-1.5756e-06,2.9693e-08,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,1.6684e-07,2.6354e-06,1.5967e-06,-1.2989e-07,2.0223e-06,-7.5666e-07,0.0000e+00,4.7257e-06,3.4736e-06,2.0774e-06,4.9572e-06,-7.2687e-07,0.0000e+00,8.7790e-07,8.5044e-07,-2.0638e-06,5.1618e-07,8.4877e-08,0.0000e+00,-6.6691e-06,-2.0963e-06,-9.8949e-06,6.7381e-08,2.8406e-07,0.0000e+00,8.1062e-07,1.8090e-07,-4.3031e-06,7.7724e-08,-2.7768e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,2.1599e-06,-1.1659e-06,-2.9914e-06,2.0094e-06,1.2789e-06,1.0358e-06,0.0000e+00,2.6090e-06,5.1172e-07,-3.2009e-06,9.8027e-07,-2.3209e-06,0.0000e+00,-2.6084e-06,2.2161e-07,3.9008e-07,-4.4392e-07,1.8580e-06,0.0000e+00,-1.3526e-06,-4.4591e-07,-1.0538e-05,-2.8442e-06,3.0056e-06,0.0000e+00,4.7455e-07,5.4003e-06,1.5300e-06,-2.1702e-07,-2.9047e-07,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,0.0000e+00,4.0020e-07,4.1238e-07,9.8479e-07,4.0339e-08,1.1243e-07,6.1000e-07,0.0000e+00,8.9801e-08,8.9362e-08,8.9801e-08,8.6026e-08,8.9958e-08,1.1104e-07,8.9958e-08,1.0756e-07,8.9976e-08,2.8643e-07,8.9976e-08,-1.0103e-05,4.1063e-05,-4.1063e-05,-2.5485e-05,2.5485e-05,3.9199e-05,-3.9199e-05,-6.4333e-05,6.4333e-05,1.4018e-05,-1.4018e-05,3.1624e-05,-3.1624e-05}
>>>> Re-trying (3/3).
After: gradient norm = 1.856629972213115E-4
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.0968,-0.0968}
Count Table 1:
---------------
h: {-0.0111,0.0111}
Count Table 2:
---------------
h: {0.6215,-0.6215}
Count Table 3:
---------------
h: {0.6334,-0.6334}
Count Table 4:
---------------
h: {1.0466,-1.0466}
Count Table 5:
---------------
h: {1.3621,-1.3621}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,-0.0213}
Activity(exp=1): {-0.0000,-0.1842}
Activity(exp=2): {-0.0000,1.0347}
Activity(exp=3): {-0.0000,0.8647}
Activity(exp=4): {-0.0000,1.1203}
Activity(exp=5): {-0.0000,1.2392}
Binding mode 1:
---------------
Mononucleotide: {-0.5550,-1.1432,-0.3520,-0.7824,-0.8408,-1.0820,-0.3379,-0.9462,-0.7358,-1.0091,-0.8856,-0.8408,-0.6018,-1.0047,-1.6042,-0.1211,-0.5380,-0.8856,-0.5484,-0.6866,-2.1088,-0.4999,-0.3736,-0.5380,0.2763,-1.5901,-1.1310,-0.6695,-1.2675,-0.3736,-0.2446,-0.4619,-1.5282,-0.6963,-0.5568,-1.2675,-0.6963,-1.5282,-0.4619,-0.2446,-1.2675,-0.5568,-0.6695,-1.1310,-1.5901,0.2763,-0.3736,-1.2675,-0.4999,-2.1088,-0.6866,-0.5484,-0.5380,-0.3736,-0.1211,-1.6042,-1.0047,-0.6018,-0.8856,-0.5380,-1.0091,-0.7358,-0.9462,-0.3379,-0.8408,-0.8856,-0.7824,-0.3520,-1.1432,-0.5550,-1.0820,-0.8408}
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Activity(exp=0): {0.0000,-0.0828}
Activity(exp=1): {0.0000,0.1863}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.2413}
Activity(exp=5): {0.0000,-2.6625}
Binding mode 2:
---------------
Mononucleotide: {-0.5984,-0.9551,-0.3981,-0.5071,-0.7090,-0.7009,-0.0624,-0.5831,-0.6349,-0.9498,-0.9294,-0.7090,-0.9170,-1.0238,-1.5682,0.5906,-0.0314,-0.9294,-0.9541,-0.7740,-1.0864,-0.6529,-0.3803,-0.0314,0.4438,-1.5284,-0.6401,-0.3747,-1.3993,-0.3803,-0.9842,0.0752,-1.1872,-0.7588,0.3753,-1.3993,-0.7588,-1.1872,0.0752,-0.9842,-1.3993,0.3753,-0.3747,-0.6401,-1.5284,0.4438,-0.3803,-1.3993,-0.6529,-1.0864,-0.7740,-0.9541,-0.0314,-0.3803,0.5906,-1.5682,-1.0238,-0.9170,-0.9294,-0.0314,-0.9498,-0.6349,-0.5831,-0.0624,-0.7090,-0.9294,-0.5071,-0.3981,-0.9551,-0.5984,-0.7009,-0.7090}
Dinucleotide(d=1): {-0.2852,-0.3383,-0.0383,0.0498,0.0811,0.0000,-0.3078,-0.3191,-0.1561,-0.1274,0.0661,0.0000,0.0152,-0.1218,-0.2809,0.0148,0.0335,0.0000,0.3188,0.3951,0.0916,-0.5135,-0.7601,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,0.1855,-0.1103,-0.2157,-0.2625,-0.2322,0.0000,-0.2209,-0.2777,-0.5658,0.6876,0.3033,0.0000,0.0680,-0.0832,0.0068,-0.2664,-0.2195,0.0000,-0.3138,-0.3114,-0.7560,0.4028,0.3790,0.0000,0.6446,0.0643,0.2799,-1.1290,-0.6986,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.9810,-0.3039,-0.3688,0.7699,0.2345,0.0000,0.1428,0.1217,-0.6904,-0.6643,0.2873,0.0000,-0.1265,0.2385,-0.1869,-0.5364,-0.3008,0.0000,0.0898,-0.0847,-1.0657,-0.8714,0.5281,0.0000,-0.4294,-1.2464,1.8672,2.4404,-2.1670,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-0.4838,0.3747,-0.9897,-1.0987,1.3858,0.0000,-0.6360,0.2941,-0.5768,-0.1106,0.2221,0.0000,-0.3309,0.4657,-0.6164,-0.2217,0.1071,0.0000,0.5207,-0.7074,-0.6066,0.2330,-0.5051,0.0000,0.2102,-1.7707,2.0090,0.1803,-1.3591,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,0.6555,0.3694,-0.8723,-0.4507,0.2967,0.0000,-0.3775,0.6762,-0.0434,0.2502,-0.0859,0.0000,-0.0010,-0.6903,0.1604,-0.1939,-0.6240,0.0000,-0.6939,0.8055,-0.2242,-0.8455,0.2949,0.0000,-0.1959,0.7481,-0.3599,-0.7802,0.2182,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.3776,-1.4645,-0.6259,0.8811,0.5652,0.0000,0.1383,0.4446,-0.3554,-0.6957,-0.2508,0.0000,1.3873,-0.7695,0.2601,-0.3554,-0.4439,0.0000,-1.1108,0.5989,-0.7695,0.4446,-0.3538,0.0000,-0.7480,-1.1108,1.3873,0.1383,-0.1841,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3065,-0.1841,-0.3538,-0.4439,-0.2508,-0.0041,0.0000,-0.7802,-0.8455,-0.1939,0.2502,0.8811,0.0000,-0.3599,-0.2242,0.1604,-0.0434,-0.6259,0.0000,0.7481,0.8055,-0.6903,0.6762,-1.4645,0.0000,-0.1959,-0.6939,-0.0010,-0.3775,0.3776,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.2383,0.2182,0.2949,-0.6240,-0.0859,0.5652,0.0000,0.1803,0.2330,-0.2217,-0.1106,-0.4507,0.0000,2.0090,-0.6066,-0.6164,-0.5768,-0.8723,0.0000,-1.7707,-0.7074,0.4657,0.2941,0.3694,0.0000,0.2102,0.5207,-0.3309,-0.6360,0.6555,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2665,-1.3591,-0.5051,0.1071,0.2221,0.2967,0.0000,2.4404,-0.8714,-0.5364,-0.6643,-1.0987,0.0000,1.8672,-1.0657,-0.1869,-0.6904,-0.9897,0.0000,-1.2464,-0.0847,0.2385,0.1217,0.3747,0.0000,-0.4294,0.0898,-0.1265,0.1428,-0.4838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0014,-2.1670,0.5281,-0.3008,0.2873,1.3858,0.0000,-1.1290,0.4028,-0.2664,0.6876,0.7699,0.0000,0.2799,-0.7560,0.0068,-0.5658,-0.3688,0.0000,0.0643,-0.3114,-0.0832,-0.2777,-0.3039,0.0000,0.6446,-0.3138,0.0680,-0.2209,-0.9810,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8117,-0.6986,0.3790,-0.2195,0.3033,0.2345,0.0000,-0.5135,0.0148,-0.1274,0.0498,-0.2625,0.0000,0.0916,-0.2809,-0.1561,-0.0383,-0.2157,0.0000,0.3951,-0.1218,-0.3191,-0.3383,-0.1103,0.0000,0.3188,0.0152,-0.3078,-0.2852,0.1855,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6493,-0.7601,0.0335,0.0661,0.0811,-0.2322,0.0000}
Activity(exp=0): {0.0199,0.0239}
Activity(exp=1): {0.0199,0.0246}
Activity(exp=2): {0.0199,-2.0682}
Activity(exp=3): {0.0199,-1.7003}
Activity(exp=4): {0.0199,-0.5432}
Activity(exp=5): {0.0199,-0.2725}
Binding mode 3:
---------------
Mononucleotide: {-0.5568,-0.6759,-0.5686,-0.1071,-0.4402,-0.6654,0.1497,-0.4767,-0.1815,-1.0275,-1.0377,-0.4402,-0.2417,-0.6507,-1.5067,1.4522,-1.0602,-1.0377,-0.6181,0.1272,-1.2231,0.7792,-1.0497,-1.0602,-0.8424,0.1036,-0.7418,0.6766,-1.1910,-1.0497,-0.4348,0.6076,-1.1273,-0.5446,-0.3546,-1.1910,0.1606,-0.8375,-0.8080,-0.4054,-0.7999,-0.3546,-0.6308,-0.9161,-0.7971,0.3614,-0.2623,-0.7999,-0.5753,-1.3884,-0.2256,-0.6523,0.0589,-0.2623,-0.1296,-1.0773,-0.5738,-0.5034,-0.8196,0.0589,-0.5199,-0.5441,-0.1528,-0.1555,-0.8221,-0.8196,-0.6926,-0.0214,-0.4805,-0.4273,-0.5700,-0.8221}
Dinucleotide(d=1): {-0.0547,0.1113,0.1935,-0.1922,-0.2024,0.0000,-0.2894,-0.0315,0.0767,-0.0886,0.3407,0.0000,0.1733,-0.3435,0.1494,-0.1579,0.0502,0.0000,-0.0341,0.1875,-0.2340,0.1998,-0.1953,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0497,0.1479,0.1324,-0.0878,-0.3462,0.1135,0.0000,-0.1439,-0.2931,0.2727,0.2858,-0.1785,0.0000,-0.7537,0.2971,0.7002,-0.3078,0.1202,0.0000,0.1189,-0.3274,0.4183,0.1027,-0.2147,0.0000,0.2583,0.4317,-0.9243,-0.3177,-0.0332,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1067,0.3975,-0.7507,0.4314,-0.0752,0.0467,0.0000,0.5285,-0.1642,0.6380,-0.9550,-0.1701,0.0000,-1.1436,0.5082,-0.5166,0.4862,0.0235,0.0000,1.1441,0.8166,0.6900,-1.7328,-0.0195,0.0000,-0.7335,-1.7282,0.2604,1.7503,0.1390,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2594,0.0228,0.6153,-0.0199,-0.5021,-0.0093,0.0000,-0.0518,0.7364,-1.3671,0.4703,0.0304,0.0000,-0.8085,1.7282,-1.1362,0.0714,0.1927,0.0000,-0.7792,0.2261,0.5641,1.1359,-0.0950,0.0000,0.8982,-1.6944,1.1565,-0.9545,-0.3594,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0365,-0.0799,-0.0755,-0.0563,-0.0458,-0.0018,0.0000,-0.6547,0.1720,-0.4211,-0.3263,0.4089,0.0000,0.7879,-0.6616,0.7882,1.2951,-1.2889,0.0000,-0.5991,0.4333,-0.3522,-1.8076,1.4867,0.0000,0.3863,0.1036,-0.4077,0.9624,-0.3673,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2331,0.1033,-0.0659,0.0571,-0.0704,-0.0606,0.0000,-0.1868,-0.3549,0.3164,-0.0333,0.2823,0.0000,0.9194,-0.7430,0.7200,-0.5748,-0.3401,0.0000,-0.1858,0.5245,-0.4446,0.2598,-0.4895,0.0000,-0.9560,0.5748,-0.7605,0.6271,0.5678,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1789,0.1287,-0.0542,0.0120,-0.2114,-0.1082,0.0000,-0.1344,0.2427,-0.3917,0.1695,-0.1667,0.0000,0.2041,0.4774,-0.2315,-0.1000,-0.4027,0.0000,-0.6246,-1.5123,1.1442,0.8354,0.0006,0.0000,0.8017,0.5886,-0.2393,-0.9055,-0.1781,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0878,-0.3707,-0.3087,-0.3840,0.2946,0.9476,0.0000,0.4610,-0.6081,-0.1200,0.3949,-0.2516,0.0000,0.3761,-0.3770,-0.4519,0.2217,-0.2812,0.0000,-0.1223,-0.5756,0.6716,-0.3183,0.2423,0.0000,-0.1892,1.0215,-0.6347,-0.5782,0.6745,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.2006,-0.5892,-0.5025,0.9240,0.3028,-0.2228,0.0000,-1.3596,0.4026,0.2905,0.4178,0.1851,0.0000,1.7998,-1.0964,-0.0789,-0.0884,-1.5779,0.0000,-0.0160,0.0435,0.2904,-0.2966,0.3677,0.0000,0.3671,-0.0281,-0.2720,-0.2729,0.2289,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1612,-0.8864,0.4048,-0.2679,0.2546,0.6956,0.0000,-0.3026,-0.1971,0.5207,0.2546,-0.3708,0.0000,-0.0770,0.0835,0.0158,-0.0367,-0.2593,0.0000,0.3975,-0.0759,-0.0148,-0.4555,0.1108,0.0000,0.4265,0.0170,-0.3124,-0.0188,-0.0979,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.1006,-0.5584,0.1243,-0.2292,0.3466,0.4779,0.0000,-0.0642,0.0595,0.2928,-0.2615,-0.1406,0.0000,-0.4234,0.0330,-0.5239,0.3953,0.4707,0.0000,0.3333,0.0233,-0.1020,-0.1908,-0.0836,0.0000,-0.2119,-0.0609,0.1306,0.2531,-0.0207,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.1392,0.2767,0.0285,0.1720,-0.2000,-0.3778,0.0000}
Activity(exp=0): {0.0449,0.0447}
Activity(exp=1): {0.0449,0.0430}
Activity(exp=2): {0.0450,0.0555}
Activity(exp=3): {0.0450,0.0538}
Activity(exp=4): {0.0450,-1.8416}
Activity(exp=5): {0.0450,-1.0378}
> Optimizing the full model (component3-4-all).
>> Starting new optimization: component3-4-all. (2021-05-21 20:27:41.985).
>>> Packing before optimization
Packing: 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Value and gradient before optimization:
=======================================
value = 3.644662722629431
gradient = 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gradient norm = 0.016039345160015758
Starting Function Value: 3.644662722629431
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 3.644077904878213 0.083815295630549 5.225605833303652 0.019707895161878
2 4 3.643581716951511 0.050875962797300 1.000000000000000 0.014359508699542
3 5 3.642906005585378 0.098783944928505 1.000000000000000 0.016608365234960
4 6 3.642041861268964 0.193834474559838 1.000000000000000 0.016669390011141
5 7 3.642013170940926 0.167522422854871 1.000000000000000 0.028083793373996
6 8 3.641518098788392 0.030012905775052 1.000000000000000 0.009855192591141
7 9 3.641337718728690 0.030978375603405 1.000000000000000 0.007168886730367
8 10 3.640940659833111 0.118619006222943 1.000000000000000 0.011403932338958
9 11 3.640537116800746 0.171865025737343 1.000000000000000 0.012132601906286
10 12 3.640098014260476 0.223967812564517 1.000000000000000 0.008885444175978
11 13 3.639961063678503 0.168180295688681 1.000000000000000 0.014209709617416
12 14 3.639755823172882 0.048499329494289 1.000000000000000 0.007445572531735
13 15 3.639563617022763 0.085531051527927 1.000000000000000 0.008047262374956
14 16 3.639304664797257 0.182456418093631 1.000000000000000 0.010489906370189
15 17 3.638981557000595 0.252955865266057 1.000000000000000 0.009169844413894
16 18 3.638686733357126 0.288579367349871 1.000000000000000 0.010205527463433
17 19 3.638431987852571 0.179595090177268 1.000000000000000 0.008987042226924
18 20 3.638219028658423 0.125277557344390 1.000000000000000 0.010294444037006
19 21 3.637909828572556 0.232980722622947 1.000000000000000 0.012829066596456
20 22 3.637834033076403 0.300528049203384 1.000000000000000 0.014275188255321
21 23 3.637652979656595 0.175493324254935 1.000000000000000 0.005412045315158
22 24 3.637577266948145 0.047335138374998 1.000000000000000 0.004568078966158
23 25 3.637432126965841 0.130368418635670 1.000000000000000 0.007752347787575
24 26 3.637213489427086 0.272264602504682 1.000000000000000 0.010558006987502
25 27 3.636911798019912 0.340918273233346 1.000000000000000 0.008803740897118
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275 289 3.631275499312143 0.020830682871892 1.000000000000000 0.000119585445894
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279 293 3.631273767825508 0.022413309914240 1.000000000000000 0.000104498236535
280 294 3.631273540185465 0.010611376262100 1.000000000000000 0.000087532408750
281 295 3.631273166440064 0.023660521141398 1.000000000000000 0.000109634060006
282 296 3.631272595107348 0.052744040736671 1.000000000000000 0.000172126100207
283 297 3.631272015506058 0.066197464235841 1.000000000000000 0.000120113045052
284 298 3.631271518724049 0.050368341125177 1.000000000000000 0.000107541293564
285 300 3.631271135855120 0.049212245915124 0.491946563547183 0.000142323160667
286 301 3.631270555887506 0.035936663908527 1.000000000000000 0.000115553506725
287 302 3.631269951572922 0.056198634960284 1.000000000000000 0.000153513218920
288 303 3.631269380041503 0.038343035462735 1.000000000000000 0.000104022101252
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290 305 3.631268285194863 0.066636421189038 1.000000000000000 0.000102298735399
291 306 3.631267825468742 0.096785213947451 1.000000000000000 0.000163306002487
292 307 3.631267144228036 0.039413588578636 1.000000000000000 0.000117363610067
293 308 3.631266617852504 0.034107211468023 1.000000000000000 0.000127240027939
294 309 3.631266343225867 0.058093615041793 1.000000000000000 0.000184820500442
295 310 3.631266069775001 0.034737646418216 1.000000000000000 0.000263915087841
296 311 3.631265709890074 0.016336328826924 1.000000000000000 0.000095323651206
297 312 3.631265330896264 0.032474595837569 1.000000000000000 0.000112794773562
298 313 3.631264929540966 0.048351901730897 1.000000000000000 0.000155300011956
299 314 3.631264327611532 0.056069334426326 1.000000000000000 0.000123968339735
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301 317 3.631262948427610 0.055957945121898 0.467057249233022 0.000221420996250
302 318 3.631262499840182 0.028648871411900 1.000000000000000 0.000159468660116
303 319 3.631261909697660 0.038481061792079 1.000000000000000 0.000131375837629
304 320 3.631261484722226 0.059527693518102 1.000000000000000 0.000273167041204
305 321 3.631261020998074 0.028724834263733 1.000000000000000 0.000172582662469
306 322 3.631260491165171 0.050883965892454 1.000000000000000 0.000133021663445
307 323 3.631260080363651 0.045814164369143 1.000000000000000 0.000113456066004
308 325 3.631259886295595 0.036477279973773 0.263079357095748 0.000327716385447
309 326 3.631259474101868 0.042405567714282 1.000000000000000 0.000120009251484
310 327 3.631259233081382 0.020287110992026 1.000000000000000 0.000122106404793
311 328 3.631259002222197 0.014878969087225 1.000000000000000 0.000143704099120
312 329 3.631258590772836 0.027591903881897 1.000000000000000 0.000126634081460
313 330 3.631258004337288 0.068404856240454 1.000000000000000 0.000108150584792
314 331 3.631257661756175 0.047650797932121 1.000000000000000 0.000184987720103
315 332 3.631257477138351 0.024793595844880 1.000000000000000 0.000183052584260
316 333 3.631257295765169 0.011609717537396 1.000000000000000 0.000069147938337
317 334 3.631257205694236 0.010436263957370 1.000000000000000 0.000056514250227
318 335 3.631257077824620 0.013483600317765 1.000000000000000 0.000084561268722
319 336 3.631256842943222 0.038122125661744 1.000000000000000 0.000100331551656
320 337 3.631256699929914 0.038714706420729 1.000000000000000 0.000270118753750
321 338 3.631256434372059 0.024027802032515 1.000000000000000 0.000102423383080
322 339 3.631256304173334 0.013924097202030 1.000000000000000 0.000062728579534
323 340 3.631256204787814 0.009532790247759 1.000000000000000 0.000086996755291
324 341 3.631256042228323 0.019314834187443 1.000000000000000 0.000107852003439
325 342 3.631255695857170 0.035913655748166 1.000000000000000 0.000100085280375
326 344 3.631255649443136 0.012456790964018 0.132108588931068 0.000171707213654
327 345 3.631255421469263 0.038069951496271 1.000000000000000 0.000089066356526
328 346 3.631255280188885 0.017088214081888 1.000000000000000 0.000059053342176
329 347 3.631255126295933 0.019613978277254 1.000000000000000 0.000085783471247
330 349 3.631255086931017 0.006488507439660 0.318207352023153 0.000164933193830
331 350 3.631254985422455 0.008858741899274 1.000000000000000 0.000114872656154
332 351 3.631254854859480 0.015239713938144 1.000000000000000 0.000062733596681
333 352 3.631254731588038 0.015511354284918 1.000000000000000 0.000078392873723
334 354 3.631254689070147 0.010067688642080 0.385441959223321 0.000142406964931
335 355 3.631254602274308 0.013607928155769 1.000000000000000 0.000109874272636
336 356 3.631254496781236 0.013658993249813 1.000000000000000 0.000071665041578
337 357 3.631254383898577 0.016576250552148 1.000000000000000 0.000053551251536
338 358 3.631254289960888 0.013774094926464 1.000000000000000 0.000062374633302
339 359 3.631254194774965 0.020331809957409 1.000000000000000 0.000197678662732
340 360 3.631254084943941 0.022110734448572 1.000000000000000 0.000089163874685
341 361 3.631254007559237 0.004586622064371 1.000000000000000 0.000066117051375
342 362 3.631253864598278 0.015956607967203 1.000000000000000 0.000063210032513
343 363 3.631253770561469 0.014673668940645 1.000000000000000 0.000062020491120
344 364 3.631253658876898 0.034505965758103 1.000000000000000 0.000197291944847
345 365 3.631253542447983 0.031876082112290 1.000000000000000 0.000159552191960
346 366 3.631253460573586 0.008860087109245 1.000000000000000 0.000066373331164
347 367 3.631253406340041 0.006319721642828 1.000000000000000 0.000046928291697
348 368 3.631253350424819 0.009841080009680 1.000000000000000 0.000062931637405
349 369 3.631253267714161 0.016030902949689 1.000000000000000 0.000056562748002
350 371 3.631253228209453 0.016486373511598 0.291991309202287 0.000113288510230
351 372 3.631253148550851 0.015438379984677 1.000000000000000 0.000056956718432
352 373 3.631253086282556 0.011696645650766 1.000000000000000 0.000059170266696
353 374 3.631253019002611 0.012032905974357 1.000000000000000 0.000076633103345
354 375 3.631252932928861 0.019108627895536 1.000000000000000 0.000077577753677
355 376 3.631252905617989 0.034518199909523 1.000000000000000 0.000207996511753
356 377 3.631252762321735 0.015849625252839 1.000000000000000 0.000066227313285
357 378 3.631252707261366 0.007361333564456 1.000000000000000 0.000044868927559
358 379 3.631252643031366 0.018330174965587 1.000000000000000 0.000082488128728
359 380 3.631252588414014 0.019009337090799 1.000000000000000 0.000084797995762
360 381 3.631252522655637 0.015586937656878 1.000000000000000 0.000058526495742
361 382 3.631252415511701 0.022937721750311 1.000000000000000 0.000053286531074
362 383 3.631252312230509 0.020898971672399 1.000000000000000 0.000097934784538
363 384 3.631252236494543 0.031948016046031 1.000000000000000 0.000098528156511
364 385 3.631252150894971 0.006113387822176 1.000000000000000 0.000055470304574
365 386 3.631252092438181 0.006000546055451 1.000000000000000 0.000052865323597
366 387 3.631252006535080 0.012457383195678 1.000000000000000 0.000062574605432
367 388 3.631251908556165 0.038063271127127 1.000000000000000 0.000139220120238
368 389 3.631251782282947 0.035424582735799 1.000000000000000 0.000087100486120
369 390 3.631251691528259 0.013320529305150 1.000000000000000 0.000066279605153
370 391 3.631251552771736 0.033798848050152 1.000000000000000 0.000065989993701
371 392 3.631251475896705 0.016328364817229 1.000000000000000 0.000070573949198
372 394 3.631251408591039 0.017834370515179 0.422784284343760 0.000127344742642
373 395 3.631251294022571 0.024032036272573 1.000000000000000 0.000073383214866
374 396 3.631251190674961 0.016735696713047 1.000000000000000 0.000051126675828
375 397 3.631251086487506 0.024126287147111 1.000000000000000 0.000066450134460
376 398 3.631250966512357 0.025899027899344 1.000000000000000 0.000069765096292
377 399 3.631250838070815 0.070471049212804 1.000000000000000 0.000120873076523
378 400 3.631250704743938 0.036585824375501 1.000000000000000 0.000063317634746
379 401 3.631250612288470 0.014957608069438 1.000000000000000 0.000039877747445
380 402 3.631250510247169 0.011151712234535 1.000000000000000 0.000052940412260
381 403 3.631250447953268 0.031812920388248 1.000000000000000 0.000133704600419
382 404 3.631250312063933 0.019292119134852 1.000000000000000 0.000057817243145
383 405 3.631250212950884 0.032737951515344 1.000000000000000 0.000047736817470
384 406 3.631250131108593 0.031759787462581 1.000000000000000 0.000053834667838
385 407 3.631249958810538 0.048289762526815 1.000000000000000 0.000056621460158
386 408 3.631249783263023 0.072707209228729 1.000000000000000 0.000112253586647
387 409 3.631249604999350 0.057852544995075 1.000000000000000 0.000075928330041
388 410 3.631249483915156 0.020714476740576 1.000000000000000 0.000041946467258
389 411 3.631249377649642 0.017248591454918 1.000000000000000 0.000047299163287
390 412 3.631249268534373 0.027243934584420 1.000000000000000 0.000065770813373
391 413 3.631249079008527 0.055344668839546 1.000000000000000 0.000062439409264
392 414 3.631249039777172 0.122278798974939 1.000000000000000 0.000190317841750
393 415 3.631248635590151 0.040582187805979 1.000000000000000 0.000073997817127
394 416 3.631248524980735 0.012885151894191 1.000000000000000 0.000044007439124
395 417 3.631248371073278 0.019370803204724 1.000000000000000 0.000044162974874
396 418 3.631248179457990 0.047905587349170 1.000000000000000 0.000106137080582
397 419 3.631248067393991 0.066637883369828 1.000000000000000 0.000148656588498
398 420 3.631247910727809 0.019115697453101 1.000000000000000 0.000052971098478
399 421 3.631247836654642 0.014132600840926 1.000000000000000 0.000050024237052
400 422 3.631247709392447 0.029776058904242 1.000000000000000 0.000055225092975
401 423 3.631247561034975 0.053265501251294 1.000000000000000 0.000098314180547
402 425 3.631247511300372 0.024843714626650 0.326587498649428 0.000111409023271
403 426 3.631247419002560 0.016458361552129 1.000000000000000 0.000053429438904
404 427 3.631247342483077 0.017603499898920 1.000000000000000 0.000062300891940
405 428 3.631247274574827 0.014546460452009 1.000000000000000 0.000081203903370
406 429 3.631247117630367 0.031484764831386 1.000000000000000 0.000086422524759
407 431 3.631247070404201 0.016842831310298 0.142530643261837 0.000126699840511
408 432 3.631246924614613 0.029772243108868 1.000000000000000 0.000073896165921
409 433 3.631246795843174 0.027490863889636 1.000000000000000 0.000055649481884
410 435 3.631246750151231 0.013747656405719 0.423555855998710 0.000161591778094
411 436 3.631246662103311 0.019020270291521 1.000000000000000 0.000097076468209
412 437 3.631246596601779 0.011437559081765 1.000000000000000 0.000076512976676
413 438 3.631246493158837 0.025014538857200 1.000000000000000 0.000056894724458
414 439 3.631246409143807 0.021990167527645 1.000000000000000 0.000051581512348
415 440 3.631246292751350 0.028368799401557 1.000000000000000 0.000051109774215
416 441 3.631246139341026 0.033639367049799 1.000000000000000 0.000051599306519
417 443 3.631246104945975 0.014608323985621 0.175114113434614 0.000111135033961
418 444 3.631245976449159 0.028187117955284 1.000000000000000 0.000061461153925
419 445 3.631245883713961 0.017920829888652 1.000000000000000 0.000041787638417
420 446 3.631245758952872 0.023803551279804 1.000000000000000 0.000055672306903
421 447 3.631245652446256 0.023574211074161 1.000000000000000 0.000064014012434
422 449 3.631245586879368 0.021762755957311 0.432967134633509 0.000123932920471
423 450 3.631245479603500 0.032977526438168 1.000000000000000 0.000051812581392
424 451 3.631245428932064 0.010935658685894 1.000000000000000 0.000038116519335
425 452 3.631245353219717 0.021877743249555 1.000000000000000 0.000042424606648
426 453 3.631245262816088 0.020159542202606 1.000000000000000 0.000043156927881
427 454 3.631245137783767 0.034552890297150 1.000000000000000 0.000082802860770
428 455 3.631245081529473 0.069569270483359 1.000000000000000 0.000142572393320
429 456 3.631245028626520 0.030389326790332 1.000000000000000 0.000139533392826
430 457 3.631244972994637 0.017541066175154 1.000000000000000 0.000034688609533
431 458 3.631244956487275 0.006165172259869 1.000000000000000 0.000033358850230
432 459 3.631244924039147 0.008881420785581 1.000000000000000 0.000059367920112
433 461 3.631244903213502 0.007984041022691 0.456681827525178 0.000094534212020
434 462 3.631244872496049 0.014443702731626 1.000000000000000 0.000060008876990
435 463 3.631244832882921 0.013505169635832 1.000000000000000 0.000039611006849
436 464 3.631244815724922 0.009968411496820 1.000000000000000 0.000036295394544
437 465 3.631244785072124 0.007373661149339 1.000000000000000 0.000088338724982
438 466 3.631244756006544 0.008945699364805 1.000000000000000 0.000056567611756
439 467 3.631244733745323 0.007577354788781 1.000000000000000 0.000042257836987
440 468 3.631244695503122 0.014330363478167 1.000000000000000 0.000040277535308
441 469 3.631244671840657 0.012866148216598 1.000000000000000 0.000058601996115
442 470 3.631244636705732 0.014809272278475 1.000000000000000 0.000049843581821
443 471 3.631244608735612 0.008827367602543 1.000000000000000 0.000037175168153
444 472 3.631244572038502 0.012764253693907 1.000000000000000 0.000040487764434
445 473 3.631244538284044 0.006295475254805 1.000000000000000 0.000039448502029
446 474 3.631244518736271 0.023788587105578 1.000000000000000 0.000148790973009
447 475 3.631244465835771 0.011455434472482 1.000000000000000 0.000040760088217
448 476 3.631244452584007 0.002718071918404 1.000000000000000 0.000032556527405
449 477 3.631244416014767 0.010229347651725 1.000000000000000 0.000035966427220
450 478 3.631244385760949 0.011335294116890 1.000000000000000 0.000044591274116
451 479 3.631244375361371 0.017201259965005 1.000000000000000 0.000099511004236
452 480 3.631244341744176 0.004739063988980 1.000000000000000 0.000032743446735
453 481 3.631244326409287 0.003234785139380 1.000000000000000 0.000038432584723
454 482 3.631244308451709 0.003798069670437 1.000000000000000 0.000052081132554
455 483 3.631244279685939 0.007023050103176 1.000000000000000 0.000052472071298
456 484 3.631244222380453 0.015778830498913 1.000000000000000 0.000050589544581
457 486 3.631244188449330 0.015617788455521 0.436166278892844 0.000051575250685
458 487 3.631244119695909 0.026754426585622 1.000000000000000 0.000037597223965
459 488 3.631244084728031 0.014499751343406 1.000000000000000 0.000058896050328
460 489 3.631244060980000 0.015155796302361 1.000000000000000 0.000091020706957
461 490 3.631244033113499 0.006643661719870 1.000000000000000 0.000036923287137
462 491 3.631244016326666 0.002757802242661 1.000000000000000 0.000028105577050
463 492 3.631243993940988 0.004482686556101 1.000000000000000 0.000047930883986
464 493 3.631243962916342 0.009625272266123 1.000000000000000 0.000063159298379
465 494 3.631243915426318 0.016849703878179 1.000000000000000 0.000056265456232
466 496 3.631243896600542 0.009980689291781 0.224194934962327 0.000081552708252
467 497 3.631243861308111 0.015253392012619 1.000000000000000 0.000035603612430
468 498 3.631243839444540 0.008414415637308 1.000000000000000 0.000038586242974
469 499 3.631243818608488 0.006035913588553 1.000000000000000 0.000053588183765
470 500 3.631243783602293 0.009144945495008 1.000000000000000 0.000054873179378
471 502 3.631243764358982 0.009841093933567 0.393912937745913 0.000081330591596
472 503 3.631243725009502 0.012751795169106 1.000000000000000 0.000039987758978
473 504 3.631243700803393 0.006209866913658 1.000000000000000 0.000031906407737
474 505 3.631243679688358 0.006144750768497 1.000000000000000 0.000052710412057
475 506 3.631243654377786 0.007069938313710 1.000000000000000 0.000061279321145
476 507 3.631243612459127 0.016434755766594 1.000000000000000 0.000072800268151
477 508 3.631243565759231 0.030342174921204 1.000000000000000 0.000068484239805
478 509 3.631243528634888 0.005369684230048 1.000000000000000 0.000037372626491
479 510 3.631243502120177 0.007193717926852 1.000000000000000 0.000044061519433
480 511 3.631243479624138 0.008196801123387 1.000000000000000 0.000046007599286
481 512 3.631243430841556 0.019180506754070 1.000000000000000 0.000045345444726
482 513 3.631243377374402 0.024403267213428 1.000000000000000 0.000066076766825
483 514 3.631243328434516 0.021674664703456 1.000000000000000 0.000036851995347
484 515 3.631243302277878 0.009701371133526 1.000000000000000 0.000025636006197
485 516 3.631243283081568 0.008115128787303 1.000000000000000 0.000026657032148
486 517 3.631243247662634 0.014197198677689 1.000000000000000 0.000029897430424
487 518 3.631243199140942 0.023316358716732 1.000000000000000 0.000046228878899
488 519 3.631243169842348 0.018589708073371 1.000000000000000 0.000051550112303
489 520 3.631243149158654 0.007061676898808 1.000000000000000 0.000031446821113
490 521 3.631243113240195 0.017724234587779 1.000000000000000 0.000030058808696
491 522 3.631243082776616 0.013921763558110 1.000000000000000 0.000033786336656
492 523 3.631243014521826 0.027180571266248 1.000000000000000 0.000030863378980
493 524 3.631243007089007 0.048178547540996 1.000000000000000 0.000101840697099
494 525 3.631242923230999 0.014976125294732 1.000000000000000 0.000026865393911
495 526 3.631242898898316 0.010127903169310 1.000000000000000 0.000023074795008
496 527 3.631242855188742 0.016719107277853 1.000000000000000 0.000029240975208
497 528 3.631242806800643 0.021497875991187 1.000000000000000 0.000045962544738
498 529 3.631242754988545 0.027911761038335 1.000000000000000 0.000044745116322
499 530 3.631242722576170 0.027558461201412 1.000000000000000 0.000064277311697
500 531 3.631242695541348 0.009056554780302 1.000000000000000 0.000036319857343
>>> Maximum iteration count reached.
After: gradient norm = 3.631985734289441E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.3269,-0.3269}
Count Table 1:
---------------
h: {0.2182,-0.2182}
Count Table 2:
---------------
h: {0.5242,-0.5242}
Count Table 3:
---------------
h: {0.5637,-0.5637}
Count Table 4:
---------------
h: {1.5655,-1.5655}
Count Table 5:
---------------
h: {1.4296,-1.4296}
Binding mode 0:
---------------
Mononucleotide: {}
Activity(exp=0): {-0.0000,0.4281}
Activity(exp=1): {-0.0000,0.2566}
Activity(exp=2): {-0.0000,0.7513}
Activity(exp=3): {-0.0000,0.5657}
Activity(exp=4): {-0.0000,2.5580}
Activity(exp=5): {-0.0000,2.0823}
Binding mode 1:
---------------
Mononucleotide: {-0.4166,-1.0603,-0.3379,-0.6075,-0.7305,-1.0077,-0.2078,-0.8288,-0.6269,-0.9094,-0.8571,-0.7305,-0.4550,-0.9351,-1.3801,-0.0144,-0.5188,-0.8571,-0.3847,-0.6414,-2.0081,-0.2378,-0.3698,-0.5188,0.3013,-1.5585,-0.8490,-0.5199,-1.1646,-0.3698,-0.2083,-0.5247,-1.0674,-0.7150,-0.4804,-1.1646,-0.7150,-1.0674,-0.5247,-0.2083,-1.1646,-0.4804,-0.5199,-0.8490,-1.5585,0.3013,-0.3698,-1.1646,-0.2378,-2.0081,-0.6414,-0.3847,-0.5188,-0.3698,-0.0144,-1.3801,-0.9351,-0.4550,-0.8571,-0.5188,-0.9094,-0.6269,-0.8288,-0.2078,-0.7305,-0.8571,-0.6075,-0.3379,-1.0603,-0.4166,-1.0077,-0.7305}
Dinucleotide(d=1): {-0.2536,-0.4187,0.0317,-0.4562,0.6802,0.0000,0.0196,-0.5290,-0.1898,0.0209,-0.3819,0.0000,0.2452,0.5221,-0.0365,-0.0696,-0.9992,0.0000,-0.0431,0.0251,-0.4544,-0.2323,0.0971,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7305,-0.1760,-0.4283,0.0221,-0.1722,-0.2533,0.0000,-0.1574,-0.2962,-1.0750,0.6293,0.6915,0.0000,-0.3421,-0.1356,-0.6556,0.7001,-0.3956,0.0000,-0.2748,-0.2267,-0.2911,0.0527,0.1131,0.0000,0.8101,0.4752,0.0563,-1.1727,-1.0782,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8571,-0.4908,-0.7518,0.5853,-0.2237,0.1504,0.0000,0.1312,0.3763,-1.5266,-0.2613,0.8255,0.0000,-0.0446,0.3216,-0.7554,-0.0895,-0.3671,0.0000,0.3805,-0.3102,-1.4939,0.3240,-0.2804,0.0000,-0.8180,-0.5707,2.6810,-0.3340,-0.9727,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5188,-0.0337,-0.4583,-0.9131,0.1231,0.4250,0.0000,-1.7395,0.8527,0.0419,0.4343,0.0259,0.0000,-0.8123,-0.1525,0.3976,-0.0682,-0.0059,0.0000,1.4028,-1.2206,-0.1495,-1.0732,-0.9675,0.0000,-0.5371,-0.2059,0.0879,0.4884,-0.0711,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3698,1.9874,-0.8322,-1.2268,-0.3012,-0.1461,0.0000,-2.3039,1.0152,-0.8855,1.0358,1.4397,0.0000,1.0659,-0.6912,-0.4182,-0.2523,-1.2628,0.0000,0.1933,-0.4497,0.0935,-0.4225,-0.2636,0.0000,1.0950,-1.2145,0.6916,-0.5394,-0.5526,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.1646,-0.2587,0.8155,-0.5488,-0.5366,0.1589,0.0000,-0.6813,0.9801,-2.0465,1.4394,0.1107,0.0000,0.6115,-1.0805,2.5447,-2.0465,-0.5752,0.0000,-0.2600,-0.6221,-1.0805,0.9801,-0.0576,0.0000,0.2340,-0.2600,0.6115,-0.6813,-0.6371,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.4617,-0.6371,-0.0576,-0.5752,0.1107,-0.0053,0.0000,-0.5394,-0.4225,-0.2523,1.0358,-0.5366,0.0000,0.6916,0.0935,-0.4182,-0.8855,-0.5488,0.0000,-1.2145,-0.4497,-0.6912,1.0152,0.8155,0.0000,1.0950,0.1933,1.0659,-2.3039,-0.2587,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.1646,-0.5526,-0.2636,-1.2628,1.4397,0.1589,0.0000,0.4884,-1.0732,-0.0682,0.4343,-0.3012,0.0000,0.0879,-0.1495,0.3976,0.0419,-1.2268,0.0000,-0.2059,-1.2206,-0.1525,0.8527,-0.8322,0.0000,-0.5371,1.4028,-0.8123,-1.7395,1.9874,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3698,-0.0711,-0.9675,-0.0059,0.0259,-0.1461,0.0000,-0.3340,0.3240,-0.0895,-0.2613,0.1231,0.0000,2.6810,-1.4939,-0.7554,-1.5266,-0.9131,0.0000,-0.5707,-0.3102,0.3216,0.3763,-0.4583,0.0000,-0.8180,0.3805,-0.0446,0.1312,-0.0337,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5188,-0.9727,-0.2804,-0.3671,0.8255,0.4250,0.0000,-1.1727,0.0527,0.7001,0.6293,-0.2237,0.0000,0.0563,-0.2911,-0.6556,-1.0750,0.5853,0.0000,0.4752,-0.2267,-0.1356,-0.2962,-0.7518,0.0000,0.8101,-0.2748,-0.3421,-0.1574,-0.4908,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.8571,-1.0782,0.1131,-0.3956,0.6915,0.1504,0.0000,-0.2323,-0.0696,0.0209,-0.4562,-0.1722,0.0000,-0.4544,-0.0365,-0.1898,0.0317,0.0221,0.0000,0.0251,0.5221,-0.5290,-0.4187,-0.4283,0.0000,-0.0431,0.2452,0.0196,-0.2536,-0.1760,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7305,0.0971,-0.9992,-0.3819,0.6802,-0.2533,0.0000}
Activity(exp=0): {0.0000,-0.7563}
Activity(exp=1): {0.0000,-0.4763}
Activity(exp=2): {0.0000,0.0000}
Activity(exp=3): {0.0000,0.0000}
Activity(exp=4): {0.0000,-2.0276}
Activity(exp=5): {0.0000,-0.9854}
Binding mode 2:
---------------
Mononucleotide: {-0.4270,-0.8267,-0.6630,-0.2817,-0.5916,-0.7925,0.0445,-0.8496,-0.5891,-0.5611,-1.0355,-0.5916,-0.7319,-0.8561,-1.3098,0.8524,-0.5013,-1.0355,-0.3238,-0.6406,-0.9787,-0.1701,-0.9677,-0.5013,0.2595,-1.1986,-0.6969,0.0989,-1.0775,-0.9677,-0.6383,-0.3038,-1.0765,-0.5069,0.0208,-1.0775,-0.5069,-1.0765,-0.3038,-0.6383,-1.0775,0.0208,0.0989,-0.6969,-1.1986,0.2595,-0.9677,-1.0775,-0.1701,-0.9787,-0.6406,-0.3238,-0.5013,-0.9677,0.8524,-1.3098,-0.8561,-0.7319,-1.0355,-0.5013,-0.5611,-0.5891,-0.8496,0.0445,-0.5916,-1.0355,-0.2817,-0.6630,-0.8267,-0.4270,-0.7925,-0.5916}
Dinucleotide(d=1): {-0.2221,-0.4144,-0.1709,0.0265,0.3524,0.0000,-0.3092,-0.4320,-0.2390,0.1856,-0.0346,0.0000,0.2563,-0.2274,0.0109,-0.0847,-0.6195,0.0000,0.1655,0.3072,-0.1459,-0.2406,-0.3689,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5929,0.1542,-0.0850,-0.0451,-0.4504,-0.3677,0.0000,0.2244,-0.1185,-0.1557,0.4294,-0.3349,0.0000,0.0252,0.1798,-0.9227,0.1053,-0.2392,0.0000,-0.1936,-0.5503,-0.2505,0.4672,-0.0627,0.0000,0.4854,0.4867,0.1393,-0.7998,-0.8753,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0382,-1.2760,-0.8563,-0.1239,0.6531,1.0102,0.0000,0.8729,0.0478,-0.8708,-0.4253,-0.3590,0.0000,-0.7912,1.1073,-1.1938,0.0297,-0.0107,0.0000,0.2190,-0.5219,-0.2999,-0.5363,-0.1744,0.0000,-0.6977,-0.9162,1.0167,1.8345,-0.3820,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5020,0.0699,-0.3616,0.3687,-1.0710,-0.0441,0.0000,-0.2819,0.3143,-0.8961,-0.4082,0.9449,0.0000,-1.1775,1.6498,-0.6590,-0.7358,0.2778,0.0000,0.7525,-1.2455,0.2982,0.5868,-1.3711,0.0000,0.2555,-0.9515,1.5927,-0.2328,-0.8323,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9702,0.7115,-0.9698,-1.0322,0.8889,-0.1004,0.0000,-0.1593,0.0883,0.0451,0.1310,0.1550,0.0000,0.0248,0.1533,-0.8536,0.6176,-1.1447,0.0000,-0.8035,0.2244,0.1696,-0.7828,0.4960,0.0000,-0.2270,0.1653,-0.1669,-0.0062,0.3336,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0811,0.5247,-0.9350,-0.2728,-0.4681,0.1810,0.0000,-0.1032,0.2084,0.0753,-0.1803,-0.6946,0.0000,0.3173,-0.1751,0.8404,0.0753,-1.4072,0.0000,-1.1672,0.0687,-0.1751,0.2084,-0.0205,0.0000,-0.4897,-1.1672,0.3173,-0.1032,1.0709,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0581,1.0709,-0.0205,-1.4072,-0.6946,-0.0207,0.0000,-0.0062,-0.7828,0.6176,0.1310,-0.4681,0.0000,-0.1669,0.1696,-0.8536,0.0451,-0.2728,0.0000,0.1653,0.2244,0.1533,0.0883,-0.9350,0.0000,-0.2270,-0.8035,0.0248,-0.1593,0.5247,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0811,0.3336,0.4960,-1.1447,0.1550,0.1810,0.0000,-0.2328,0.5868,-0.7358,-0.4082,0.8889,0.0000,1.5927,0.2982,-0.6590,-0.8961,-1.0322,0.0000,-0.9515,-1.2455,1.6498,0.3143,-0.9698,0.0000,0.2555,0.7525,-1.1775,-0.2819,0.7115,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9702,-0.8323,-1.3711,0.2778,0.9449,-0.1004,0.0000,1.8345,-0.5363,0.0297,-0.4253,-1.0710,0.0000,1.0167,-0.2999,-1.1938,-0.8708,0.3687,0.0000,-0.9162,-0.5219,1.1073,0.0478,-0.3616,0.0000,-0.6977,0.2190,-0.7912,0.8729,0.0699,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5020,-0.3820,-0.1744,-0.0107,-0.3590,-0.0441,0.0000,-0.7998,0.4672,0.1053,0.4294,0.6531,0.0000,0.1393,-0.2505,-0.9227,-0.1557,-0.1239,0.0000,0.4867,-0.5503,0.1798,-0.1185,-0.8563,0.0000,0.4854,-0.1936,0.0252,0.2244,-1.2760,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0382,-0.8753,-0.0627,-0.2392,-0.3349,1.0102,0.0000,-0.2406,-0.0847,0.1856,0.0265,-0.4504,0.0000,-0.1459,0.0109,-0.2390,-0.1709,-0.0451,0.0000,0.3072,-0.2274,-0.4320,-0.4144,-0.0850,0.0000,0.1655,0.2563,-0.3092,-0.2221,0.1542,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.5929,-0.3689,-0.6195,-0.0346,0.3524,-0.3677,0.0000}
Activity(exp=0): {0.0034,0.0041}
Activity(exp=1): {0.0034,0.0042}
Activity(exp=2): {0.0034,-1.3465}
Activity(exp=3): {0.0034,-1.1642}
Activity(exp=4): {0.0034,-0.6247}
Activity(exp=5): {0.0034,-0.6859}
Binding mode 3:
---------------
Mononucleotide: {-0.9004,-1.1031,-0.5530,-0.4382,-0.4117,-0.5888,0.0491,-0.3980,-0.9074,-1.2013,-1.1258,-0.4117,-0.8611,-1.5597,-1.8733,1.8089,-0.3895,-1.1258,-1.2172,-1.1727,-1.1288,0.5740,-0.6662,-0.3895,-0.1684,-1.9256,-0.6495,0.5878,-1.1786,-0.6662,-1.0282,0.9077,-1.3786,-1.5322,0.2095,-1.1786,-0.2305,-1.2156,-0.6198,-1.4192,-0.7248,0.2095,-0.9075,-0.9830,-1.6156,0.3061,-0.0757,-0.7248,-0.7655,-1.8673,-0.5092,-0.8834,0.1006,-0.0757,0.1332,-1.5524,-0.9672,-0.8773,-0.8375,0.1006,-0.9603,-0.7146,-0.5226,-0.1929,-0.7672,-0.8375,-0.7303,-0.1365,-1.0323,-0.6119,-0.7170,-0.7672}
Dinucleotide(d=1): {-0.3426,-0.1893,0.0787,-0.1382,-0.2380,0.0000,-0.4298,-0.0684,0.0299,-0.1850,-0.3319,0.0000,0.0439,-0.5157,-0.3508,-0.0025,0.3480,0.0000,0.3611,0.5834,0.1586,-0.8265,-0.7095,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.3273,0.3808,-0.1161,-0.7757,0.0271,0.0028,0.0000,-0.5313,0.1066,-0.4393,1.1131,-0.2357,0.0000,-0.2203,0.1572,0.2008,-0.4391,-0.0048,0.0000,-1.0072,0.0239,-0.3878,1.2726,-0.7608,0.0000,0.3218,-0.8986,-0.5521,-0.7566,0.7604,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.9286,0.5964,-0.9472,-0.2806,0.3148,-0.0106,0.0000,-0.7688,1.0500,-0.7168,-0.3882,-0.0168,0.0000,-1.0228,-0.4170,-0.6547,0.5545,-0.0182,0.0000,2.0069,-0.7553,-1.0656,-1.6405,-0.0045,0.0000,-1.2112,-1.0591,1.8895,2.3265,-0.4409,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.2515,-0.1462,-0.0052,-0.1891,-0.5770,-0.0111,0.0000,0.0850,-0.4195,-1.2986,0.4851,0.0060,0.0000,-0.6452,-0.1373,-0.4971,0.0267,0.0665,0.0000,0.0084,0.1054,-0.6539,0.0471,-0.2437,0.0000,0.6002,-1.1739,2.4038,-0.7190,-0.8357,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.4915,-0.2132,-0.1595,-0.6203,0.7481,-0.0066,0.0000,-0.0864,0.8997,-0.0232,-1.5874,0.6326,0.0000,-0.1193,-0.5587,-0.5115,1.1521,-1.7474,0.0000,-0.5102,0.5723,-0.3856,-1.2291,0.8864,0.0000,-0.2943,0.6519,-0.2860,0.2934,0.2229,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0135,0.0611,-0.7654,-0.0359,-0.0583,0.3069,0.0000,-0.0463,-0.4684,0.2321,-1.3569,0.6903,0.0000,1.3861,-0.7342,1.5513,-0.1038,-1.2997,0.0000,-0.7321,1.1579,-0.7961,0.2539,-1.1258,0.0000,-0.3424,-0.8386,-1.4359,0.0124,1.1753,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.3014,-0.5718,-0.1972,-0.0589,-0.1433,-0.0422,0.0000,-0.2484,-0.0889,-0.2105,0.5111,-0.2699,0.0000,-0.2973,-0.3969,0.9227,-0.1590,-1.1499,0.0000,-0.5394,-0.3484,-1.4878,0.9235,0.9444,0.0000,0.1384,0.1143,-0.5671,-1.1359,0.1126,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6021,0.1266,-0.1936,-0.1532,0.1548,0.3668,0.0000,0.2355,-0.4979,-0.1365,-0.0232,-0.3980,0.0000,0.6280,-0.7311,-0.1870,-0.1028,-0.5205,0.0000,-0.5762,-0.6437,-0.4546,-0.0048,0.1835,0.0000,0.0964,1.1850,-0.6005,-1.2481,0.8616,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0041,-1.0610,-1.1199,0.9753,0.6119,-0.0084,0.0000,0.1029,-0.2714,-0.4396,-0.0900,0.0208,0.0000,2.9579,-1.7140,-0.1805,-0.6706,-2.2004,0.0000,-0.9984,-0.0148,-0.0018,-0.0279,0.6396,0.0000,-0.0651,-0.0746,0.0234,-0.4132,-0.2375,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.1183,-1.8581,0.6609,-0.2764,0.4136,1.0640,0.0000,-1.1005,-0.0051,0.3772,0.8316,0.0359,0.0000,0.2060,-0.5816,-0.1540,-0.5580,-0.3263,0.0000,0.0840,-0.1388,-0.2292,-0.6198,0.0289,0.0000,0.6660,-0.3335,-0.1575,-0.4298,-0.5333,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.7136,-0.7459,0.4298,-0.3362,0.6255,0.1451,0.0000,-0.6825,-0.0077,-0.1018,-0.1941,0.0958,0.0000,-0.2777,-0.2723,-0.3363,0.2147,0.0424,0.0000,0.2688,0.1725,-0.4362,-0.3156,-0.1892,0.0000,0.0552,-0.0666,0.0824,-0.1174,-0.1042,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.6495,0.0098,0.0557,-0.1628,-0.1265,-0.4898,0.0000}
Activity(exp=0): {0.0077,0.0077}
Activity(exp=1): {0.0077,0.0074}
Activity(exp=2): {0.0078,0.0096}
Activity(exp=3): {0.0078,0.0093}
Activity(exp=4): {0.0078,-1.8950}
Activity(exp=5): {0.0078,-2.0770}
> Optimization done.
Probound Model
±
Optimized model:
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0","freezingLevel":0,"includeComponent":true,"bindingModes":[0,1],"variationDescription":[],"modifications":[]},{"variationsOptimized":false,"bindingSaturation":false,"cumulativeEnrichment":true,"concentration":1,"modelType":"SELEX","bindingModeInteractions":[],"componentName":"SELEX enrichment model 1","freezingLevel":0,"includeComponent":true,"bindingModes":[0,1],"variationDescription":[],"modifications":[]},{"variationsOptimized":false,"bindingSaturation":false,"cumulativeEnrichment":true,"concentration":1,"modelType":"SELEX","bindingModeInteractions":[],"componentName":"SELEX enrichment model 2","freezingLevel":0,"includeComponent":true,"bindingModes":[0,2],"variationDescription":[],"modifications":[]},{"variationsOptimized":false,"bindingSaturation":false,"cumulativeEnrichment":true,"concentration":1,"modelType":"SELEX","bindingModeInteractions":[],"componentName":"SELEX enrichment model 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