Status
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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": "addTable",
- "leftFlank": "",
- "nColumns": 2,
- "modeledColumns": [
],
- 0,
- 1
- "countTableFile": "jobs/fefdadcaefe5/countTable.0.tsv.gz",
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- {
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- "function": "addTable",
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- {
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- "function": "addTable",
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- "rightFlank": "",
- "inputFileType": "tsv.gz",
- "variableRegionLength": 200
- {
},
- "function": "addSELEX"
- {
},
- "function": "addSELEX"
- {
},
- "function": "addSELEX"
- {
},
- "function": "addNS"
- {
},
- "function": "addBindingMode",
- "flankLength": 0,
- "dinucleotideDistance": 0,
- "size": 15
- {
},
- "function": "optimizerSetting",
- "lambdaL2": 0.000001
- {
},
- "function": "bindingModeConstraints",
- "index": 1,
- "roundSpecificActivity": true,
- "experimentSpecificActivity": true
- {
},
- "function": "bindingModeSeed",
- "index": 1,
- "mononucleotideString": "AG.ACA...TGT.CT"
- {
},
- "function": "symmetry",
- "index": 1,
- "symmetryString": "abcdefg1GFEDCBA"
- {
}
- "function": "output",
- "outputPath": "jobs/fefdadcaefe5",
- "baseName": "fit",
- "storeHessian": false,
- "printTrajectory": false
Configuration File
±
ProBound configuration file:
{
- "modelSeeding": {
- "bindingModes": []
- "optimizerSetting": {
- "nThreads": 4,
- "likelihoodThreshold": 0,
- "lambdaL2": 0.000001,
- "patternSearchSettings": {},
- "pseudocount": 0,
- "minimizerType": "lbfgs",
- "nRetries": 3,
- "hkSettings": {},
- "output": {
- "storeHessian": false,
- "outputPath": "jobs/fefdadcaefe5",
- "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": [
- -1
- "modifications": []
- {
- "r0KUsed": 1,
- "round": 1,
- "bindingSaturation": false,
- "concentration": 1,
- "modelType": "SELEX",
- "bindingModeInteractions": [
- -1
- "r0KsTested": [
- 1
- "bindingModes": [
- -1
- "modifications": []
- {
- "r0KUsed": 1,
- "round": 1,
- "bindingSaturation": false,
- "concentration": 1,
- "modelType": "SELEX",
- "bindingModeInteractions": [
- -1
- "r0KsTested": [
- 1
- "bindingModes": [
- -1
- "modifications": []
- {
- "countTable": [
- {
- "leftFlank": "",
- "transliterate": {
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- "out": []
- "variableRegionLength": 200,
- "modeledColumns": [
- 0,
- 1
- "inputFileType": "tsv.gz",
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- "rightFlank": "",
- "countTableFile": "jobs/fefdadcaefe5/countTable.0.tsv.gz"
- {
- "leftFlank": "",
- "transliterate": {
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- {
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- "countTableFile": "jobs/fefdadcaefe5/countTable.2.tsv.gz"
- {
- "bindingModeInteractions": [],
- "bindingModes": [],
- "letterComplement": "C-G,A-T"
- "enrichmentModel": [
- "modelFittingConstraints": {
- "enrichmentModel": [
- {
- "fitDelta": [
- false
- "roundSpecificGamma": true,
- "fitRho": false,
- "roundSpecificDelta": true,
- "fitGamma": false,
- "trySaturation": false,
- "roundSpecificRho": true
- "fitDelta": [
- {
- "fitDelta": [
- false
- "roundSpecificGamma": true,
- "fitRho": false,
- "roundSpecificDelta": true,
- "fitGamma": false,
- "trySaturation": false,
- "roundSpecificRho": true
- "fitDelta": [
- {
- "fitDelta": [
- false
- "roundSpecificGamma": true,
- "fitRho": false,
- "roundSpecificDelta": true,
- "fitGamma": false,
- "trySaturation": false,
- "roundSpecificRho": true
- "fitDelta": [
- {
- "nShifts": 0,
- "countTable": [
- {},
- {},
- {}
- "addBindingModesSequentially": true,
- "flankLengths": [
- 0
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- "singleModeLengthSweep": false,
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- {
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- "positionBiasBinWidth": 1,
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- "maxSize": -1,
- "optimizeFlankLength": false,
- "symmetryString": "null",
- "roundSpecificActivity": true,
- "informationThreshold": 0.1,
- "optimizeMotifShift": false,
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- "optimizeMotifShiftHeuristic": false,
- "experimentSpecificPositionBias": true,
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- "experimentSpecificActivity": true,
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- {
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- "informationThreshold": 0.1,
- "optimizeMotifShift": false,
- "fittingStages": [],
- "optimizeMotifShiftHeuristic": false,
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- "experimentSpecificActivity": true,
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- {
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Probound Text Output
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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}],"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":"abcdefg1GFEDCBA","optimizeFlankLength":false,"roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"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":"abcdefg1GFEDCBA","optimizeFlankLength":false,"roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"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}] > Builds likelihood object. >> Creating CombinedLikelihood object. Alphabet ======== Letter Complement: C-G,A-T Letter Order: ACGT 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 1 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 16:33:11.129). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]}],"bindingModeInteractions":[],"bindingModes":[{},{}]} Value and gradient before optimization: ======================================= value = 13.48916481067059 gradient = {0.4999,-0.4999,0.4999,-0.4999,0.4999,-0.4999} gradient norm = 1.2244402463764148 Starting Function Value: 13.48916481067059 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 7.387135231367192 5.000000000000000 4.083498573978522 1.206802887527609 2 7 2.302825766830394 6.968729812589974 0.020369521766198 0.454973544030718 3 9 2.080077992239129 0.955491218148372 0.500794469986259 0.000075483608422 4 10 2.080077986556125 0.000158549642737 1.000000000000000 0.000003791529997 5 11 2.080077986542296 0.000158549642737 1.000000000000000 0.000000000000028 Convergence criteria met. After: gradient norm = 2.8273603066674934E-14 >>> Parameters after optimization Count Table 0: --------------- h: {-4.4961,4.4961} Count Table 1: --------------- h: {-4.4961,4.4961} Count Table 2: --------------- h: {-4.4961,4.4961} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-8.9922,-8.9922} Activity(exp=1): {-8.9922,-8.9922} Activity(exp=2): {-8.9922,-8.9922} Binding mode 1: --------------- Mononucleotide: {0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000} Activity(exp=0): {0.0000,0.0000} Activity(exp=1): {0.0000,0.0000} Activity(exp=2): {0.0000,0.0000} > Initial optimization (component0-1-f0). >> Starting new optimization: component0-1-f0. (2021-05-21 16:33:12.974). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[6,7]},{"h":[8,9]},{"h":[10,11]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5]]},{}]} Value and gradient before optimization: ======================================= value = 2.080077986542501 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} gradient norm = 5.615612157603672E-5 Starting Function Value: 2.080077986542501 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 2.080077977432690 0.000321472079216 5.724613278011847 0.000101584460433 2 7 2.080076792139533 0.024410583302448 85.000000000000000 0.000186682210103 3 8 2.079920709866871 4.461539920125083 1.000000000000000 0.008082789248141 4 9 2.079757080346703 6.240945851470735 1.000000000000000 0.011770071739059 5 10 2.079556952003967 9.883316620786223 1.000000000000000 0.010194396763882 6 11 2.079483145648375 4.455367677355632 1.000000000000000 0.004137132486471 7 12 2.079471974525198 0.049334798963376 1.000000000000000 0.000539266147070 8 13 2.079471546825102 0.417127785324951 1.000000000000000 0.000001473686162 9 14 2.079471541693515 0.068992628130223 1.000000000000000 0.000003176426398 10 15 2.079471541679484 0.002724387016917 1.000000000000000 0.000000174704081 >>>> Exception caugth. Parameters reverted. > Parameter: {2.1343e-06,2.1268e-06,2.1343e-06,2.0060e-06,2.1343e-06,2.0686e-06,1.0563e-06,-1.0563e-06,1.1865e-06,-1.1865e-06,1.1178e-06,-1.1178e-06} > Gradient: {4.2685e-12,3.5516e-09,4.2686e-12,-9.1744e-08,4.2686e-12,-4.1751e-08,-3.5452e-09,3.5452e-09,9.1750e-08,-9.1750e-08,4.1758e-08,-4.1758e-08} >>>> Re-trying (1/3). Starting Function Value: 2.079471541679484 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 2.079471541679178 0.000000220398505 1.261553271375516 0.000000009404762 2 4 2.079471541678233 0.000000220398505 1.000000000000000 0.000000000011659 Convergence criteria met. After: gradient norm = 1.1659306138570689E-11 >>> 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} 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} Binding mode 1: --------------- Mononucleotide: {0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000} Activity(exp=0): {0.0000,0.0000} Activity(exp=1): {0.0000,0.0000} Activity(exp=2): {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 16:33:17.397). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[6,7]},{"h":[8,9]},{"h":[10,11]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5]]},{}]} Value and gradient before optimization: ======================================= value = 2.0794715416782332 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} gradient norm = 1.165930582770322E-11 Already at minimum! After: gradient norm = 1.165930582770322E-11 >>> 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} 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} Binding mode 1: --------------- Mononucleotide: {0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000} Activity(exp=0): {0.0000,0.0000} Activity(exp=1): {0.0000,0.0000} Activity(exp=2): {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 16:33:17.495). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[6,7]},{"h":[8,9]},{"h":[10,11]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5]]},{}]} Value and gradient before optimization: ======================================= value = 2.0794715416782332 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} gradient norm = 1.165930598296555E-11 Already at minimum! After: gradient norm = 1.165930598296555E-11 >>> 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} 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} Binding mode 1: --------------- Mononucleotide: {0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000} Activity(exp=0): {0.0000,0.0000} Activity(exp=1): {0.0000,0.0000} Activity(exp=2): {0.0000,0.0000} ================================== == Starts fiting Binding mode 1 == ================================== > Optimizing h (component1-0-h). >> Starting new optimization: component1-0-h. (2021-05-21 16:33:18.369). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[0,1]},{"h":[2,3]},{"h":[4,5]}],"bindingModeInteractions":[],"bindingModes":[{},{}]} Value and gradient before optimization: ======================================= value = 4.862915874110651 gradient = {-0.4586,0.4586,-0.4586,0.4586,-0.4597,0.4597} gradient norm = 1.1242388812184285 Starting Function Value: 4.862915874110651 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 2 3.789541527923842 1.000000000000000 0.889490673829230 1.008966954688266 2 4 2.100361579860996 2.563573276936788 0.292818817648625 0.158988471622782 3 5 2.080522114240854 0.479293592165320 1.000000000000000 0.076696055985879 4 6 2.074553506085069 0.155970604316203 1.000000000000000 0.000215017518864 5 7 2.074553459289241 0.155970604316203 1.000000000000000 0.000000310073935 Convergence criteria met. After: gradient norm = 3.100739345927095E-7 >>> Parameters after optimization Count Table 0: --------------- h: {1.5806,-1.5806} Count Table 1: --------------- h: {1.5816,-1.5816} Count Table 2: --------------- h: {1.5979,-1.5979} 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} Binding mode 1: --------------- Mononucleotide: {0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000} Activity(exp=0): {3.5081,3.5081} Activity(exp=1): {3.5081,3.5081} Activity(exp=2): {3.5081,3.5081} > Initial optimization (component1-1-f0). >> Starting new optimization: component1-1-f0. (2021-05-21 16:34:20.871). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[36,37]},{"h":[38,39]},{"h":[40,41]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,3,2,5,4,7,6,9,8,11,10,13,12,15,14,17,16,19,18,21,20,23,22,25,24,27,26,29,28,28,29,26,27,24,25,22,23,20,21,18,19,16,17,14,15,12,13,10,11,8,9,6,7,4,5,2,3,0,1],"activity":[[30,31],[32,33],[34,35]]}]} Value and gradient before optimization: ======================================= value = 2.0745534592892416 gradient = {-0.0049,0.0176,0.0011,-0.0126,-0.0004,0.0011,0.0027,-0.0022,-0.0014,-0.0005,0.0054,-0.0022,-0.0026,0.0059,0.0017,-0.0037,-0.0061,0.0031,0.0050,-0.0008,-0.0040,0.0119,-0.0013,-0.0053,-0.0029,0.0043,0.0057,-0.0058,-0.0011,0.0017,0.0000,0.0003,0.0000,0.0003,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000} gradient norm = 0.030958214303740364 Starting Function Value: 2.0745534592892416 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 2.073690728554003 0.061770841978998 1.995297318280238 0.105872500121439 2 4 2.072210338481798 0.050225509341088 1.000000000000000 0.078899038457751 3 5 2.069586973210066 0.283642054638224 1.000000000000000 0.061792307892103 4 6 2.069151786995589 0.058576412048795 1.000000000000000 0.017664531808241 5 7 2.069016206774240 0.011880761990521 1.000000000000000 0.018658371890503 6 8 2.067428105840486 0.172940538851923 1.000000000000000 0.057342341599985 7 9 2.065051385588439 0.316472651418250 1.000000000000000 0.028305799977570 8 11 2.063841632601536 0.218256636644455 0.504762825463624 0.054173041061593 9 12 2.062614169905646 0.135826214090730 1.000000000000000 0.017917843359452 10 13 2.062359514051110 0.027581258095850 1.000000000000000 0.013474268983200 11 14 2.061938771747971 0.055508367970572 1.000000000000000 0.013367268030045 12 15 2.061399766286905 0.109433158206263 1.000000000000000 0.018146768435276 13 16 2.060893192218785 0.112408439482187 1.000000000000000 0.019361317592907 14 17 2.060754896847425 0.045940192880197 1.000000000000000 0.004987108154957 15 18 2.060713006154841 0.037013921771379 1.000000000000000 0.013647291843383 16 19 2.060684740705677 0.005383839259898 1.000000000000000 0.009128919007338 17 20 2.060553023110279 0.045048709442033 1.000000000000000 0.021032383921036 18 21 2.060503303351176 0.031499829313660 1.000000000000000 0.026477274349950 19 22 2.060434486606177 0.042851811385263 1.000000000000000 0.025382982361834 20 23 2.060297185361886 0.065267050702426 1.000000000000000 0.019495740265286 21 24 2.060079211676884 0.131623995900634 1.000000000000000 0.009567383927707 22 25 2.059995129889372 0.075478635043060 1.000000000000000 0.002580888099462 23 26 2.059976499485868 0.030082628733997 1.000000000000000 0.003354497103206 24 27 2.059968299899617 0.012232310006378 1.000000000000000 0.003607785094588 25 28 2.059936031299497 0.031832449262686 1.000000000000000 0.002738959599396 26 29 2.059890529801764 0.058948247505346 1.000000000000000 0.001989638822979 27 30 2.059874712979800 0.030482298206458 1.000000000000000 0.001954680843976 28 32 2.059868695695422 0.016683103484718 0.412655394135517 0.002034400839499 29 33 2.059862619369127 0.012182017003433 1.000000000000000 0.001384067616261 30 34 2.059854142695489 0.017226753684559 1.000000000000000 0.001399366305198 31 35 2.059839072818339 0.038797392655041 1.000000000000000 0.002273112806950 32 36 2.059818168850546 0.056522800899200 1.000000000000000 0.003636913722550 33 37 2.059795037934378 0.078683582149886 1.000000000000000 0.001818961927420 34 38 2.059779302761853 0.050923366169143 1.000000000000000 0.002750336921948 35 39 2.059759406533408 0.056183976190719 1.000000000000000 0.002547838921900 36 40 2.059721243130226 0.097120600243301 1.000000000000000 0.005267911723008 37 41 2.059662503454485 0.145518620840810 1.000000000000000 0.010895559341142 38 42 2.059522119440097 0.397708512534194 1.000000000000000 0.025641654895427 39 43 2.059355545101417 0.296588169770153 1.000000000000000 0.030199704124566 40 44 2.058929355398475 0.746165288250948 1.000000000000000 0.058496894061661 41 45 2.058180322777941 0.490440461366901 1.000000000000000 0.039094996543546 42 47 2.057877099468315 0.278081274791609 0.188322770051649 0.060453166890025 43 49 2.056863787001408 0.412794036124822 0.272694967610552 0.066522490068919 44 50 2.054367057960342 0.500471716488724 1.000000000000000 0.042840284659745 45 51 2.053013409003781 0.190420987704267 1.000000000000000 0.020104119432743 46 53 2.051376801818488 0.422595265155654 0.342211235229119 0.028438787158402 47 55 2.050777898732307 0.240788360098424 0.311694778011642 0.040428773599362 48 56 2.049800594089707 0.187178407915511 1.000000000000000 0.032226918744939 49 57 2.048362341439809 0.311761599413763 1.000000000000000 0.034886361482022 50 58 2.047535314635866 0.226345434597723 1.000000000000000 0.023936538604963 51 59 2.046796409914041 0.322201232812134 1.000000000000000 0.026427550064678 52 60 2.046420095894303 0.334998516414954 1.000000000000000 0.027263290389420 53 61 2.045907254340095 0.275632961023569 1.000000000000000 0.012814488219411 54 62 2.045786288236797 0.111032587759118 1.000000000000000 0.005523780375209 55 63 2.045698950111991 0.035752715650770 1.000000000000000 0.005391080524611 56 64 2.045501944319815 0.123011164906946 1.000000000000000 0.003626638081962 57 65 2.045382724123479 0.083543277694737 1.000000000000000 0.003267974247088 58 66 2.045258789155094 0.125629129879663 1.000000000000000 0.006320364817513 59 67 2.045211669469511 0.047995971667460 1.000000000000000 0.006633553650989 60 68 2.045147356829288 0.069612765911676 1.000000000000000 0.005614091111630 61 69 2.045111070203525 0.058919004544735 1.000000000000000 0.003511120368437 62 70 2.045089676096569 0.056340978859304 1.000000000000000 0.001319475782680 63 71 2.045079772179331 0.039534415568383 1.000000000000000 0.001251576319435 64 72 2.045073078090967 0.028875856718967 1.000000000000000 0.002174147934294 65 73 2.045065059405048 0.028338343540955 1.000000000000000 0.002758728487068 66 74 2.045051021871182 0.043553831830000 1.000000000000000 0.002682714904935 67 75 2.045024759495908 0.076827396315152 1.000000000000000 0.001949186169692 68 76 2.044995185861689 0.111248771769081 1.000000000000000 0.001263476974329 69 77 2.044979167385569 0.064778348591122 1.000000000000000 0.001836287894023 70 78 2.044958510279319 0.070776351750985 1.000000000000000 0.002227637498412 71 79 2.044907999619072 0.178392800833392 1.000000000000000 0.003968378491282 72 80 2.044820399836500 0.379155691364099 1.000000000000000 0.011284762823516 73 81 2.044720929753753 0.303116116358403 1.000000000000000 0.014927522834180 74 82 2.044551110075345 0.262582573864541 1.000000000000000 0.005811941784292 75 84 2.044496253782643 0.176874000130304 0.267732666884656 0.013439385120557 76 85 2.044316991562400 0.319859554557631 1.000000000000000 0.016832055178855 77 86 2.044136025313606 0.108677671369175 1.000000000000000 0.005390674327828 78 87 2.043970464328657 0.491376989344451 1.000000000000000 0.022124749368286 79 88 2.043717425224427 0.134366800529792 1.000000000000000 0.006138567237839 80 89 2.043573991644553 0.224430031671859 1.000000000000000 0.009013028044196 81 90 2.043455725456750 0.179926367035562 1.000000000000000 0.005992647400701 82 91 2.043370785286175 0.148704740428656 1.000000000000000 0.005905599695679 83 92 2.043342699341765 0.086033085637260 1.000000000000000 0.003618097126302 84 93 2.043315413615597 0.097853046783632 1.000000000000000 0.004405674787493 85 94 2.043303993074042 0.030890725190902 1.000000000000000 0.004068936153064 86 95 2.043252910899078 0.096904670885572 1.000000000000000 0.003931902624272 87 96 2.043198234841562 0.093600486563912 1.000000000000000 0.003656968112154 88 97 2.043113630414266 0.199018437044943 1.000000000000000 0.005250141767824 89 98 2.043064948228675 0.151715946600401 1.000000000000000 0.003262989583216 90 99 2.043044647615364 0.104214939832501 1.000000000000000 0.002312483731879 91 100 2.043033442831671 0.085068422000576 1.000000000000000 0.001932520253234 92 101 2.043027593754105 0.041304483192624 1.000000000000000 0.000662895720636 93 102 2.043024985244059 0.050674422024345 1.000000000000000 0.000744204689647 94 103 2.043023488490862 0.020489890317046 1.000000000000000 0.000302692829441 95 104 2.043021914358564 0.023142317643628 1.000000000000000 0.000350335302433 96 105 2.043020303470405 0.014639485372299 1.000000000000000 0.000389993295421 97 106 2.043015163327207 0.042813025117906 1.000000000000000 0.000337232605129 98 107 2.043009185896196 0.074201055546949 1.000000000000000 0.000307558162672 99 108 2.043006343808197 0.056397091896473 1.000000000000000 0.000487820955323 100 109 2.043005069052745 0.027710787436498 1.000000000000000 0.000480028497384 101 110 2.043003728786829 0.029255037254679 1.000000000000000 0.000408139112926 102 111 2.043002485998949 0.032534534835765 1.000000000000000 0.000313401173098 103 112 2.043001657746054 0.025685226149329 1.000000000000000 0.000207870817347 104 113 2.043001278080153 0.014817144704986 1.000000000000000 0.000093720960850 105 114 2.043001099749151 0.007110344963863 1.000000000000000 0.000086723377232 106 115 2.043000941273756 0.006957604388617 1.000000000000000 0.000105591044266 107 116 2.043000752552767 0.008989113830888 1.000000000000000 0.000172035470165 108 117 2.043000484714456 0.012342737595510 1.000000000000000 0.000181836411191 109 118 2.043000159818391 0.013710012741808 1.000000000000000 0.000174870717942 110 119 2.042999544073394 0.034098279966846 1.000000000000000 0.000169714987155 111 121 2.042998996388644 0.041795331065787 0.408953299217686 0.000192559931834 112 122 2.042997774293442 0.045208512140404 1.000000000000000 0.000201010975359 113 123 2.042992669233467 0.256352189788700 1.000000000000000 0.000675987553655 114 124 2.042989229582596 0.193386070671001 1.000000000000000 0.000587343467078 115 125 2.042983745251218 0.295885540825371 1.000000000000000 0.000638688670976 116 126 2.042971950075275 0.888383614979563 1.000000000000000 0.001530710539031 117 127 2.042958394205538 0.051939206036272 1.000000000000000 0.000547410580783 118 128 2.042945214858727 0.488895755422445 1.000000000000000 0.000776014023789 119 130 2.042942719849503 0.114560742556797 0.110503144747512 0.000850408208402 120 131 2.042934478843847 0.169243337780508 1.000000000000000 0.001345315708031 121 132 2.042928120891954 0.058850719488696 1.000000000000000 0.000525348968574 122 133 2.042922599248073 0.140183573479415 1.000000000000000 0.000663863660868 123 134 2.042919655679240 0.043686339558362 1.000000000000000 0.000777285286020 124 135 2.042913077026566 0.081319509147815 1.000000000000000 0.000703795624713 125 137 2.042911895920383 0.021962037712918 0.142091217859789 0.000646358573292 126 138 2.042909367112950 0.039820857004827 1.000000000000000 0.000275414636914 127 139 2.042908240085259 0.019410941164344 1.000000000000000 0.000170597863341 128 140 2.042907768050989 0.011876688069262 1.000000000000000 0.000177924692368 129 141 2.042907366817275 0.007801702502095 1.000000000000000 0.000099699240693 130 142 2.042907159543508 0.008051052341476 1.000000000000000 0.000090406836518 131 143 2.042907020846082 0.006564164007542 1.000000000000000 0.000050705760579 132 144 2.042906937729534 0.006770940543886 1.000000000000000 0.000045791725277 133 145 2.042906815399808 0.008227248427343 1.000000000000000 0.000052427789528 134 146 2.042906581953487 0.023176503575901 1.000000000000000 0.000073072758156 135 147 2.042906313602264 0.025821785811893 1.000000000000000 0.000102565466563 136 148 2.042905690573800 0.068991515526318 1.000000000000000 0.000113086069866 137 149 2.042904481491642 0.129168680999824 1.000000000000000 0.000188389546025 138 150 2.042901334673993 0.360052938061749 1.000000000000000 0.000275426532389 139 151 2.042895042939233 0.725477599270898 1.000000000000000 0.000440300688117 140 152 2.042883025171637 1.464817352897565 1.000000000000000 0.000528633430317 141 153 2.042865992400525 2.332543673826821 1.000000000000000 0.000852705671085 142 154 2.042850737353047 2.001377010814208 1.000000000000000 0.000513980331526 143 155 2.042846799218040 0.912291970817569 1.000000000000000 0.000640543988671 144 156 2.042842733005831 0.482291017719359 1.000000000000000 0.000230318490310 145 157 2.042842274634327 0.215754661798749 1.000000000000000 0.000212422469604 146 158 2.042841517592071 0.127277729865136 1.000000000000000 0.000249785450927 147 160 2.042841285600830 0.031412773698674 0.253054795675592 0.000104566171282 148 161 2.042841051718159 0.179762157563414 1.000000000000000 0.000059026871647 149 162 2.042840968684344 0.179997507388755 1.000000000000000 0.000026270368677 150 163 2.042840960596610 0.006266930207879 1.000000000000000 0.000012595073782 151 164 2.042840958375841 0.001794828313719 1.000000000000000 0.000009000016651 152 165 2.042840956361424 0.006526320523599 1.000000000000000 0.000010115773006 153 166 2.042840953666038 0.006101194063475 1.000000000000000 0.000016489666185 154 167 2.042840949017792 0.006406683905566 1.000000000000000 0.000025653779238 155 168 2.042840941296952 0.007042275742232 1.000000000000000 0.000033271966011 156 169 2.042840928753600 0.018147990630501 1.000000000000000 0.000059966692958 157 170 2.042840906855602 0.012283484139791 1.000000000000000 0.000057769672292 158 171 2.042840863818375 0.021273460727502 1.000000000000000 0.000068523101151 159 172 2.042840719986602 0.069039846808316 1.000000000000000 0.000115154671965 160 173 2.042840454596135 0.127519560638228 1.000000000000000 0.000177723887453 161 174 2.042839869831725 0.262334692065814 1.000000000000000 0.000272565281489 162 175 2.042838891363892 0.448818542020894 1.000000000000000 0.000304767298569 163 176 2.042838061216045 0.489067959743716 1.000000000000000 0.000487107659563 164 177 2.042837656172281 0.157574135054082 1.000000000000000 0.000117692317500 165 178 2.042837546724720 0.079036388859166 1.000000000000000 0.000022054662094 166 179 2.042837534306784 0.037721701111267 1.000000000000000 0.000006586466026 167 180 2.042837533874616 0.004680171380446 1.000000000000000 0.000003703366142 168 181 2.042837533816787 0.001132795617210 1.000000000000000 0.000001041640310 169 182 2.042837533801381 0.001132795617210 1.000000000000000 0.000000205474441 Convergence criteria met. After: gradient norm = 2.0547444126960997E-7 >>> Parameters after optimization Count Table 0: --------------- h: {0.0065,-0.0065} Count Table 1: --------------- h: {0.0685,-0.0685} Count Table 2: --------------- h: {0.3167,-0.3167} 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} Binding mode 1: --------------- Mononucleotide: {-0.3634,-1.0821,-0.1306,-1.4181,-0.8797,-1.5315,0.6107,-1.1938,-0.3317,-1.0062,-0.8030,-0.8487,0.7094,-1.5860,-0.9291,-1.1885,-2.1481,1.4316,-1.1328,-1.1450,-0.0039,-1.6773,-0.2714,-1.0417,-0.9329,-0.7262,-0.5800,-0.7505,-0.6786,-0.8162,-0.8162,-0.6786,-0.7505,-0.5800,-0.7262,-0.9329,-1.0417,-0.2714,-1.6773,-0.0039,-1.1450,-1.1328,1.4316,-2.1481,-1.1885,-0.9291,-1.5860,0.7094,-0.8487,-0.8030,-1.0062,-0.3317,-1.1938,0.6107,-1.5315,-0.8797,-1.4181,-0.1306,-1.0821,-0.3634} Activity(exp=0): {0.0410,-3.2377} Activity(exp=1): {0.0410,-0.8188} Activity(exp=2): {0.0410,0.9590} Suggested variations: key=15;0;0, description = Initial model. > Optimizing variation "Initial model." (component1-2-variation0). >> Starting new optimization: component1-2-variation0. (2021-05-21 17:19:41.129). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[36,37]},{"h":[38,39]},{"h":[40,41]}],"bindingModeInteractions":[],"bindingModes":[{},{"mononucleotide":[1,0,3,2,5,4,7,6,9,8,11,10,13,12,15,14,17,16,19,18,21,20,23,22,25,24,27,26,29,28,28,29,26,27,24,25,22,23,20,21,18,19,16,17,14,15,12,13,10,11,8,9,6,7,4,5,2,3,0,1],"activity":[[30,31],[32,33],[34,35]]}]} Value and gradient before optimization: ======================================= value = 2.042837533801381 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} gradient norm = 2.0547444126960631E-7 Already at minimum! After: gradient norm = 2.0547444126960631E-7 >>> Parameters after optimization Count Table 0: --------------- h: {0.0065,-0.0065} Count Table 1: --------------- h: {0.0685,-0.0685} Count Table 2: --------------- h: {0.3167,-0.3167} 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} Binding mode 1: --------------- Mononucleotide: {-0.3634,-1.0821,-0.1306,-1.4181,-0.8797,-1.5315,0.6107,-1.1938,-0.3317,-1.0062,-0.8030,-0.8487,0.7094,-1.5860,-0.9291,-1.1885,-2.1481,1.4316,-1.1328,-1.1450,-0.0039,-1.6773,-0.2714,-1.0417,-0.9329,-0.7262,-0.5800,-0.7505,-0.6786,-0.8162,-0.8162,-0.6786,-0.7505,-0.5800,-0.7262,-0.9329,-1.0417,-0.2714,-1.6773,-0.0039,-1.1450,-1.1328,1.4316,-2.1481,-1.1885,-0.9291,-1.5860,0.7094,-0.8487,-0.8030,-1.0062,-0.3317,-1.1938,0.6107,-1.5315,-0.8797,-1.4181,-0.1306,-1.0821,-0.3634} Activity(exp=0): {0.0410,-3.2377} Activity(exp=1): {0.0410,-0.8188} Activity(exp=2): {0.0410,0.9590} The Likelihood DID NOT improve. Discarding fit component1-2-variation0. > No varitions possible for Binding mode 1. > Optimizing the full model (component1-4-all). >> Starting new optimization: component1-4-all. (2021-05-21 17:19:56.714). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{}],"countTable":[{"h":[42,43]},{"h":[44,45]},{"h":[46,47]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[],"activity":[[0,1],[2,3],[4,5]]},{"mononucleotide":[7,6,9,8,11,10,13,12,15,14,17,16,19,18,21,20,23,22,25,24,27,26,29,28,31,30,33,32,35,34,34,35,32,33,30,31,28,29,26,27,24,25,22,23,20,21,18,19,16,17,14,15,12,13,10,11,8,9,6,7],"activity":[[36,37],[38,39],[40,41]]}]} Value and gradient before optimization: ======================================= value = 2.042837533801381 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} gradient norm = 7.047275391702686E-6 Starting Function Value: 2.042837533801381 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 2.042837533688548 0.000031144405251 4.419354079369641 0.000010495706187 2 4 2.042837533531461 0.000027600137070 1.000000000000000 0.000010656864299 3 5 2.042837527316177 0.002897991564827 1.000000000000000 0.000070235553433 4 6 2.042837523888509 0.001398232641857 1.000000000000000 0.000091182956763 5 7 2.042837520295207 0.000360010610141 1.000000000000000 0.000048627846391 6 8 2.042837515398324 0.000610797675055 1.000000000000000 0.000020277239409 7 9 2.042837510015171 0.002023412210463 1.000000000000000 0.000034890777083 8 10 2.042837506516432 0.002063341760278 1.000000000000000 0.000028969661522 9 11 2.042837500074549 0.003090216054229 1.000000000000000 0.000040749281816 10 12 2.042837484010596 0.007685737363165 1.000000000000000 0.000048017243538 11 13 2.042837455483515 0.011503897291027 1.000000000000000 0.000098627250891 12 14 2.042837407190174 0.019542939187926 1.000000000000000 0.000100684747938 13 15 2.042837371466560 0.014657215096677 1.000000000000000 0.000105635900289 14 16 2.042837352785856 0.005585480986564 1.000000000000000 0.000025629969868 15 17 2.042837348031834 0.002754947422262 1.000000000000000 0.000030045089385 16 18 2.042837343205991 0.001735473910084 1.000000000000000 0.000031754846416 17 19 2.042837334473721 0.002890417500271 1.000000000000000 0.000018581437491 18 20 2.042837327378899 0.005645311357061 1.000000000000000 0.000013310463199 19 21 2.042837321338225 0.005622218445697 1.000000000000000 0.000022911643940 20 22 2.042837310642847 0.008426492247079 1.000000000000000 0.000036693632848 21 23 2.042837291079276 0.011226062034493 1.000000000000000 0.000046758473388 22 24 2.042837244331212 0.021733304316195 1.000000000000000 0.000057469970928 23 25 2.042837124937044 0.051314668548603 1.000000000000000 0.000066302972135 24 26 2.042836887442966 0.149055484596354 1.000000000000000 0.000157375704708 25 27 2.042836579666882 0.095369219440237 1.000000000000000 0.000113866623410 26 28 2.042835709598950 0.338802200809913 1.000000000000000 0.000080540088337 27 29 2.042835296798777 0.156787680975331 1.000000000000000 0.000130296620422 28 30 2.042834377867177 0.392607701615535 1.000000000000000 0.000132072479714 29 31 2.042833105520913 0.631246387194953 1.000000000000000 0.000503559380300 30 32 2.042832535790081 0.255891223405227 1.000000000000000 0.000221831455480 31 33 2.042832409771395 0.011187184505538 1.000000000000000 0.000065890484951 32 34 2.042832385598709 0.017597239272485 1.000000000000000 0.000042366297407 33 35 2.042832343082395 0.010551370683584 1.000000000000000 0.000069592768741 34 36 2.042832300240828 0.022302418019407 1.000000000000000 0.000087421345187 35 37 2.042832200143711 0.063042101212377 1.000000000000000 0.000091924552865 36 38 2.042832051897241 0.068692937224911 1.000000000000000 0.000093333160180 37 39 2.042832046510880 0.088174044686390 1.000000000000000 0.000101238414911 38 40 2.042832012356040 0.054502425625694 1.000000000000000 0.000009635601990 39 41 2.042832011002286 0.005060636753433 1.000000000000000 0.000007002590265 40 42 2.042832008563233 0.001421959071793 1.000000000000000 0.000008655608658 41 43 2.042832005143821 0.004947177728507 1.000000000000000 0.000015172854914 42 44 2.042832003221489 0.001200202944423 1.000000000000000 0.000011071072462 43 45 2.042832001427809 0.001524828978723 1.000000000000000 0.000003264575113 44 46 2.042832001159955 0.000601466897967 1.000000000000000 0.000002319369354 45 47 2.042832001079688 0.000220544431707 1.000000000000000 0.000002401434681 46 48 2.042832000978764 0.000349610274889 1.000000000000000 0.000001394374273 47 49 2.042832000867503 0.000584419278928 1.000000000000000 0.000001402649238 48 50 2.042832000811145 0.000220736973912 1.000000000000000 0.000001995168089 49 51 2.042832000707437 0.000295723608099 1.000000000000000 0.000002135823006 50 52 2.042832000536115 0.000505004017867 1.000000000000000 0.000001696847847 51 53 2.042832000419129 0.000641095369353 1.000000000000000 0.000001256102345 52 54 2.042832000371163 0.000122484406349 1.000000000000000 0.000000672009147 53 55 2.042832000362159 0.000122484406349 1.000000000000000 0.000000377982610 Convergence criteria met. After: gradient norm = 3.7798260995006115E-7 >>> Parameters after optimization Count Table 0: --------------- h: {0.7514,-0.7514} Count Table 1: --------------- h: {0.3171,-0.3171} Count Table 2: --------------- h: {0.1626,-0.1626} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {0.0000,1.4900} Activity(exp=1): {0.0000,0.4972} Activity(exp=2): {0.0000,-0.3085} Binding mode 1: --------------- Mononucleotide: {-0.3295,-1.0480,-0.0967,-1.3842,-0.8458,-1.4972,0.6445,-1.1599,-0.3001,-0.9744,-0.7713,-0.8171,0.7432,-1.5519,-0.8951,-1.1546,-2.1141,1.4654,-1.0987,-1.1110,0.0300,-1.6432,-0.2374,-1.0078,-0.9012,-0.6945,-0.5482,-0.7189,-0.6469,-0.7845,-0.7845,-0.6469,-0.7189,-0.5482,-0.6945,-0.9012,-1.0078,-0.2374,-1.6432,0.0300,-1.1110,-1.0987,1.4654,-2.1141,-1.1546,-0.8951,-1.5519,0.7432,-0.8171,-0.7713,-0.9744,-0.3001,-1.1599,0.6445,-1.4972,-0.8458,-1.3842,-0.0967,-1.0480,-0.3295} Activity(exp=0): {0.0002,-2.2608} Activity(exp=1): {0.0002,-0.8188} Activity(exp=2): {0.0002,0.1536} > Optimization done.
Probound Model
±
Optimized model:
{
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- {
Model Viewer
±
Binding Mode 0
Size
0
Flank length
0
Binding Mode 1
Size
15
Flank length
0
Mononucleotide (15bp)