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": "addTable", "leftFlank": "ACACTCTTTCCCTACACGACGCTCTTCCGATCTTGACGTC", "nColumns": 2, "inputFileType": "tsv.gz", "countTableFile": "jobs/133d27f6506e/countTable.0.tsv.gz", "rightFlank": "GACGTCAGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG", "variableRegionLength": 30}, {"function": "addTable", "leftFlank": "CGGAGTCGGCAAGCAGAAGACGGCATACGATAGC", "nColumns": 5, "inputFileType": "tsv.gz", "countTableFile": "jobs/133d27f6506e/countTable.1.tsv.gz", "rightFlank": "TCGCTAGATCGGAAGAGCGTCG", "variableRegionLength": 20}, {"function": "addSELEX"}, {"function": "addSELEX"}, {"function": "addBindingMode", "singleStrand": true, "positionBias": true, "size": 1}, {"function": "addBindingMode", "flankLength": 5, "size": 12}, {"function": "addBindingMode", "flankLength": 5, "size": 12}, {"function": "bindingModeConstraints", "index": 0, "experimentSpecificPositionBias": true}, {"function": "bindingModeConstraints", "index": 1, "maxFlankLength": -1, "fittingStages": [{"optimizeFlankLength": true}, {"optimizeMotifShiftHeuristic": true}, {"optimizeSizeHeuristic": true}], "maxSize": 18}, {"function": "bindingModeConstraints", "index": 2, "maxFlankLength": -1, "fittingStages": [{"optimizeFlankLength": true}, {"optimizeMotifShiftHeuristic": true}, {"optimizeSizeHeuristic": true}], "maxSize": 18}, {"function": "optimizerSetting", "likelihoodThreshold": 0.0002, "pseudocount": 20, "nThreads": 20, "lambdaL2": 1e-06}, {"function": "output", "outputPath": "jobs/133d27f6506e", "baseName": "fit", "storeHessian": false, "printTrajectory": false}]Configuration File
±
ProBound configuration file:
{
"optimizerSetting": {
"likelihoodThreshold": 2.0E-4,
"nThreads": 20,
"lambdaL2": 1.0E-6,
"pseudocount": 20,
"patternSearchSettings": {},
"minimizerType": "lbfgs",
"nRetries": 3,
"hkSettings": {},
"output": {
"storeHessian": false,
"outputPath": "jobs/133d27f6506e",
"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": []
}
],
"countTable": [
{
"leftFlank": "ACACTCTTTCCCTACACGACGCTCTTCCGATCTTGACGTC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 30,
"modeledColumns": [-1],
"inputFileType": "tsv.gz",
"nColumns": 2,
"rightFlank": "GACGTCAGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG",
"countTableFile": "jobs/133d27f6506e/countTable.0.tsv.gz"
},
{
"leftFlank": "CGGAGTCGGCAAGCAGAAGACGGCATACGATAGC",
"transliterate": {
"in": [],
"out": []
},
"variableRegionLength": 20,
"modeledColumns": [-1],
"inputFileType": "tsv.gz",
"nColumns": 5,
"rightFlank": "TCGCTAGATCGGAAGAGCGTCG",
"countTableFile": "jobs/133d27f6506e/countTable.1.tsv.gz"
}
],
"bindingModeInteractions": [],
"bindingModes": [
{
"size": 1,
"fitLogActivity": true,
"flankLength": 0,
"dinucleotideDistance": 0,
"positionBias": true,
"singleStrand": true,
"modifications": []
},
{
"size": 12,
"fitLogActivity": true,
"flankLength": 5,
"dinucleotideDistance": 0,
"positionBias": false,
"singleStrand": false,
"modifications": []
},
{
"size": 12,
"fitLogActivity": true,
"flankLength": 5,
"dinucleotideDistance": 0,
"positionBias": false,
"singleStrand": false,
"modifications": []
}
],
"letterComplement": "C-G,A-T"
},
"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
}
],
"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,
"maxSize": 18,
"optimizeSizeHeuristic": false,
"optimizeFlankLength": false,
"symmetryString": "null",
"roundSpecificActivity": true,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [
{"optimizeFlankLength": true},
{"optimizeMotifShiftHeuristic": true},
{"optimizeSizeHeuristic": true}
],
"optimizeMotifShiftHeuristic": false,
"experimentSpecificPositionBias": true,
"minSize": -1,
"experimentSpecificActivity": true,
"optimizeSize": false
},
{
"maxFlankLength": -1,
"positionBiasBinWidth": 1,
"maxSize": 18,
"optimizeSizeHeuristic": false,
"optimizeFlankLength": false,
"symmetryString": "null",
"roundSpecificActivity": true,
"informationThreshold": 0.1,
"optimizeMotifShift": false,
"fittingStages": [
{"optimizeFlankLength": true},
{"optimizeMotifShiftHeuristic": true},
{"optimizeSizeHeuristic": 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}],"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,"maxSize":18,"optimizeSizeHeuristic":false,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true},{"optimizeMotifShiftHeuristic":true},{"optimizeSizeHeuristic":true}],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"maxSize":18,"optimizeSizeHeuristic":false,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true},{"optimizeMotifShiftHeuristic":true},{"optimizeSizeHeuristic":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,"maxSize":18,"optimizeSizeHeuristic":false,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true},{"optimizeMotifShiftHeuristic":true},{"optimizeSizeHeuristic":true}],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"maxSize":18,"optimizeSizeHeuristic":false,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[{"optimizeFlankLength":true},{"optimizeMotifShiftHeuristic":true},{"optimizeSizeHeuristic":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}]
> Builds likelihood object.
>> Creating CombinedLikelihood object.
Alphabet
========
Letter Complement: C-G,A-T
Letter Order: ACGT
Optimizer settings:
===================
lambdaL2 = 1.0E-6
pseudocount = 20.0
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 2
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 2
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. (2021-05-22 06:17:07.679).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[0,1]},{"h":[2,3,4,5,6]}],"bindingModeInteractions":[],"bindingModes":[{},{},{}]}
Value and gradient before optimization:
=======================================
value = 9.042757630763937
gradient = {0.3925,-0.3925,0.7834,-0.1777,-0.2015,-0.2021,-0.2021}
gradient norm = 1.0371289777337034
Starting Function Value: 9.042757630763937
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 8.028696374673165 1.000000000000000 0.964200231089063 0.984567634944557
2 4 4.537337662131590 7.255835785791192 0.285495209626287 0.737188835699477
3 5 3.609857839159709 2.644563684193720 1.000000000000000 0.544907693695451
4 6 2.970958413712301 2.544137397410154 1.000000000000000 0.431551013635649
5 7 2.646967359900885 1.948620247862860 1.000000000000000 0.374405404899492
6 8 2.447997184351596 2.321986295605589 1.000000000000000 0.329180349533683
7 9 2.305062493059687 0.938211015937210 1.000000000000000 0.081545047152055
8 10 2.292577026116157 0.432296932553057 1.000000000000000 0.041437031909691
9 11 2.289322160551695 0.229419366153158 1.000000000000000 0.013277737817011
10 12 2.288921836689638 0.061625062697156 1.000000000000000 0.001349221282462
11 13 2.288918230751476 0.004713345842188 1.000000000000000 0.000597817676979
12 14 2.288917499968597 0.002016989295184 1.000000000000000 0.000221206604261
13 15 2.288917382518689 0.000966735632580 1.000000000000000 0.000037996190949
14 16 2.288917379006109 0.000172774048566 1.000000000000000 0.000004390786374
15 17 2.288917378964315 0.000172774048566 1.000000000000000 0.000000244916670
Convergence criteria met.
After: gradient norm = 2.4491667048660147E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {-1.6766,1.6766}
Count Table 1:
---------------
h: {-7.4199,-3.6781,0.0106,3.6993,7.3881}
Binding mode 0:
---------------
Mononucleotide: {-0.0002,-0.0032,0.0023,-0.0038}
Activity(exp=0): {-7.0889,-7.0889}
Activity(exp=1): {-6.6834,-6.6834,-6.6834,-6.6834,-6.6834}
Position Bias(exp=0, s=0): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {0.0039,0.0042,-0.0050,-0.0044,-0.0035,-0.0037,-0.0050,0.0027,-0.0018,-0.0047,-0.0035,0.0025,0.0028,0.0019,0.0026,-0.0022,-0.0001,-0.0003,0.0049,0.0042,0.0003,-0.0000,-0.0041,0.0035,-0.0029,-0.0039,-0.0023,-0.0000,0.0029,-0.0005,-0.0015,-0.0048,0.0018,-0.0016,0.0037,0.0036,0.0011,-0.0033,-0.0007,-0.0048,0.0020,-0.0046,-0.0014,0.0032,-0.0031,-0.0027,0.0016,-0.0019}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
> Initial optimization (component0-1-f1).
>> Starting new optimization: component0-1-f1. (2021-05-22 06:17:14.876).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[11,12]},{"h":[13,14,15,16,17]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[0,1,2,3],"activity":[[4,5],[6,7,8,9,10]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 2.289476720960297
gradient = {0.0406,-0.0391,-0.0268,0.0253,-0.0000,-0.0000,-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 = 0.06732352964490815
Starting Function Value: 2.289476720960297
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 2.258066589890719 1.000000000000000 14.853647829732180 0.204258024772747
2 3 2.237242291324899 0.342796709827694 1.000000000000000 0.058231148448181
3 4 2.230129856467299 0.459723796996915 1.000000000000000 0.043336961612666
4 5 2.228097111378653 0.237939792794566 1.000000000000000 0.044607679363053
5 7 2.226415359348381 0.279689005010387 0.447539047541378 0.046882572271709
6 8 2.224483325733713 0.357363835307384 1.000000000000000 0.028145909533196
7 9 2.223594801038293 0.138064275784824 1.000000000000000 0.013389156751762
8 10 2.222812620895924 0.384048387771354 1.000000000000000 0.016572598481677
9 11 2.222466822757097 0.235948586434538 1.000000000000000 0.006426312706155
10 12 2.222202398558379 0.410774051938882 1.000000000000000 0.010313239177026
11 13 2.222103917560685 0.213311671199742 1.000000000000000 0.005343374575569
12 14 2.222060760169056 0.202317972578508 1.000000000000000 0.002543806689462
13 15 2.222042643983821 0.184051303982829 1.000000000000000 0.001328510980380
14 16 2.222039021451385 0.098373250826110 1.000000000000000 0.000207533457822
15 17 2.222038680565087 0.040221319015239 1.000000000000000 0.000250792590049
16 18 2.222038597754851 0.003808815138024 1.000000000000000 0.000131364667414
17 19 2.222038540891222 0.002453500265299 1.000000000000000 0.000222025461489
18 20 2.222038314114262 0.006614261709539 1.000000000000000 0.000465090917176
19 21 2.222037791465859 0.012939613247796 1.000000000000000 0.000811103237256
20 22 2.222036396429995 0.032972224620378 1.000000000000000 0.001367253712236
21 23 2.222033117925564 0.077656197476707 1.000000000000000 0.002083733878421
22 24 2.222026265493284 0.170741037264250 1.000000000000000 0.002631473725311
23 25 2.222017373974325 0.268104585719233 1.000000000000000 0.002263881059694
24 26 2.222016840957100 0.164264539609860 1.000000000000000 0.001864363458213
25 27 2.222012670120039 0.018660521128410 1.000000000000000 0.000933384187381
26 28 2.222012036491358 0.043859070415918 1.000000000000000 0.000561050810273
27 29 2.222011786108155 0.037588624112517 1.000000000000000 0.000073267467809
28 30 2.222011776379414 0.003220640776632 1.000000000000000 0.000055980627971
29 31 2.222011764735726 0.000632221680047 1.000000000000000 0.000067459194559
30 32 2.222011710511219 0.002257427068736 1.000000000000000 0.000142320103355
31 33 2.222011594106409 0.004889264621160 1.000000000000000 0.000261296556250
32 34 2.222011260509169 0.014391534235490 1.000000000000000 0.000480064310533
33 35 2.222010417673032 0.037590872407174 1.000000000000000 0.000823875612820
34 36 2.222008191725921 0.101757643393366 1.000000000000000 0.001385511931534
35 37 2.222002460119886 0.266777731174455 1.000000000000000 0.002273155694092
36 38 2.221987873775947 0.689109743545692 1.000000000000000 0.003641218783591
37 39 2.221952579122488 1.696888828610172 1.000000000000000 0.005569626513244
38 40 2.221876625937263 3.761271518409681 1.000000000000000 0.007688494322724
39 41 2.221751941757324 6.514526698669026 1.000000000000000 0.008427143106925
40 42 2.221631643126849 6.696169955215413 1.000000000000000 0.005796421533310
41 43 2.221585311610440 2.453259884706959 1.000000000000000 0.002617965083985
42 44 2.221574513944987 0.656949484958025 1.000000000000000 0.000230333050741
43 45 2.221573946820634 0.578946473352530 1.000000000000000 0.000042992892329
44 46 2.221573931749494 0.111943823152969 1.000000000000000 0.000008655429474
45 47 2.221573931607875 0.000739931457238 1.000000000000000 0.000005789074142
46 48 2.221573931566899 0.000739931457238 1.000000000000000 0.000000543907648
Convergence criteria met.
After: gradient norm = 5.439076484317336E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.0391,-1.0391}
Count Table 1:
---------------
h: {1.3850,0.5111,0.0337,-0.4626,-1.4673}
Binding mode 0:
---------------
Mononucleotide: {-4.7064,0.1224,0.0169,-3.1505}
Activity(exp=0): {-0.0000,-1.0392}
Activity(exp=1): {-0.0000,-1.3851,-1.8962,-1.9300,-1.4673}
Position Bias(exp=0, s=0): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {0.0039,0.0042,-0.0050,-0.0044,-0.0035,-0.0037,-0.0050,0.0027,-0.0018,-0.0047,-0.0035,0.0025,0.0028,0.0019,0.0026,-0.0022,-0.0001,-0.0003,0.0049,0.0042,0.0003,-0.0000,-0.0041,0.0035,-0.0029,-0.0039,-0.0023,-0.0000,0.0029,-0.0005,-0.0015,-0.0048,0.0018,-0.0016,0.0037,0.0036,0.0011,-0.0033,-0.0007,-0.0048,0.0020,-0.0046,-0.0014,0.0032,-0.0031,-0.0027,0.0016,-0.0019}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
Suggested variations:
key=1;0;0, description = Initial model.
> Optimizing variation "Initial model." (component0-2-variation0).
>> Starting new optimization: component0-2-variation0. (2021-05-22 06:17:47.471).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[11,12]},{"h":[13,14,15,16,17]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[0,1,2,3],"activity":[[4,5],[6,7,8,9,10]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 2.2215739315668985
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}
gradient norm = 5.439076484353114E-7
Already at minimum!
After: gradient norm = 5.439076484353114E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.0391,-1.0391}
Count Table 1:
---------------
h: {1.3850,0.5111,0.0337,-0.4626,-1.4673}
Binding mode 0:
---------------
Mononucleotide: {-4.7064,0.1224,0.0169,-3.1505}
Activity(exp=0): {-0.0000,-1.0392}
Activity(exp=1): {-0.0000,-1.3851,-1.8962,-1.9300,-1.4673}
Position Bias(exp=0, s=0): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {0.0039,0.0042,-0.0050,-0.0044,-0.0035,-0.0037,-0.0050,0.0027,-0.0018,-0.0047,-0.0035,0.0025,0.0028,0.0019,0.0026,-0.0022,-0.0001,-0.0003,0.0049,0.0042,0.0003,-0.0000,-0.0041,0.0035,-0.0029,-0.0039,-0.0023,-0.0000,0.0029,-0.0005,-0.0015,-0.0048,0.0018,-0.0016,0.0037,0.0036,0.0011,-0.0033,-0.0007,-0.0048,0.0020,-0.0046,-0.0014,0.0032,-0.0031,-0.0027,0.0016,-0.0019}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
The Likelihood DID NOT improve. Discarding fit component0-2-variation0.
> No varitions possible for Binding mode 0.
> Unfreezing component (component0-3-f0).
>> Starting new optimization: component0-3-f0. (2021-05-22 06:17:48.134).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[61,62]},{"h":[63,64,65,66,67]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[0,1,2,3],"activity":[[54,55],[56,57,58,59,60]],"positionBias":[[[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],[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1]],[[34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53],[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1]]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 2.221573931566899
gradient = {-0.0000,-0.0000,-0.0000,-0.0000,0.0002,0.0003,-0.0002,0.0000,-0.0001,-0.0002,-0.0002,-0.0002,-0.0001,-0.0000,0.0001,0.0000,0.0000,-0.0001,-0.0000,0.0000,0.0000,0.0000,0.0001,0.0001,0.0001,-0.0001,-0.0002,-0.0000,-0.0001,-0.0000,0.0001,0.0001,-0.0000,0.0001,-0.0007,0.0036,0.0002,-0.0013,0.0036,0.0031,-0.0034,0.0033,-0.0055,-0.0081,0.0037,-0.0036,0.0055,0.0071,-0.0029,0.0001,0.0014,-0.0028,-0.0004,-0.0033,-0.0000,0.0000,-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 = 0.017117758582418843
Starting Function Value: 2.221573931566899
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 2.209083426716151 1.000000000000000 58.418863380108140 0.061900760707875
2 3 2.204396359156503 2.148580199800610 1.000000000000000 0.061622031948290
3 5 2.201444368398355 0.103629256034690 0.311457799333190 0.014630561535924
4 6 2.200488377454278 0.438926607633898 1.000000000000000 0.034794701923277
5 8 2.200017724344741 0.165925129867851 0.474816805260053 0.004617007288409
6 9 2.199994871637269 0.020819197164873 1.000000000000000 0.003913273596911
7 10 2.199958825354786 0.027721415433353 1.000000000000000 0.004594716100416
8 11 2.199894932298589 0.054473510207640 1.000000000000000 0.005065689770650
9 12 2.199810076787550 0.072152912963893 1.000000000000000 0.004963888056051
10 13 2.199618377324530 0.244246245271764 1.000000000000000 0.008180517731291
11 14 2.199515450513584 0.246930103503362 1.000000000000000 0.007010674140790
12 15 2.199431848525255 0.065875824892371 1.000000000000000 0.002375518937524
13 16 2.199406945304374 0.025519477158450 1.000000000000000 0.002169018882939
14 17 2.199379125174728 0.027886253677621 1.000000000000000 0.002263126373447
15 18 2.199259606471550 0.152593697104094 1.000000000000000 0.003153650354259
16 19 2.199151307358374 0.206747985484466 1.000000000000000 0.004657280142891
17 20 2.199076102701615 0.273657578394306 1.000000000000000 0.006143089846458
18 21 2.199005747778198 0.042802553959310 1.000000000000000 0.001974932809689
19 22 2.198972251723594 0.078613231525921 1.000000000000000 0.002165311857238
20 23 2.198936020851666 0.082251736032452 1.000000000000000 0.002905434399083
21 24 2.198799665033048 0.364998385395992 1.000000000000000 0.003550409567234
22 26 2.198746526991414 0.188379062282064 0.374185435237085 0.005382878732549
23 27 2.198641185101033 0.324970414191956 1.000000000000000 0.003441051616244
24 28 2.198589438551904 0.093351759341797 1.000000000000000 0.002744873227718
25 29 2.198571645688837 0.062861711788337 1.000000000000000 0.001634223889792
26 30 2.198550869333832 0.068994961159380 1.000000000000000 0.002138626257041
27 31 2.198494898126553 0.095776807473615 1.000000000000000 0.002599851394335
28 32 2.198437633400047 0.115385862544241 1.000000000000000 0.004053477907854
29 33 2.198402231966704 0.127471380000168 1.000000000000000 0.003579138278430
30 34 2.198369995210627 0.146252300522655 1.000000000000000 0.001526993333527
31 35 2.198342413611072 0.194938001758238 1.000000000000000 0.001661275138902
32 36 2.198321937926405 0.145293029444317 1.000000000000000 0.003257413048394
33 37 2.198297730211030 0.167524667800425 1.000000000000000 0.004013831519534
34 38 2.198264622761396 0.134016796618079 1.000000000000000 0.004816249544672
35 39 2.198214269082427 0.228040133753291 1.000000000000000 0.002456672604193
36 40 2.198184174193870 0.182078522914118 1.000000000000000 0.001572759255590
37 41 2.198167706843902 0.045584797492306 1.000000000000000 0.001497112465205
38 42 2.198154739735716 0.048752335528257 1.000000000000000 0.001977438101103
39 43 2.198143546503128 0.063347010635314 1.000000000000000 0.002158123253761
40 44 2.198119588026447 0.216342893278532 1.000000000000000 0.001951792726668
41 45 2.198105564307316 0.166571911726572 1.000000000000000 0.001099725474652
42 46 2.198095887425549 0.140324919604616 1.000000000000000 0.000859630549625
43 47 2.198092377188196 0.050147541023804 1.000000000000000 0.001211325673844
44 48 2.198086845425788 0.047997939839315 1.000000000000000 0.001461297263698
45 49 2.198075445326395 0.077574954361062 1.000000000000000 0.001377827802935
46 50 2.198062613841071 0.085430883160321 1.000000000000000 0.000784684425863
47 51 2.198056118976506 0.048984783476526 1.000000000000000 0.000449811844525
48 52 2.198053293906827 0.018035273777634 1.000000000000000 0.000551308585377
49 53 2.198049677594817 0.030664532204156 1.000000000000000 0.000775548041661
50 54 2.198044069805338 0.068607000306517 1.000000000000000 0.000918380359521
51 55 2.198035784539079 0.119521737496645 1.000000000000000 0.000810745598319
52 56 2.198023281086986 0.173658671269381 1.000000000000000 0.000751735286457
53 57 2.198010128967165 0.233529525442219 1.000000000000000 0.000734772003970
54 58 2.198004522026701 0.076758148460592 1.000000000000000 0.000559496650040
55 59 2.198001838083989 0.053201946523273 1.000000000000000 0.000417826266973
56 60 2.198000360440707 0.020842088462366 1.000000000000000 0.000301729926163
57 61 2.197999169271494 0.016462424888846 1.000000000000000 0.000224769189265
58 62 2.197998230009863 0.013984564589385 1.000000000000000 0.000366867681722
59 63 2.197996733121156 0.031632883568916 1.000000000000000 0.000488211815813
60 64 2.197994376359195 0.057846407126583 1.000000000000000 0.000436260169350
61 65 2.197990301102239 0.093845667932271 1.000000000000000 0.000294417165937
62 66 2.197986109387052 0.129724042402001 1.000000000000000 0.000143523720866
63 67 2.197984372661516 0.058544666707751 1.000000000000000 0.000156649677134
64 68 2.197983110378748 0.049229141601639 1.000000000000000 0.000148851534924
65 69 2.197981425820312 0.054977927806572 1.000000000000000 0.000215846709791
66 70 2.197978453424037 0.129503948621204 1.000000000000000 0.000146857036778
67 71 2.197976320141607 0.096883070520974 1.000000000000000 0.000207938557822
68 72 2.197973586213238 0.151984811662226 1.000000000000000 0.000202924427813
69 73 2.197972316180202 0.084193693543231 1.000000000000000 0.000126119821144
70 74 2.197971616068362 0.042762069936755 1.000000000000000 0.000096580798830
71 75 2.197970933548711 0.045085273653116 1.000000000000000 0.000098174120274
72 76 2.197970086762909 0.055787378300496 1.000000000000000 0.000123053430318
73 77 2.197969186962203 0.073378428734567 1.000000000000000 0.000113485770441
74 78 2.197968479059938 0.056796069165243 1.000000000000000 0.000122684067138
75 79 2.197967795466809 0.065078687531572 1.000000000000000 0.000072235611256
76 80 2.197967372827507 0.034377791400135 1.000000000000000 0.000076440535328
77 81 2.197966931311771 0.041422974845212 1.000000000000000 0.000082315306741
78 82 2.197966719295087 0.023204129757230 1.000000000000000 0.000068335100448
79 83 2.197966553292566 0.020627860323028 1.000000000000000 0.000059699966192
80 84 2.197966298607327 0.036665553827826 1.000000000000000 0.000047531531205
81 85 2.197966057906412 0.039305794779059 1.000000000000000 0.000071615838709
82 86 2.197965808480859 0.039054798078075 1.000000000000000 0.000097101438501
83 87 2.197965633496322 0.021843286977863 1.000000000000000 0.000080325357689
84 88 2.197965485778692 0.017045521565213 1.000000000000000 0.000050482857105
85 89 2.197965346747681 0.023969241963663 1.000000000000000 0.000039940917044
86 90 2.197965237040806 0.020223252452698 1.000000000000000 0.000081083017325
87 91 2.197965091006617 0.021783951982289 1.000000000000000 0.000126313518648
88 92 2.197964923950831 0.025044465969101 1.000000000000000 0.000135316367065
89 93 2.197964675032061 0.043458112653925 1.000000000000000 0.000114988031546
90 94 2.197964517450833 0.039407149258832 1.000000000000000 0.000056827358484
91 95 2.197964423801820 0.034811376750239 1.000000000000000 0.000037027092907
92 96 2.197964369101134 0.019424555925564 1.000000000000000 0.000072991557664
93 97 2.197964282677585 0.023624772274461 1.000000000000000 0.000115989402440
94 98 2.197964198077212 0.017263015783581 1.000000000000000 0.000121591011127
95 99 2.197964049458812 0.026207608810746 1.000000000000000 0.000094851865693
96 100 2.197963883659649 0.039639399412716 1.000000000000000 0.000021797564889
97 101 2.197963845762395 0.010147249286084 1.000000000000000 0.000025853360628
98 102 2.197963827638132 0.002962765397194 1.000000000000000 0.000031842228212
99 103 2.197963794156130 0.005765735550826 1.000000000000000 0.000025114601452
100 104 2.197963650065530 0.037037460898762 1.000000000000000 0.000039789481182
101 105 2.197963515661776 0.043535056631601 1.000000000000000 0.000071774120779
102 106 2.197963376300332 0.053878579315448 1.000000000000000 0.000080490480180
103 107 2.197963279597160 0.027446152389283 1.000000000000000 0.000042044507167
104 108 2.197963210002796 0.026647062254246 1.000000000000000 0.000064652894227
105 109 2.197963189500906 0.015021801097371 1.000000000000000 0.000056894118431
106 110 2.197963160397441 0.011157092813786 1.000000000000000 0.000070859745132
107 111 2.197963107848217 0.011221301799999 1.000000000000000 0.000114035509872
108 112 2.197963067501103 0.017536581548694 1.000000000000000 0.000099805997186
109 113 2.197963044146801 0.023162821527118 1.000000000000000 0.000054017230981
110 114 2.197963028247671 0.024117313936770 1.000000000000000 0.000020745204239
111 115 2.197963022456615 0.012364084164290 1.000000000000000 0.000044806821539
112 116 2.197963018408272 0.005158776641759 1.000000000000000 0.000056027717328
113 117 2.197963006763039 0.007865707977303 1.000000000000000 0.000073501136352
114 118 2.197962981826604 0.009666103289098 1.000000000000000 0.000087052085159
115 120 2.197962969651951 0.009277287695403 0.219109562304940 0.000130932665562
116 121 2.197962916861719 0.014193915340635 1.000000000000000 0.000114617903707
117 122 2.197962827360060 0.032883356689960 1.000000000000000 0.000068882768116
118 123 2.197962777030341 0.028669519821895 1.000000000000000 0.000032478498777
119 124 2.197962769582240 0.013815376702887 1.000000000000000 0.000069419848902
120 125 2.197962760131869 0.003244721841026 1.000000000000000 0.000016505119021
121 126 2.197962758644107 0.002900816989503 1.000000000000000 0.000014754793395
122 127 2.197962755278194 0.003236904708394 1.000000000000000 0.000017839621436
123 128 2.197962743675175 0.005463810710167 1.000000000000000 0.000034942777026
124 129 2.197962715643433 0.009280096513157 1.000000000000000 0.000059031266545
125 130 2.197962661112606 0.017746992856054 1.000000000000000 0.000088843827112
126 132 2.197962624452820 0.027673505985017 0.426788524392549 0.000134789790228
127 133 2.197962545352389 0.032570976845022 1.000000000000000 0.000083672410286
128 134 2.197962486829418 0.039198869661917 1.000000000000000 0.000042947412403
129 136 2.197962478864093 0.013678007279457 0.464325267083158 0.000049043571469
130 137 2.197962472414918 0.005010283517034 1.000000000000000 0.000016714104370
131 138 2.197962470488159 0.001435427609049 1.000000000000000 0.000014126876084
132 139 2.197962467139755 0.002078435966278 1.000000000000000 0.000014421575622
133 140 2.197962463064109 0.001693446821317 1.000000000000000 0.000015341229853
134 141 2.197962452679077 0.002970365662304 1.000000000000000 0.000020873562911
135 142 2.197962430899488 0.012553711902945 1.000000000000000 0.000033195549677
136 144 2.197962410525132 0.015476428392487 0.492491298211238 0.000056244701171
137 145 2.197962371338962 0.016595858841983 1.000000000000000 0.000038410226560
138 146 2.197962306945345 0.040854558463111 1.000000000000000 0.000040186126082
139 147 2.197962302811096 0.006409440575509 1.000000000000000 0.000060806261074
140 148 2.197962299015437 0.003640390347561 1.000000000000000 0.000013866717269
141 149 2.197962298371180 0.001609981323976 1.000000000000000 0.000008328940064
142 150 2.197962297530137 0.001159885338908 1.000000000000000 0.000008929495724
143 151 2.197962294796839 0.001237595854783 1.000000000000000 0.000015204912364
144 152 2.197962287654869 0.002487532668410 1.000000000000000 0.000028874094537
145 153 2.197962273089984 0.006765116160416 1.000000000000000 0.000048294085160
146 154 2.197962244459333 0.016915586321422 1.000000000000000 0.000065154635305
147 155 2.197962203681640 0.031673212978528 1.000000000000000 0.000072142255477
148 157 2.197962192048980 0.012380948061526 0.113294920174965 0.000089808529540
149 158 2.197962164873982 0.015400918302566 1.000000000000000 0.000066055127851
150 159 2.197962147278889 0.010242678738853 1.000000000000000 0.000027261252284
151 160 2.197962144084923 0.001228547945871 1.000000000000000 0.000014843906632
152 161 2.197962141881560 0.003181816578655 1.000000000000000 0.000011069973061
153 162 2.197962140533276 0.002821640521732 1.000000000000000 0.000014112011267
154 163 2.197962138782478 0.002655983723490 1.000000000000000 0.000016868060682
155 164 2.197962134599154 0.004182222582646 1.000000000000000 0.000021321020326
156 165 2.197962125176430 0.007015782290901 1.000000000000000 0.000026361311646
157 166 2.197962106601965 0.012894345812146 1.000000000000000 0.000038151457234
158 167 2.197962082920320 0.019344223401046 1.000000000000000 0.000035731846189
159 168 2.197962061423648 0.017217640412602 1.000000000000000 0.000029332309943
160 169 2.197962049283440 0.010677864949217 1.000000000000000 0.000033463885344
161 170 2.197962046320703 0.012152024308477 1.000000000000000 0.000040548491116
162 171 2.197962043477039 0.006029100604941 1.000000000000000 0.000017025320342
163 172 2.197962042488252 0.002458898590940 1.000000000000000 0.000008856388355
164 173 2.197962041092517 0.003783811749628 1.000000000000000 0.000009398683884
165 174 2.197962040211846 0.001943195075057 1.000000000000000 0.000013129041370
166 175 2.197962038340023 0.002631413435971 1.000000000000000 0.000016897787297
167 176 2.197962033707630 0.004499538588515 1.000000000000000 0.000021912285079
168 177 2.197962022436188 0.008916801586302 1.000000000000000 0.000027756476854
169 178 2.197961999505405 0.017083211726206 1.000000000000000 0.000039162206533
170 179 2.197961969176138 0.029797213737163 1.000000000000000 0.000022817287808
171 180 2.197961945673140 0.022896356764351 1.000000000000000 0.000046455926919
172 181 2.197961928662279 0.006625726257191 1.000000000000000 0.000025187733639
173 182 2.197961918463669 0.005105278511369 1.000000000000000 0.000030205427559
174 183 2.197961913078323 0.003394276151739 1.000000000000000 0.000031770588023
175 184 2.197961900590632 0.011883895518643 1.000000000000000 0.000027767194216
176 185 2.197961893309809 0.009487151143356 1.000000000000000 0.000019702657724
177 186 2.197961887659348 0.008722108076034 1.000000000000000 0.000012156007676
178 187 2.197961883450564 0.005448669310334 1.000000000000000 0.000020781981534
179 188 2.197961877039007 0.006036136842750 1.000000000000000 0.000038743813254
180 189 2.197961868624718 0.005904623706745 1.000000000000000 0.000054022045513
181 190 2.197961859881280 0.005767713944162 1.000000000000000 0.000054510448014
182 191 2.197961848268302 0.008276728267695 1.000000000000000 0.000058329042191
183 192 2.197961834886603 0.015791347157704 1.000000000000000 0.000023783695570
184 193 2.197961828073027 0.005598308115547 1.000000000000000 0.000014447277231
185 194 2.197961823336827 0.005971499694761 1.000000000000000 0.000024059410665
186 195 2.197961821418333 0.002535716572523 1.000000000000000 0.000027184376148
187 196 2.197961817702526 0.004451713669148 1.000000000000000 0.000026620736122
188 197 2.197961811807981 0.006413164012671 1.000000000000000 0.000022397457834
189 198 2.197961802403015 0.011885831634435 1.000000000000000 0.000017911493941
190 199 2.197961793659062 0.009382340654768 1.000000000000000 0.000030004393253
191 200 2.197961786024955 0.008265229504674 1.000000000000000 0.000039189148623
192 201 2.197961780316041 0.005329802447563 1.000000000000000 0.000037301391299
193 202 2.197961771675586 0.008481108648643 1.000000000000000 0.000026459248744
194 203 2.197961767150017 0.013332832318145 1.000000000000000 0.000022705778955
195 204 2.197961759558404 0.006940985648748 1.000000000000000 0.000020181111971
196 205 2.197961752841076 0.003041783543641 1.000000000000000 0.000026120176631
197 206 2.197961731672404 0.014091873311764 1.000000000000000 0.000045858350311
198 207 2.197961706258540 0.023210593908727 1.000000000000000 0.000054929107283
199 208 2.197961674833616 0.034576509048081 1.000000000000000 0.000061136315603
200 209 2.197961667007373 0.037524428824720 1.000000000000000 0.000046933665893
201 210 2.197961656116302 0.012874777296145 1.000000000000000 0.000010952473437
202 211 2.197961653118798 0.001925143209581 1.000000000000000 0.000012027745413
203 212 2.197961646765612 0.008487529912298 1.000000000000000 0.000030721451318
204 213 2.197961638141816 0.008745243095342 1.000000000000000 0.000040912691524
205 214 2.197961612470760 0.026908050190778 1.000000000000000 0.000062586497453
206 215 2.197961578676348 0.043577668319207 1.000000000000000 0.000069618778060
207 217 2.197961561240498 0.030373341567027 0.353740754849208 0.000095379918037
208 218 2.197961532167680 0.023460788689002 1.000000000000000 0.000062836815223
209 219 2.197961515280964 0.008977447906483 1.000000000000000 0.000025475093409
210 220 2.197961510463292 0.002395886763542 1.000000000000000 0.000013191205058
211 221 2.197961504195785 0.005018343452960 1.000000000000000 0.000017317899265
212 222 2.197961498587280 0.005940034252496 1.000000000000000 0.000021832520196
213 224 2.197961497120707 0.008028650257500 0.073120129182106 0.000031187461002
214 225 2.197961489252308 0.010070826351054 1.000000000000000 0.000024329190846
215 226 2.197961476033429 0.015863428584516 1.000000000000000 0.000013456806930
216 227 2.197961461251805 0.020493748202897 1.000000000000000 0.000017579632671
217 228 2.197961457426363 0.015438486195142 1.000000000000000 0.000063578462125
218 229 2.197961448403245 0.005528492019984 1.000000000000000 0.000026332629816
219 230 2.197961445122131 0.004589077608317 1.000000000000000 0.000021019960653
220 231 2.197961440329470 0.004737935279332 1.000000000000000 0.000016639131607
221 232 2.197961436101350 0.003410352561287 1.000000000000000 0.000017897459696
222 233 2.197961431224778 0.009445309376890 1.000000000000000 0.000039133642133
223 234 2.197961426320987 0.009938965841735 1.000000000000000 0.000030130518398
224 235 2.197961419915243 0.010433614478752 1.000000000000000 0.000026367809263
225 236 2.197961399840550 0.031050511803851 1.000000000000000 0.000025151668142
226 237 2.197961376851127 0.026940837582663 1.000000000000000 0.000030372153616
227 238 2.197961355616162 0.032960876142653 1.000000000000000 0.000034909773641
228 240 2.197961350645985 0.010979492075951 0.256377342983826 0.000032799468675
229 241 2.197961343991265 0.008955085548918 1.000000000000000 0.000022113665441
230 242 2.197961340021187 0.007212337699477 1.000000000000000 0.000015944845451
231 243 2.197961336613815 0.007396552216008 1.000000000000000 0.000013657446843
232 244 2.197961330101776 0.011739671655970 1.000000000000000 0.000035442083015
233 245 2.197961323678823 0.011856606422057 1.000000000000000 0.000026517753535
234 246 2.197961316815964 0.018128583560522 1.000000000000000 0.000014624439327
235 247 2.197961311769134 0.011374493942658 1.000000000000000 0.000010945112667
236 248 2.197961298741122 0.023873747891301 1.000000000000000 0.000031731708393
237 249 2.197961279706163 0.027947201390610 1.000000000000000 0.000051264229536
238 250 2.197961257039429 0.023964554768316 1.000000000000000 0.000051346967367
239 251 2.197961231006206 0.022112381798933 1.000000000000000 0.000077641818555
240 252 2.197961212234423 0.014686948150519 1.000000000000000 0.000035924367810
241 253 2.197961200111390 0.008602644070903 1.000000000000000 0.000015835111829
242 254 2.197961194174715 0.008985087639008 1.000000000000000 0.000017605983256
243 255 2.197961193756676 0.016849259804160 1.000000000000000 0.000063191445268
244 256 2.197961187764935 0.008409383014303 1.000000000000000 0.000013874055234
245 257 2.197961186792129 0.003514696536886 1.000000000000000 0.000008432884358
246 258 2.197961185142518 0.008093073152882 1.000000000000000 0.000011812875817
247 259 2.197961182939786 0.007249639269615 1.000000000000000 0.000017654294845
248 260 2.197961175934855 0.016850468779848 1.000000000000000 0.000028651398297
249 261 2.197961161927043 0.024148616051684 1.000000000000000 0.000042321857632
250 262 2.197961140046238 0.028472438333499 1.000000000000000 0.000041632713458
251 263 2.197961117115681 0.044439534961643 1.000000000000000 0.000048999740299
252 264 2.197961098771862 0.015450548698373 1.000000000000000 0.000017018142834
253 265 2.197961091055388 0.017703509098175 1.000000000000000 0.000022346969901
254 266 2.197961089299152 0.003586185628684 1.000000000000000 0.000019513761814
255 267 2.197961086607925 0.011720430602124 1.000000000000000 0.000013159708919
256 268 2.197961084596605 0.005385418287215 1.000000000000000 0.000007932124920
257 269 2.197961082559974 0.005181614182989 1.000000000000000 0.000012359148907
258 270 2.197961080038897 0.004747022886115 1.000000000000000 0.000019357331935
259 271 2.197961076338113 0.004338384074116 1.000000000000000 0.000024056589167
260 272 2.197961069451104 0.006479105297352 1.000000000000000 0.000033852671181
261 273 2.197961058038050 0.009670208604265 1.000000000000000 0.000032499470691
262 274 2.197961057325009 0.029170298530955 1.000000000000000 0.000052615513239
263 275 2.197961038768613 0.010299098187416 1.000000000000000 0.000036573185868
264 276 2.197961034384421 0.020611612666384 1.000000000000000 0.000024876732644
265 277 2.197961027584523 0.008445283999304 1.000000000000000 0.000005404550675
266 278 2.197961025809923 0.006832595580365 1.000000000000000 0.000007214358469
267 279 2.197961025021349 0.004641487256438 1.000000000000000 0.000005270980504
268 280 2.197961024010578 0.006837456832782 1.000000000000000 0.000005069773189
269 281 2.197961022483575 0.004124963907586 1.000000000000000 0.000017697149405
270 282 2.197961021050502 0.004181561148121 1.000000000000000 0.000010920102335
271 283 2.197961019625564 0.006500097151847 1.000000000000000 0.000005216608639
272 284 2.197961018588789 0.002230840235251 1.000000000000000 0.000004585505064
273 285 2.197961015308229 0.006954579531598 1.000000000000000 0.000011692619450
274 286 2.197961012059274 0.007666254298600 1.000000000000000 0.000023829297645
275 287 2.197961008669160 0.013139608933676 1.000000000000000 0.000020644292256
276 288 2.197961005661841 0.006562458570050 1.000000000000000 0.000018080060597
277 289 2.197961003123375 0.006535235845955 1.000000000000000 0.000004350981895
278 290 2.197961001881660 0.005254896486672 1.000000000000000 0.000012073422793
279 291 2.197961001220625 0.003034459604010 1.000000000000000 0.000013034570701
280 292 2.197960999762708 0.006480420269714 1.000000000000000 0.000014880720975
281 294 2.197960999191126 0.006414115426511 0.315136292638078 0.000005377591452
282 295 2.197960998130344 0.005256525616409 1.000000000000000 0.000003790927041
283 296 2.197960997426513 0.003845272244491 1.000000000000000 0.000007899491957
284 297 2.197960996758284 0.003285392740792 1.000000000000000 0.000010084367951
285 298 2.197960995831374 0.002869726710611 1.000000000000000 0.000006872178557
286 299 2.197960994572862 0.006399382445598 1.000000000000000 0.000008620712635
287 301 2.197960993905667 0.003717968988755 0.098823574009301 0.000011003329205
288 302 2.197960992874875 0.003357410721990 1.000000000000000 0.000012074384644
289 303 2.197960989947045 0.010752243051685 1.000000000000000 0.000013871779742
290 304 2.197960988619875 0.004142169507478 1.000000000000000 0.000006806973933
291 305 2.197960987409152 0.006285489331938 1.000000000000000 0.000004622092032
292 306 2.197960986875331 0.005849918389472 1.000000000000000 0.000007956137865
293 307 2.197960986445565 0.004102193132677 1.000000000000000 0.000009320655193
294 308 2.197960985600532 0.004264919507921 1.000000000000000 0.000009498486025
295 309 2.197960984437739 0.003002111022542 1.000000000000000 0.000010137029567
296 311 2.197960983885122 0.003432326913397 0.365997214163758 0.000006833187087
297 312 2.197960983375110 0.004290595529544 1.000000000000000 0.000003855242955
298 313 2.197960983041399 0.004425704900461 1.000000000000000 0.000003661713178
299 314 2.197960982750951 0.001898983484554 1.000000000000000 0.000005842710133
300 315 2.197960981945841 0.003089504272874 1.000000000000000 0.000008133010997
301 316 2.197960980575186 0.003311692268233 1.000000000000000 0.000016059054627
302 317 2.197960978892946 0.008743488974024 1.000000000000000 0.000011472117183
303 318 2.197960976674584 0.006892363195520 1.000000000000000 0.000012576125520
304 319 2.197960974961965 0.008286268062008 1.000000000000000 0.000012451319657
305 320 2.197960973771077 0.004714967916415 1.000000000000000 0.000007623550022
306 321 2.197960973230642 0.002541951918180 1.000000000000000 0.000003100630821
307 322 2.197960973020255 0.002550342092357 1.000000000000000 0.000002075689522
308 323 2.197960972957274 0.001528781788755 1.000000000000000 0.000001643956716
309 324 2.197960972951007 0.001526782604013 1.000000000000000 0.000003265497785
310 325 2.197960972915954 0.000619550459531 1.000000000000000 0.000001004229049
311 326 2.197960972894612 0.000358662799957 1.000000000000000 0.000001209719825
312 327 2.197960972841456 0.000566039515812 1.000000000000000 0.000001835166031
313 328 2.197960972771404 0.000979840302579 1.000000000000000 0.000001669348039
314 330 2.197960972712439 0.001066710729470 0.280865024412477 0.000003020885233
315 331 2.197960972593766 0.001233659689904 1.000000000000000 0.000001643794084
316 332 2.197960972278125 0.004059312940735 1.000000000000000 0.000003758969022
317 333 2.197960971990356 0.002474182079970 1.000000000000000 0.000005289351950
318 334 2.197960971473882 0.002442781811298 1.000000000000000 0.000004480622494
319 336 2.197960971448602 0.000803124273106 0.032770677131061 0.000006207533743
320 337 2.197960971121829 0.003271391100778 1.000000000000000 0.000002878878949
321 338 2.197960970987126 0.003271391100778 1.000000000000000 0.000000850179793
Convergence criteria met.
After: gradient norm = 8.501797934176925E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.9574,-0.9574}
Count Table 1:
---------------
h: {1.2555,0.4807,0.0461,-0.4178,-1.3645}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {0.0039,0.0042,-0.0050,-0.0044,-0.0035,-0.0037,-0.0050,0.0027,-0.0018,-0.0047,-0.0035,0.0025,0.0028,0.0019,0.0026,-0.0022,-0.0001,-0.0003,0.0049,0.0042,0.0003,-0.0000,-0.0041,0.0035,-0.0029,-0.0039,-0.0023,-0.0000,0.0029,-0.0005,-0.0015,-0.0048,0.0018,-0.0016,0.0037,0.0036,0.0011,-0.0033,-0.0007,-0.0048,0.0020,-0.0046,-0.0014,0.0032,-0.0031,-0.0027,0.0016,-0.0019}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
> Optimizing the full model (component0-4-all).
>> Starting new optimization: component0-4-all. (2021-05-22 06:21:29.166).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[61,62]},{"h":[63,64,65,66,67]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[0,1,2,3],"activity":[[54,55],[56,57,58,59,60]],"positionBias":[[[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],[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1]],[[34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53],[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1]]]},{},{}]}
Value and gradient before optimization:
=======================================
value = 2.1979609709871264
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}
gradient norm = 8.501797934186908E-7
Already at minimum!
After: gradient norm = 8.501797934186908E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.9574,-0.9574}
Count Table 1:
---------------
h: {1.2555,0.4807,0.0461,-0.4178,-1.3645}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {0.0039,0.0042,-0.0050,-0.0044,-0.0035,-0.0037,-0.0050,0.0027,-0.0018,-0.0047,-0.0035,0.0025,0.0028,0.0019,0.0026,-0.0022,-0.0001,-0.0003,0.0049,0.0042,0.0003,-0.0000,-0.0041,0.0035,-0.0029,-0.0039,-0.0023,-0.0000,0.0029,-0.0005,-0.0015,-0.0048,0.0018,-0.0016,0.0037,0.0036,0.0011,-0.0033,-0.0007,-0.0048,0.0020,-0.0046,-0.0014,0.0032,-0.0031,-0.0027,0.0016,-0.0019}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
==================================
== Starts fiting Binding mode 1 ==
==================================
> Optimizing h (component1-0-h).
>> Starting new optimization: component1-0-h. (2021-05-22 06:21:32.812).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[0,1]},{"h":[2,3,4,5,6]}],"bindingModeInteractions":[],"bindingModes":[{},{},{}]}
Value and gradient before optimization:
=======================================
value = 2.20622715821962
gradient = {-0.0229,0.0229,-0.0314,-0.0157,0.0005,0.0159,0.0307}
gradient norm = 0.058935470283782
Starting Function Value: 2.20622715821962
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.199715421176437 0.219966414324175 3.732326445602412 0.031391286542224
2 4 2.198124548891400 0.105216807308655 1.000000000000000 0.003482423353755
3 5 2.198103484923611 0.012110843157316 1.000000000000000 0.000643193562343
4 6 2.198102503845035 0.002556577045935 1.000000000000000 0.000166762463489
5 7 2.198102442462540 0.000763599819224 1.000000000000000 0.000001767576744
6 8 2.198102442456826 0.000763599819224 1.000000000000000 0.000000041035173
Convergence criteria met.
After: gradient norm = 4.103517340773488E-8
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.0044,-1.0044}
Count Table 1:
---------------
h: {1.4480,0.5632,0.0343,-0.5124,-1.5331}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {0.0039,0.0042,-0.0050,-0.0044,-0.0035,-0.0037,-0.0050,0.0027,-0.0018,-0.0047,-0.0035,0.0025,0.0028,0.0019,0.0026,-0.0022,-0.0001,-0.0003,0.0049,0.0042,0.0003,-0.0000,-0.0041,0.0035,-0.0029,-0.0039,-0.0023,-0.0000,0.0029,-0.0005,-0.0015,-0.0048,0.0018,-0.0016,0.0037,0.0036,0.0011,-0.0033,-0.0007,-0.0048,0.0020,-0.0046,-0.0014,0.0032,-0.0031,-0.0027,0.0016,-0.0019}
Activity(exp=0): {-3.8483,-4.8057}
Activity(exp=1): {-3.8216,-5.0771,-5.5578,-5.6039,-5.1861}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
> Initial optimization (component1-1-f0).
>> Starting new optimization: component1-1-f0. (2021-05-22 06:21:38.32).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[55,56]},{"h":[57,58,59,60,61]}],"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],"activity":[[48,49],[50,51,52,53,54]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.204814549140245
gradient = {0.0006,-0.0005,0.0008,0.0005,0.0006,-0.0004,0.0007,0.0006,0.0005,-0.0003,0.0005,0.0006,0.0006,-0.0002,0.0004,0.0006,0.0007,-0.0001,0.0002,0.0006,0.0007,0.0000,0.0001,0.0007,0.0007,0.0001,0.0000,0.0007,0.0006,0.0002,-0.0001,0.0006,0.0006,0.0004,-0.0002,0.0006,0.0006,0.0005,-0.0003,0.0005,0.0006,0.0007,-0.0004,0.0006,0.0005,0.0008,-0.0005,0.0006,-0.0000,-0.0001,-0.0000,-0.0003,0.0001,0.0008,0.0009,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000}
gradient norm = 0.003822769618555603
Starting Function Value: 2.204814549140245
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.204543192872230 0.209730765448737 54.863563953922590 0.012980305154506
2 4 2.204066462299705 0.137489419776397 1.000000000000000 0.008568825779657
3 5 2.203521785116541 0.362164436352694 1.000000000000000 0.009406077334832
4 6 2.203352514698096 0.101685094772601 1.000000000000000 0.005123848117111
5 7 2.203146143511281 0.215363917486967 1.000000000000000 0.005778006472798
6 8 2.202831859417329 0.408936621628085 1.000000000000000 0.006885763818341
7 12 2.195014141079096 4.539414467874750 3.886617256363161 0.039239659296080
8 14 2.194924848200693 0.090691231461790 0.001769229733965 0.040255845477341
9 15 2.191546492448218 0.383103038544762 1.000000000000000 0.036932364443334
10 16 2.183967992406071 0.801307085856275 1.000000000000000 0.044649125977673
11 17 2.166405595405503 1.683384132490545 1.000000000000000 0.041487722828893
12 23 2.151009839890689 1.381755858008043 0.053905998338619 0.046225235347202
> Parameters: {1.6683e+01,-1.7098e+01,2.3712e+01,1.3204e+01,1.4173e+01,-7.9144e+00,1.7087e+01,1.3147e+01,1.4930e+01,-6.2292e+00,1.2388e+01,1.5406e+01,1.7065e+01,-6.0035e+00,9.5918e+00,1.5854e+01,1.6825e+01,1.1630e+00,1.3422e+00,1.7181e+01,1.8372e+01,-3.1793e+00,-4.8356e+00,2.6144e+01,2.6071e+01,-4.5901e+00,-3.4682e+00,1.8480e+01,1.7153e+01,1.6938e+00,9.0755e-01,1.6744e+01,1.5877e+01,9.2870e+00,-5.8684e+00,1.7215e+01,1.5573e+01,1.2251e+01,-5.9907e+00,1.4660e+01,1.3077e+01,1.6991e+01,-7.7852e+00,1.4218e+01,1.3215e+01,2.4138e+01,-1.7488e+01,1.6630e+01,-4.0358e+00,-1.3030e+01,-4.0078e+00,-1.7439e+01,-2.6092e+00,2.1353e+01,2.0719e+01,3.5508e+00,-3.5508e+00,1.3500e+01,5.5421e+00,1.4331e+00,-4.5239e+00,-1.5951e+01}
>>>> Exception caugth. Parameters reverted.
> Parameter: {-3.5063e-01,1.0619e+00,-6.2392e-01,-5.5860e-01,-4.1417e-01,1.2359e+00,-6.9298e-01,-6.0816e-01,-2.2314e-01,1.0830e+00,-6.6666e-01,-6.7065e-01,-2.7691e-01,7.9899e-01,-4.8453e-01,-5.0243e-01,-4.2370e-01,7.5542e-01,-4.1105e-01,-3.8199e-01,-3.4682e-01,1.3696e-01,-2.2482e-01,-3.5649e-02,-4.2991e-02,-2.2985e-01,1.5693e-01,-3.6319e-01,-3.9339e-01,-4.2323e-01,7.6607e-01,-4.2327e-01,-5.0176e-01,-4.7850e-01,7.9198e-01,-2.7421e-01,-6.8037e-01,-6.6344e-01,1.0993e+00,-2.3321e-01,-6.0672e-01,-6.8711e-01,1.2313e+00,-4.0825e-01,-5.5499e-01,-6.1862e-01,1.0461e+00,-3.4850e-01,-3.8341e+00,-4.8395e+00,-3.8076e+00,-4.6264e+00,-5.3199e+00,-6.0458e+00,-5.7725e+00,1.0694e+00,-1.0694e+00,1.7849e+00,7.2444e-01,7.4370e-02,-6.2212e-01,-1.9615e+00}
> Gradient: {-3.2311e-03,9.6642e-03,-1.2573e-03,1.4166e-03,9.9993e-04,1.6559e-03,2.2896e-03,1.6470e-03,-4.1643e-03,6.9690e-03,1.7699e-03,2.0178e-03,-2.1612e-03,9.6626e-03,-1.6090e-04,-7.4812e-04,2.5588e-03,-1.4980e-03,4.3388e-03,1.1928e-03,2.2700e-03,8.6970e-03,7.9241e-03,-1.2299e-02,-1.2306e-02,7.8715e-03,8.6143e-03,2.4125e-03,1.2728e-03,4.2004e-03,-1.3814e-03,2.5006e-03,-6.3752e-04,-3.1399e-04,1.0060e-02,-2.5157e-03,1.9996e-03,1.8343e-03,6.5025e-03,-3.7439e-03,1.6363e-03,2.3049e-03,1.6877e-03,9.6346e-04,1.4136e-03,-1.5690e-03,1.0167e-02,-3.4189e-03,-7.6682e-06,3.8825e-03,-7.6151e-06,3.0903e-03,2.8544e-03,-3.2300e-03,-5.7048e-05,-4.6400e-03,4.6400e-03,2.4106e-02,-6.7481e-03,-1.0205e-02,-8.8496e-03,1.6971e-03}
>>>> Re-trying (1/3).
Starting Function Value: 2.1510098398906883
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.141575138995071 0.420045580722881 9.086932225825976 0.064627115355089
2 4 2.132311064662129 0.341036201211611 1.000000000000000 0.046706058146311
3 5 2.122163880115474 0.572167247603948 1.000000000000000 0.066235976932088
4 6 2.111565573097089 0.539853910916306 1.000000000000000 0.066272846863640
5 7 2.101747374176673 0.603509005649443 1.000000000000000 0.040013753083201
6 8 2.098991133536238 0.294522259112470 1.000000000000000 0.020895272930616
7 9 2.097976997748957 0.185774376007543 1.000000000000000 0.010131755437702
8 10 2.097324094867379 0.107433084994641 1.000000000000000 0.010832882059391
9 11 2.094989063899497 0.437951347259371 1.000000000000000 0.023501182958207
10 12 2.090634321338941 0.959283159830666 1.000000000000000 0.038580539338023
11 13 2.087084004630868 1.148159086492127 1.000000000000000 0.057967958030108
12 14 2.082627779452393 0.394298407359885 1.000000000000000 0.034806382191881
13 15 2.080238588193072 0.247708984878037 1.000000000000000 0.018019905297598
14 16 2.078275615256374 0.198211682081356 1.000000000000000 0.020836099353619
15 17 2.075671648847068 0.308752174005192 1.000000000000000 0.034929667928805
16 18 2.072815171228352 0.410800481734209 1.000000000000000 0.040576617909726
17 19 2.070126937598213 0.424051870606717 1.000000000000000 0.039263893208807
18 20 2.068126529061522 0.431701477292465 1.000000000000000 0.010868875385094
19 21 2.067563397458934 0.221247225999161 1.000000000000000 0.010937704562236
20 22 2.066995500822442 0.199095309548063 1.000000000000000 0.009277469325810
21 23 2.066303975246812 0.351949065136796 1.000000000000000 0.006579130245928
22 24 2.065920386006403 0.250446063998208 1.000000000000000 0.005537814976229
23 25 2.065650202114388 0.206189922711844 1.000000000000000 0.003926519689336
24 26 2.065448420858526 0.138325661725649 1.000000000000000 0.003169497771123
25 27 2.065217751150564 0.192410470199444 1.000000000000000 0.003263403588502
26 29 2.065139284352072 0.105107071067688 0.448953789135209 0.004689521312595
27 30 2.065012968801989 0.121425678135803 1.000000000000000 0.002986671179536
28 31 2.064883161372830 0.169926861666748 1.000000000000000 0.001821407587757
29 32 2.064780879379504 0.197018360433238 1.000000000000000 0.001704851151915
30 33 2.064671607473144 0.219735072982914 1.000000000000000 0.001601867924774
31 34 2.064546279447016 0.331457289031862 1.000000000000000 0.001446522641913
32 35 2.064494484793220 0.323964375526065 1.000000000000000 0.003767111006118
33 36 2.064450550562497 0.049400903226784 1.000000000000000 0.001030276683618
34 37 2.064429073836422 0.059338820668945 1.000000000000000 0.001015685047401
35 38 2.064408826128985 0.076930438259079 1.000000000000000 0.001113002309284
36 39 2.064356338909810 0.220307671136128 1.000000000000000 0.001117023092321
37 40 2.064323185234224 0.182671238410132 1.000000000000000 0.000612600937896
38 41 2.064303201782814 0.131572560743506 1.000000000000000 0.000837400287862
39 42 2.064285279821865 0.121398261008832 1.000000000000000 0.000834133526970
40 43 2.064268591266806 0.107342217559301 1.000000000000000 0.000818427973024
41 44 2.064240787054061 0.230853827785964 1.000000000000000 0.000671840247642
42 45 2.064231537082769 0.069485395345712 1.000000000000000 0.000428361567591
43 46 2.064229249248728 0.026641609534081 1.000000000000000 0.000189072018054
44 47 2.064227806181672 0.023057898260570 1.000000000000000 0.000268078582547
45 48 2.064226126513865 0.022900481246071 1.000000000000000 0.000283132884921
46 49 2.064223129680936 0.048543237032032 1.000000000000000 0.000241526151899
47 50 2.064221356101808 0.050668662311012 1.000000000000000 0.000213234219669
48 51 2.064220649660753 0.019872090846836 1.000000000000000 0.000110376000216
49 52 2.064220181464295 0.018010076357090 1.000000000000000 0.000092352760725
50 53 2.064219786348549 0.012300621992524 1.000000000000000 0.000092054301847
51 54 2.064218874930594 0.035022596783029 1.000000000000000 0.000101715995572
52 55 2.064217990756298 0.040810639032805 1.000000000000000 0.000110213868347
53 56 2.064216909747529 0.059885508812945 1.000000000000000 0.000130308056715
54 57 2.064216058533911 0.070900932549152 1.000000000000000 0.000189338557761
55 58 2.064215438182014 0.011554895749522 1.000000000000000 0.000083965165905
56 59 2.064214906002235 0.024037686900936 1.000000000000000 0.000084200591129
57 60 2.064214477695409 0.021020291731083 1.000000000000000 0.000104417209740
58 61 2.064213526928179 0.067776604080099 1.000000000000000 0.000085016137371
59 62 2.064212630315184 0.056246227100952 1.000000000000000 0.000149485813518
60 63 2.064211516672117 0.088103231023987 1.000000000000000 0.000100561610497
61 64 2.064210796430447 0.051204955076433 1.000000000000000 0.000089577342876
62 65 2.064209441290681 0.099165182111868 1.000000000000000 0.000088811204126
63 66 2.064207846069737 0.123663995965198 1.000000000000000 0.000114194932820
64 67 2.064205860594743 0.164268000031079 1.000000000000000 0.000121734411262
65 68 2.064203549286358 0.269045082043655 1.000000000000000 0.000251435523706
66 69 2.064201486648755 0.110527402718771 1.000000000000000 0.000126589136379
67 70 2.064198903605205 0.163807343826846 1.000000000000000 0.000171201478607
68 71 2.064196558322419 0.166513771114949 1.000000000000000 0.000206565442984
69 72 2.064189735181738 0.560066674395114 1.000000000000000 0.000260569424672
70 73 2.064181540438428 0.817416904832937 1.000000000000000 0.000313320515730
71 74 2.064173076453055 1.018812976114720 1.000000000000000 0.000360925737278
72 75 2.064165245861994 1.100076616607177 1.000000000000000 0.000289076200560
73 76 2.064158695027080 1.183586179741936 1.000000000000000 0.000395866806348
74 77 2.064155154590272 0.637261399471110 1.000000000000000 0.000139044489930
75 78 2.064153096848421 0.296406820021281 1.000000000000000 0.000200145469587
76 79 2.064151070412964 0.118492988906608 1.000000000000000 0.000208381183167
77 80 2.064147059793115 0.198207149486125 1.000000000000000 0.000201432608742
78 81 2.064142790271398 0.202583298780094 1.000000000000000 0.000266700430192
79 82 2.064138869673409 0.169077637889487 1.000000000000000 0.000345106757757
80 83 2.064133435378390 0.217378870459345 1.000000000000000 0.000392309437630
81 84 2.064125551358204 0.309184491009798 1.000000000000000 0.000467249157275
82 85 2.064113984949766 0.616582548592726 1.000000000000000 0.000442069790731
83 86 2.064101737312851 1.444636618366934 1.000000000000000 0.000371872712994
84 87 2.064093819061221 0.459702629856929 1.000000000000000 0.000186065748687
85 88 2.064089797644863 0.250921597518480 1.000000000000000 0.000295043709236
86 89 2.064085748599081 0.135360975676479 1.000000000000000 0.000236601350192
87 90 2.064079151204229 0.538251291421443 1.000000000000000 0.000220296258640
88 91 2.064075096641092 0.485422948991384 1.000000000000000 0.000218962555596
89 92 2.064072331511149 0.490139986418908 1.000000000000000 0.000217408004585
90 93 2.064069260086726 0.348241425243415 1.000000000000000 0.000179050363560
91 94 2.064065899554046 0.308900427180743 1.000000000000000 0.000111273856543
92 95 2.064065143441919 0.097385591740573 1.000000000000000 0.000053071825520
93 96 2.064064916618790 0.069630837546662 1.000000000000000 0.000046244781216
94 97 2.064064660413297 0.052303955256753 1.000000000000000 0.000041790192704
95 98 2.064064398917413 0.030027562113029 1.000000000000000 0.000031744703001
96 99 2.064064283458349 0.065367896571729 1.000000000000000 0.000033741178391
97 100 2.064064229699580 0.046583041288116 1.000000000000000 0.000027287728589
98 101 2.064064212230342 0.015589372771085 1.000000000000000 0.000009656449413
99 102 2.064064208063553 0.004865833060119 1.000000000000000 0.000004672428217
100 103 2.064064206305096 0.008306041135760 1.000000000000000 0.000006592727464
101 104 2.064064205151578 0.005007947823396 1.000000000000000 0.000005196493766
102 105 2.064064203443466 0.002185465386752 1.000000000000000 0.000002830057154
103 106 2.064064202325964 0.002644359872950 1.000000000000000 0.000004573021410
104 107 2.064064201869750 0.003338265323097 1.000000000000000 0.000004886193077
105 108 2.064064201421714 0.002453678937452 1.000000000000000 0.000003668057078
106 109 2.064064201189787 0.000722697783632 1.000000000000000 0.000001778309761
107 110 2.064064201074242 0.000894714623374 1.000000000000000 0.000002473703181
108 111 2.064064201004913 0.001502243236611 1.000000000000000 0.000002777283137
109 112 2.064064200941499 0.001238794387180 1.000000000000000 0.000002223455610
110 113 2.064064200895990 0.000417434885505 1.000000000000000 0.000001013161310
111 114 2.064064200879224 0.000417434885505 1.000000000000000 0.000000444456973
Convergence criteria met.
After: gradient norm = 4.444569726786931E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.1032,-1.1032}
Count Table 1:
---------------
h: {1.4986,0.7508,0.2910,-0.5385,-2.0019}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-1.1818,0.4256,-1.5067,-1.2798,-1.6687,1.1847,-1.7071,-1.3517,-0.2561,0.1293,-1.7747,-1.6412,-1.4843,0.7056,-2.8721,0.1081,-1.4146,1.3068,-1.8988,-1.5361,-1.4983,-1.2198,-1.7227,0.8981,-0.0754,-1.7930,-0.7154,-0.9589,-1.8229,-0.7933,0.0284,-0.9549,-0.9171,-0.3175,-2.0571,-0.2510,-2.0483,-1.1687,0.6086,-0.9343,-0.9880,-1.9324,0.1070,-0.7292,-1.0114,-0.7793,-1.4054,-0.3466}
Activity(exp=0): {-0.0001,1.5627}
Activity(exp=1): {-0.0001,-1.9359,-0.7565,-0.4434,-1.9706}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
Suggested variations:
key=12;5;0, description = Initial model.
> Optimizing variation "Initial model." (component1-2-variation0).
>> Starting new optimization: component1-2-variation0. (2021-05-22 06:23:55.686).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[55,56]},{"h":[57,58,59,60,61]}],"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],"activity":[[48,49],[50,51,52,53,54]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.0640642008792236
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}
gradient norm = 4.444569726784024E-7
Already at minimum!
After: gradient norm = 4.444569726784024E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.1032,-1.1032}
Count Table 1:
---------------
h: {1.4986,0.7508,0.2910,-0.5385,-2.0019}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-1.1818,0.4256,-1.5067,-1.2798,-1.6687,1.1847,-1.7071,-1.3517,-0.2561,0.1293,-1.7747,-1.6412,-1.4843,0.7056,-2.8721,0.1081,-1.4146,1.3068,-1.8988,-1.5361,-1.4983,-1.2198,-1.7227,0.8981,-0.0754,-1.7930,-0.7154,-0.9589,-1.8229,-0.7933,0.0284,-0.9549,-0.9171,-0.3175,-2.0571,-0.2510,-2.0483,-1.1687,0.6086,-0.9343,-0.9880,-1.9324,0.1070,-0.7292,-1.0114,-0.7793,-1.4054,-0.3466}
Activity(exp=0): {-0.0001,1.5627}
Activity(exp=1): {-0.0001,-1.9359,-0.7565,-0.4434,-1.9706}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
The Likelihood DID NOT improve. Discarding fit component1-2-variation0.
Suggested variations:
key=12;6;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation1).
>> Starting new optimization: component1-2-variation1. (2021-05-22 06:23:56.75).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[55,56]},{"h":[57,58,59,60,61]}],"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],"activity":[[48,49],[50,51,52,53,54]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.0635628946809828
gradient = {0.0001,0.0001,0.0001,0.0001,0.0000,0.0003,0.0000,0.0000,0.0001,0.0001,0.0001,0.0000,0.0000,0.0001,0.0000,0.0001,0.0000,0.0003,0.0000,0.0000,0.0000,0.0001,0.0000,0.0002,0.0001,0.0000,0.0000,0.0001,-0.0000,0.0001,0.0002,0.0000,0.0001,0.0001,0.0000,0.0001,0.0000,0.0001,0.0001,0.0000,0.0001,0.0000,0.0002,0.0000,0.0000,0.0001,0.0000,0.0002,-0.0000,0.0003,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0022,0.0022,-0.0001,-0.0001,0.0000,0.0001,0.0001}
gradient norm = 0.003274608201852622
Starting Function Value: 2.0635628946809828
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.063552566390888 0.006140642478470 1.875229676330895 0.000813743941601
2 4 2.063551680156359 0.001605974778632 1.000000000000000 0.000394191360007
3 5 2.063551199847314 0.001748588967941 1.000000000000000 0.000304826566062
4 6 2.063550689589354 0.002676062098584 1.000000000000000 0.000363852500379
5 7 2.063549886035113 0.005339850234602 1.000000000000000 0.000369260126900
6 8 2.063548687787480 0.010188017719005 1.000000000000000 0.000378845683997
7 9 2.063548202708615 0.018442025698504 1.000000000000000 0.000656665223796
8 10 2.063546998707669 0.004019394872174 1.000000000000000 0.000227925885886
9 11 2.063546613732109 0.003611706820818 1.000000000000000 0.000168698412332
10 12 2.063546154250628 0.008873816592813 1.000000000000000 0.000167730420690
11 13 2.063545764526475 0.009265006439866 1.000000000000000 0.000180104008417
12 14 2.063545486438442 0.012061432224124 1.000000000000000 0.000160146830245
13 15 2.063545341286865 0.002065557779645 1.000000000000000 0.000091896476573
14 16 2.063545235221471 0.002820263649479 1.000000000000000 0.000084077947704
15 17 2.063545128144085 0.004041498627214 1.000000000000000 0.000099623708528
16 18 2.063545012891439 0.007207035019186 1.000000000000000 0.000110562090975
17 19 2.063544937858446 0.002426041500235 1.000000000000000 0.000065565264359
18 20 2.063544877513495 0.002984894433844 1.000000000000000 0.000052230779858
19 21 2.063544829501825 0.002551847554230 1.000000000000000 0.000050696696221
20 22 2.063544714470506 0.006986786023770 1.000000000000000 0.000073414251466
21 23 2.063544601254907 0.009030874854069 1.000000000000000 0.000065665085136
22 24 2.063544493268008 0.008996721783021 1.000000000000000 0.000062584427189
23 25 2.063544374412725 0.009633135941090 1.000000000000000 0.000071090528922
24 26 2.063544285784410 0.007289860899304 1.000000000000000 0.000040890142702
25 27 2.063544235345067 0.003764654213823 1.000000000000000 0.000032891973565
26 28 2.063544165307390 0.006146931563199 1.000000000000000 0.000032014496459
27 29 2.063544106573898 0.007140997592072 1.000000000000000 0.000030689232622
28 30 2.063544034993778 0.009159594845255 1.000000000000000 0.000040109423737
29 31 2.063543979335473 0.010000412899454 1.000000000000000 0.000026360065151
30 32 2.063543966947036 0.001928646940830 1.000000000000000 0.000011437090962
31 33 2.063543961166052 0.001006504861169 1.000000000000000 0.000011933667338
32 34 2.063543947711111 0.002376468025985 1.000000000000000 0.000011146967858
33 35 2.063543934170379 0.003941919111706 1.000000000000000 0.000007293855908
34 36 2.063543928798877 0.002580902762582 1.000000000000000 0.000009353613444
35 37 2.063543926049243 0.001385730316056 1.000000000000000 0.000004618542038
36 38 2.063543924538688 0.000824990222229 1.000000000000000 0.000003804129311
37 39 2.063543923218515 0.000823698595030 1.000000000000000 0.000002922502465
38 40 2.063543922363825 0.000978285755763 1.000000000000000 0.000003673668774
39 41 2.063543921795700 0.000525124575995 1.000000000000000 0.000002232146445
40 42 2.063543921334726 0.000440330225821 1.000000000000000 0.000002340136555
41 43 2.063543920497107 0.001102060402338 1.000000000000000 0.000002421940695
42 44 2.063543919665172 0.001446906566799 1.000000000000000 0.000004839072165
43 45 2.063543919142715 0.000953848464763 1.000000000000000 0.000002077057130
44 46 2.063543918929933 0.000412762952704 1.000000000000000 0.000001415781519
45 47 2.063543918769652 0.000289177360507 1.000000000000000 0.000001742601098
46 48 2.063543918403509 0.000741500281211 1.000000000000000 0.000002315673254
47 49 2.063543917920439 0.001150890029912 1.000000000000000 0.000002248877579
48 50 2.063543917557255 0.001129269320929 1.000000000000000 0.000002169492578
49 51 2.063543917435812 0.001129269320929 1.000000000000000 0.000000904503687
Convergence criteria met.
After: gradient norm = 9.045036871940389E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.1110,-1.1110}
Count Table 1:
---------------
h: {1.5006,0.7523,0.2913,-0.5400,-2.0043}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-1.1705,0.4423,-1.5274,-1.2580,-1.6430,1.1682,-1.6984,-1.3404,-0.2476,0.1366,-1.7713,-1.6313,-1.4560,0.7142,-2.8901,0.1183,-1.3921,1.2628,-1.8701,-1.5142,-1.4810,-1.2507,-1.6947,0.9129,-0.0680,-1.7840,-0.7040,-0.9576,-1.7868,-0.7973,0.0218,-0.9513,-0.9191,-0.3127,-2.0353,-0.2466,-2.0027,-1.1844,0.6041,-0.9306,-0.9830,-1.9230,0.1073,-0.7148,-1.0019,-0.7719,-1.3976,-0.3421}
Activity(exp=0): {-0.0001,1.5728}
Activity(exp=1): {-0.0001,-1.9199,-0.7603,-0.4418,-1.9653}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;7;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component1-2-variation2).
>> Starting new optimization: component1-2-variation2. (2021-05-22 06:24:49.865).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[55,56]},{"h":[57,58,59,60,61]}],"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],"activity":[[48,49],[50,51,52,53,54]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.0635417830804403
gradient = {0.0000,0.0000,0.0000,0.0000,0.0000,0.0001,0.0000,-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,-0.0000,0.0001,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0001,0.0001,-0.0002,-0.0002,-0.0000,0.0003,0.0002}
gradient norm = 5.389149697105867E-4
Starting Function Value: 2.0635417830804403
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.063541134829511 0.002423777004332 4.497512855569795 0.000449181533717
2 4 2.063540841275303 0.001522504544340 1.000000000000000 0.000154787851283
3 5 2.063540775060158 0.000586887572408 1.000000000000000 0.000127733820734
4 6 2.063540657829120 0.001757802805471 1.000000000000000 0.000074196545944
5 7 2.063540604111978 0.001216662013070 1.000000000000000 0.000079816304305
6 8 2.063540530848800 0.004494636016974 1.000000000000000 0.000150809282771
7 9 2.063540468089380 0.001221609256643 1.000000000000000 0.000080238777824
8 10 2.063540445456374 0.000457509651231 1.000000000000000 0.000066165354698
9 11 2.063540374006965 0.002239213944445 1.000000000000000 0.000062322435495
10 12 2.063540282245375 0.004573188886547 1.000000000000000 0.000072172750325
11 13 2.063540217814196 0.005461098092188 1.000000000000000 0.000095642858691
12 14 2.063540178982471 0.004772775791638 1.000000000000000 0.000051861704897
13 15 2.063540159377259 0.001128272126419 1.000000000000000 0.000029125182102
14 16 2.063540141880938 0.001050689337024 1.000000000000000 0.000034169734309
15 17 2.063540123252952 0.002050157970214 1.000000000000000 0.000053421098591
16 18 2.063540104512693 0.002603340138795 1.000000000000000 0.000035419167700
17 19 2.063540092383013 0.001426709567682 1.000000000000000 0.000023360069556
18 20 2.063540077265123 0.002171757222254 1.000000000000000 0.000029069829691
19 21 2.063540064109651 0.001836400002717 1.000000000000000 0.000031195099723
20 22 2.063540035717074 0.004037948607587 1.000000000000000 0.000026023557648
21 23 2.063540003407045 0.005665724773312 1.000000000000000 0.000018654874154
22 24 2.063539980377807 0.005426638191127 1.000000000000000 0.000026538382039
23 25 2.063539969056850 0.002732417059864 1.000000000000000 0.000016297825493
24 26 2.063539962406392 0.001555975044315 1.000000000000000 0.000016475090954
25 27 2.063539948950992 0.003419609353794 1.000000000000000 0.000015093720340
26 28 2.063539941379265 0.002768900882807 1.000000000000000 0.000011983958413
27 29 2.063539938567184 0.001113582634703 1.000000000000000 0.000007279285140
28 30 2.063539936374193 0.001005302792070 1.000000000000000 0.000011239246546
29 31 2.063539933392277 0.001316921874799 1.000000000000000 0.000011518451457
30 32 2.063539927743268 0.003172448522983 1.000000000000000 0.000008396873512
31 34 2.063539926364422 0.001100411328941 0.471998471245335 0.000006749403447
32 35 2.063539925217776 0.000670400406874 1.000000000000000 0.000003038002806
33 36 2.063539924579223 0.000502529076553 1.000000000000000 0.000004141232265
34 37 2.063539923867022 0.000660106556626 1.000000000000000 0.000005197254204
35 38 2.063539922806672 0.001227211820758 1.000000000000000 0.000004288713002
36 39 2.063539922134708 0.001162912492838 1.000000000000000 0.000002380440414
37 40 2.063539921934446 0.000445353426417 1.000000000000000 0.000001296532264
38 41 2.063539921879082 0.000445353426417 1.000000000000000 0.000000909262114
Convergence criteria met.
After: gradient norm = 9.092621139334198E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.1120,-1.1120}
Count Table 1:
---------------
h: {1.5032,0.7547,0.2919,-0.5424,-2.0075}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-1.1629,0.4434,-1.5306,-1.2508,-1.6423,1.1660,-1.7000,-1.3246,-0.2422,0.1370,-1.7693,-1.6264,-1.4415,0.7055,-2.8741,0.1091,-1.3852,1.2526,-1.8688,-1.4996,-1.4808,-1.2513,-1.6804,0.9116,-0.0622,-1.7912,-0.6979,-0.9496,-1.7795,-0.7959,0.0220,-0.9476,-0.9155,-0.3112,-2.0310,-0.2432,-1.9878,-1.1831,0.6026,-0.9326,-0.9812,-1.9194,0.1091,-0.7094,-0.9963,-0.7671,-1.4004,-0.3371}
Activity(exp=0): {-0.0001,1.5737}
Activity(exp=1): {-0.0001,-1.9237,-0.7568,-0.4355,-1.9596}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
The Likelihood DID NOT improve. Discarding fit component1-2-variation2.
Suggested variations:
key=12;6;1, description = Heuristic shift (1).
> Optimizing variation "Heuristic shift (1)." (component1-2-variation3).
>> Starting new optimization: component1-2-variation3. (2021-05-22 06:25:34.348).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[55,56]},{"h":[57,58,59,60,61]}],"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],"activity":[[48,49],[50,51,52,53,54]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.083018539966859
gradient = {0.0098,0.0103,0.0211,0.0103,0.0053,0.0391,0.0030,0.0041,0.0013,0.0471,0.0014,0.0017,0.0185,0.0264,0.0038,0.0027,0.0020,0.0343,0.0005,0.0148,0.0016,0.0477,0.0009,0.0014,0.0024,0.0032,0.0016,0.0443,0.0290,0.0035,0.0116,0.0074,0.0034,0.0104,0.0309,0.0068,0.0072,0.0206,0.0020,0.0218,0.0014,0.0050,0.0397,0.0055,0.0077,0.0024,0.0320,0.0094,-0.0000,0.0228,-0.0000,0.0007,0.0045,0.0100,0.0134,-0.0449,0.0449,-0.0070,-0.0077,-0.0057,-0.0048,0.0252}
gradient norm = 0.15118784021117085
Starting Function Value: 2.083018539966859
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.067467357022718 0.213449561247056 1.411816988382935 0.021281607232364
2 4 2.066929466713100 0.029386612922138 1.000000000000000 0.016126233593664
3 5 2.065569564075110 0.132108685081416 1.000000000000000 0.013572842608896
4 6 2.064599801910184 0.127634790840950 1.000000000000000 0.016025941638511
5 7 2.062020584580663 0.444538697689521 1.000000000000000 0.019826767772208
6 9 2.061050859947170 0.285558144840121 0.473402057544133 0.016986461800928
7 10 2.060125488871895 0.258418492189863 1.000000000000000 0.007670973333156
8 11 2.059835292529205 0.163895426210262 1.000000000000000 0.003611480841407
9 12 2.059691830298429 0.107037433753399 1.000000000000000 0.004619334417364
10 13 2.059477079925267 0.152660840758561 1.000000000000000 0.005070146284420
11 14 2.059237920429579 0.173479457372715 1.000000000000000 0.004020789070815
12 16 2.059149265874073 0.099447290579067 0.457132220690458 0.002847909709921
13 17 2.059083699178318 0.078062740136434 1.000000000000000 0.001745684661184
14 18 2.059044827565180 0.051942682774803 1.000000000000000 0.001952663709842
15 19 2.058991506748460 0.083660513958658 1.000000000000000 0.002110040705482
16 20 2.058933734016291 0.137842847650272 1.000000000000000 0.002870590280221
17 21 2.058880843168297 0.187852029070841 1.000000000000000 0.002237930890969
18 22 2.058847615198458 0.041239292628515 1.000000000000000 0.001282071531252
19 23 2.058819810879360 0.068261979701519 1.000000000000000 0.001268789345046
20 24 2.058799739912455 0.052175389698730 1.000000000000000 0.001285714116214
21 25 2.058744758622381 0.177046237622486 1.000000000000000 0.001296122005464
22 26 2.058704660194082 0.161097155698391 1.000000000000000 0.001476463615527
23 27 2.058677919518975 0.198009564959957 1.000000000000000 0.001329952914552
24 28 2.058662740697799 0.029669969606774 1.000000000000000 0.000600523558656
25 29 2.058654140356345 0.028957219431586 1.000000000000000 0.000640093707684
26 30 2.058640905296699 0.051151256856466 1.000000000000000 0.000677583470550
27 31 2.058611501893141 0.158365435891616 1.000000000000000 0.000690335306087
28 32 2.058587196856387 0.198927921437561 1.000000000000000 0.000741171856294
29 33 2.058577878204950 0.110149941344504 1.000000000000000 0.000224875465442
30 34 2.058575790864010 0.028488613818254 1.000000000000000 0.000179520232029
31 35 2.058573941465680 0.025103667987506 1.000000000000000 0.000216690649040
32 36 2.058571690324306 0.033189194493476 1.000000000000000 0.000187112689328
33 37 2.058569271023283 0.049437245537686 1.000000000000000 0.000178392887388
34 38 2.058568583893676 0.033968494654773 1.000000000000000 0.000170328641847
35 39 2.058568291372470 0.006901323117478 1.000000000000000 0.000056159629970
36 40 2.058568173644435 0.004797430410796 1.000000000000000 0.000049540188181
37 41 2.058567989941815 0.007512249683912 1.000000000000000 0.000047551394189
38 42 2.058567542688587 0.023523053871533 1.000000000000000 0.000053445923625
39 43 2.058567393129692 0.024454239517316 1.000000000000000 0.000172520547367
40 44 2.058567261944111 0.003586189746171 1.000000000000000 0.000046388855844
41 45 2.058567224352987 0.002679879251721 1.000000000000000 0.000023319450472
42 46 2.058567195929182 0.003101716994201 1.000000000000000 0.000021762054456
43 47 2.058567116488106 0.008896119063751 1.000000000000000 0.000020487326137
44 48 2.058567029485376 0.012119156709630 1.000000000000000 0.000017792938478
45 49 2.058567024947696 0.012467748576599 1.000000000000000 0.000051108943352
46 50 2.058566977236858 0.003659376231162 1.000000000000000 0.000013869095887
47 51 2.058566964082458 0.001721896469907 1.000000000000000 0.000010149464705
48 52 2.058566938580915 0.005313359110349 1.000000000000000 0.000014770295329
49 53 2.058566911401901 0.007720858566402 1.000000000000000 0.000015533561322
50 54 2.058566856240852 0.015973843043082 1.000000000000000 0.000021391236303
51 55 2.058566817036119 0.017691446067288 1.000000000000000 0.000014580871950
52 56 2.058566803040036 0.004639642278623 1.000000000000000 0.000007851901113
53 57 2.058566795541414 0.002477529169713 1.000000000000000 0.000007202063842
54 58 2.058566786778791 0.003115165998020 1.000000000000000 0.000006660783104
55 59 2.058566772832665 0.006930898378661 1.000000000000000 0.000013993823303
56 60 2.058566760726423 0.006582345997431 1.000000000000000 0.000009287844689
57 61 2.058566746087533 0.008436116298445 1.000000000000000 0.000009279832817
58 62 2.058566720590508 0.013837505449594 1.000000000000000 0.000012565188636
59 63 2.058566669157836 0.030130970284880 1.000000000000000 0.000015806997520
60 64 2.058566588597102 0.054882845505434 1.000000000000000 0.000050877089058
61 65 2.058566504518133 0.047810242867392 1.000000000000000 0.000048165113205
62 66 2.058566367490641 0.085529567674418 1.000000000000000 0.000024417333190
63 67 2.058566284046407 0.048160439201364 1.000000000000000 0.000026093239202
64 68 2.058566178334495 0.052269578492168 1.000000000000000 0.000032661829364
65 69 2.058565968124162 0.115511376502356 1.000000000000000 0.000038123863907
66 70 2.058565601772630 0.217304728130151 1.000000000000000 0.000057386211318
67 71 2.058565119711507 0.349589914348269 1.000000000000000 0.000031124127400
68 72 2.058564819405994 0.212896942736302 1.000000000000000 0.000044762204750
69 73 2.058564580024471 0.165908649947732 1.000000000000000 0.000050812195033
70 74 2.058564481838188 0.012937152952819 1.000000000000000 0.000032336326254
71 75 2.058564403484692 0.012896515628991 1.000000000000000 0.000018338508101
72 76 2.058564338412835 0.038335267281732 1.000000000000000 0.000016532738507
73 77 2.058564279518629 0.059340774465516 1.000000000000000 0.000021012013096
74 78 2.058564213245132 0.064850824313355 1.000000000000000 0.000018742508771
75 79 2.058564151758165 0.047990679682315 1.000000000000000 0.000012193605081
76 80 2.058564145718505 0.007590645848030 1.000000000000000 0.000018937621960
77 81 2.058564138956157 0.007602241736027 1.000000000000000 0.000003749686461
78 82 2.058564138181665 0.003030097326774 1.000000000000000 0.000003154934247
79 83 2.058564136284092 0.002010315168176 1.000000000000000 0.000002119986780
80 84 2.058564134825992 0.003224000027945 1.000000000000000 0.000001396158430
81 85 2.058564134511478 0.004599145527469 1.000000000000000 0.000002815443657
82 86 2.058564134387657 0.004599145527469 1.000000000000000 0.000000588611737
Convergence criteria met.
After: gradient norm = 5.886117372317741E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.0984,-1.0984}
Count Table 1:
---------------
h: {1.4768,0.7318,0.2839,-0.5206,-1.9719}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-1.5221,-1.5400,0.4637,-1.3974,-1.2859,0.5199,-1.4461,-1.7839,-1.6387,1.3019,-1.9516,-1.7076,-0.2909,0.1449,-2.0940,-1.7559,-1.5824,0.5838,-2.9134,-0.0839,-1.6401,1.4382,-2.0768,-1.7174,-1.5411,-1.3198,-1.8936,0.7584,-0.2077,-1.8785,-0.8226,-1.0872,-1.9227,-0.9293,-0.0675,-1.0765,-1.0469,-0.4884,-2.0060,-0.4547,-2.3903,-1.1806,0.5405,-0.9657,-1.1313,-1.9558,-0.0141,-0.8948}
Activity(exp=0): {-0.0000,1.9184}
Activity(exp=1): {-0.0000,-1.7272,-0.7981,-0.8900,-2.4991}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
The Likelihood DID improve.
Suggested variations:
key=12;6;2, description = Heuristic shift (1).
> Optimizing variation "Heuristic shift (1)." (component1-2-variation4).
>> Starting new optimization: component1-2-variation4. (2021-05-22 06:27:03.911).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[55,56]},{"h":[57,58,59,60,61]}],"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],"activity":[[48,49],[50,51,52,53,54]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.0714920662613445
gradient = {0.0115,0.0028,0.0059,0.0052,0.0016,0.0021,0.0193,0.0023,0.0015,0.0197,0.0017,0.0024,0.0006,0.0235,0.0006,0.0006,0.0084,0.0150,0.0006,0.0014,0.0010,0.0181,0.0003,0.0060,0.0005,0.0241,0.0003,0.0005,0.0015,0.0022,0.0010,0.0206,0.0135,0.0021,0.0060,0.0038,0.0022,0.0052,0.0138,0.0042,0.0033,0.0129,0.0014,0.0077,0.0006,0.0025,0.0181,0.0042,-0.0000,0.0137,-0.0000,0.0006,0.0028,0.0047,0.0036,-0.0239,0.0239,-0.0045,-0.0046,-0.0019,0.0018,0.0093}
gradient norm = 0.07610894646125836
Starting Function Value: 2.0714920662613445
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.066675768997069 0.129914960892489 1.706960442010845 0.016503547290338
2 4 2.066290827872390 0.027026249564197 1.000000000000000 0.012856686295149
3 5 2.065232305505655 0.139475428276288 1.000000000000000 0.009564759595416
4 6 2.064605529029689 0.110122252329105 1.000000000000000 0.010967514437127
5 7 2.063215838344870 0.417878142803513 1.000000000000000 0.012885678913102
6 8 2.062945113019601 0.299545564035023 1.000000000000000 0.017244723288203
7 9 2.062522357810634 0.085549662856191 1.000000000000000 0.004147171041751
8 10 2.062456235981772 0.021661589411434 1.000000000000000 0.003287685093066
9 11 2.062346415867899 0.057246616479952 1.000000000000000 0.004712007416351
10 12 2.062191658586911 0.097136212817474 1.000000000000000 0.005515785655121
11 13 2.061927228041681 0.201609875907035 1.000000000000000 0.004875266594454
12 14 2.061796112547982 0.266632048572904 1.000000000000000 0.005747882997016
13 15 2.061682916279036 0.045129050337172 1.000000000000000 0.002791682767403
14 16 2.061623415834450 0.056845855444175 1.000000000000000 0.002146449684745
15 17 2.061562033580079 0.104204060612385 1.000000000000000 0.002242502078806
16 18 2.061515070867402 0.147344582316694 1.000000000000000 0.003891168450700
17 19 2.061465156609519 0.055267198435639 1.000000000000000 0.001687815581251
18 20 2.061438411731662 0.039467694403554 1.000000000000000 0.001218745100018
19 21 2.061414066894701 0.054200813158298 1.000000000000000 0.001375021169940
20 22 2.061384251155715 0.092231191981240 1.000000000000000 0.002135243366745
21 23 2.061351917313782 0.088122842915569 1.000000000000000 0.001488044858541
22 24 2.061315792414496 0.111330616371212 1.000000000000000 0.001212446268062
23 25 2.061287298073426 0.111995411138136 1.000000000000000 0.000800024639490
24 26 2.061271467220057 0.073064343426033 1.000000000000000 0.000464271058892
25 27 2.061259804796678 0.063795995462428 1.000000000000000 0.000464681312164
26 28 2.061249442401298 0.067410980150622 1.000000000000000 0.000490076360810
27 29 2.061238222354387 0.084662672733466 1.000000000000000 0.000306080893328
28 30 2.061230906323888 0.079784715151849 1.000000000000000 0.000253208671635
29 31 2.061227048129684 0.049414573117014 1.000000000000000 0.000276666659973
30 32 2.061223853239799 0.050455063163599 1.000000000000000 0.000243165686366
31 33 2.061221207474973 0.047988803387216 1.000000000000000 0.000194139671143
32 34 2.061219652463381 0.034856761589455 1.000000000000000 0.000152669941682
33 35 2.061218579800531 0.026951071240044 1.000000000000000 0.000164540351889
34 36 2.061217421683455 0.031480440483845 1.000000000000000 0.000125231838901
35 37 2.061216724867860 0.026445939203299 1.000000000000000 0.000066749306713
36 38 2.061216419901452 0.013360179365304 1.000000000000000 0.000059209683167
37 39 2.061216187212454 0.011726915949217 1.000000000000000 0.000069449651880
38 40 2.061215895620970 0.016460450380496 1.000000000000000 0.000057383434250
39 41 2.061215640421036 0.018862079772973 1.000000000000000 0.000040300376103
40 42 2.061215478096059 0.015958172747229 1.000000000000000 0.000036083306936
41 43 2.061215343478716 0.013401634495171 1.000000000000000 0.000049214955455
42 44 2.061215190364073 0.017238140974380 1.000000000000000 0.000036178372147
43 45 2.061215090957409 0.012652791160568 1.000000000000000 0.000035529829283
44 46 2.061215030116618 0.009092411522894 1.000000000000000 0.000018048930813
45 47 2.061215000626681 0.004610002917866 1.000000000000000 0.000022721614130
46 48 2.061214953750855 0.007453131057279 1.000000000000000 0.000022003139762
47 49 2.061214912244882 0.013056782721498 1.000000000000000 0.000038482607430
48 50 2.061214884441068 0.004343609645021 1.000000000000000 0.000010807615568
49 51 2.061214874360000 0.002324358104659 1.000000000000000 0.000012075934377
50 52 2.061214862700016 0.003038304676455 1.000000000000000 0.000013976163022
51 53 2.061214837984859 0.007231890168305 1.000000000000000 0.000013520709673
52 54 2.061214809376335 0.011366260260016 1.000000000000000 0.000023142333424
53 55 2.061214787082040 0.009126946984556 1.000000000000000 0.000010236497223
54 56 2.061214771259010 0.007022386823771 1.000000000000000 0.000011818627503
55 57 2.061214754139585 0.006649466624626 1.000000000000000 0.000013866127290
56 58 2.061214727473549 0.011802546625746 1.000000000000000 0.000009807324218
57 59 2.061214703312665 0.013435341053741 1.000000000000000 0.000015147597259
58 60 2.061214674506330 0.015629851286634 1.000000000000000 0.000015404618625
59 61 2.061214642620490 0.015557871199056 1.000000000000000 0.000020784093328
60 62 2.061214578712136 0.029713517145905 1.000000000000000 0.000025636710196
61 63 2.061214431923345 0.077855438288580 1.000000000000000 0.000035615031635
62 64 2.061214212973305 0.150856406328059 1.000000000000000 0.000043042091827
63 65 2.061213948267491 0.124777974999856 1.000000000000000 0.000033098975852
64 66 2.061213583894426 0.183661104330946 1.000000000000000 0.000038183536861
65 67 2.061213312878619 0.127803692368505 1.000000000000000 0.000040213681687
66 68 2.061212875177079 0.249276150182243 1.000000000000000 0.000049694689196
67 69 2.061212528360179 0.202035171858648 1.000000000000000 0.000036655198282
68 70 2.061212204219096 0.187281727050700 1.000000000000000 0.000044545720932
69 71 2.061211866079615 0.185613439592301 1.000000000000000 0.000035661560992
70 72 2.061211666212907 0.123630674200817 1.000000000000000 0.000030919427995
71 73 2.061211584408405 0.032413306073214 1.000000000000000 0.000020120942581
72 74 2.061211532415227 0.011249878457524 1.000000000000000 0.000021563718412
73 75 2.061211444284270 0.036061031528955 1.000000000000000 0.000019402361911
74 76 2.061211383943748 0.054783655710999 1.000000000000000 0.000032484607704
75 77 2.061211372985009 0.012998215990471 1.000000000000000 0.000005314868271
76 78 2.061211371398483 0.002481081376948 1.000000000000000 0.000005250992488
77 79 2.061211368700745 0.001210592650112 1.000000000000000 0.000004388894293
78 80 2.061211363523828 0.003310590860627 1.000000000000000 0.000002980746461
79 81 2.061211362594298 0.001590604969591 1.000000000000000 0.000003831151891
80 82 2.061211362156406 0.000284352775615 1.000000000000000 0.000001669917783
81 83 2.061211361763340 0.000561483536834 1.000000000000000 0.000001370807537
82 84 2.061211361499086 0.000610749874050 1.000000000000000 0.000001301147944
83 85 2.061211361117019 0.000610749874050 1.000000000000000 0.000000832541008
Convergence criteria met.
After: gradient norm = 8.325410078128275E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.0799,-1.0799}
Count Table 1:
---------------
h: {1.4790,0.7340,0.2867,-0.5185,-1.9811}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-0.6619,-0.1688,-2.1082,-1.1359,-1.6065,-1.9339,0.6120,-1.1466,-0.8534,0.8150,-2.0560,-1.9806,-1.5839,1.4466,-2.1678,-1.7700,-0.3548,-0.0535,-1.7924,-1.8743,-1.5481,0.4655,-2.8977,-0.0948,-1.6331,1.2994,-2.1433,-1.5981,-1.4816,-1.4065,-1.9284,0.7415,-0.2768,-1.9007,-0.8072,-1.0904,-1.9794,-0.9385,-0.0524,-1.1048,-1.0133,-0.6628,-1.9248,-0.4741,-2.4285,-1.0061,0.5710,-1.2114}
Activity(exp=0): {-0.0000,1.8510}
Activity(exp=1): {-0.0000,-2.0035,-0.9674,-0.7792,-2.1760}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
The Likelihood DID NOT improve. Discarding fit component1-2-variation4.
informationThreshold = 0.1
>>> Information used for optimizeSizeHeuristic: I[0] = 0.6454831481192835, I[1] = 0.6861141722567494, I[k-2] = 0.6679738699821263, I[k-1] = 0.31302305982701284
Suggested variations:
key=14;7;2, description = Expands: deltaLeft = 1, deltaRight = 1, deltaFlank = 1.
> Optimizing variation "Expands: deltaLeft = 1, deltaRight = 1, deltaFlank = 1." (component1-2-variation5).
>> Starting new optimization: component1-2-variation5. (2021-05-22 06:28:31.635).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[63,64]},{"h":[65,66,67,68,69]}],"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],"activity":[[56,57],[58,59,60,61,62]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.059682815984945
gradient = {0.0030,-0.0065,0.0017,0.0018,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0022,0.0011,0.0027,-0.0060,-0.0000,0.0000,-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 = 0.010362099955439975
Starting Function Value: 2.059682815984945
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 2.056407565640204 1.000000000000000 96.505535007410570 0.031017997004732
2 4 2.055703065735650 0.072712183624184 0.197080058983872 0.007865125629096
3 5 2.055297430873270 0.233570950553703 1.000000000000000 0.004130880623146
4 6 2.055030624814002 0.140566766469604 1.000000000000000 0.007624506901435
5 7 2.054755861867188 0.139998118050481 1.000000000000000 0.005688959209150
6 8 2.054548037155295 0.140529913264261 1.000000000000000 0.003540912869007
7 9 2.054405998395546 0.141528309867257 1.000000000000000 0.002740349226878
8 10 2.054312641711514 0.098440131039105 1.000000000000000 0.003068550870315
9 11 2.054218894229492 0.098446185231705 1.000000000000000 0.002478338838451
10 12 2.054148044786096 0.109464670179551 1.000000000000000 0.001879730420737
11 13 2.054110027106005 0.062024742568253 1.000000000000000 0.001719171870636
12 14 2.054077724228482 0.056228935671292 1.000000000000000 0.001594692050425
13 15 2.054046094938220 0.087818387472709 1.000000000000000 0.001261388623880
14 16 2.054030271043814 0.038105169252721 1.000000000000000 0.000938209251736
15 17 2.054018686404086 0.030911766440276 1.000000000000000 0.001068674930727
16 18 2.053997745060617 0.072130502532356 1.000000000000000 0.001241447589386
17 19 2.053976775974894 0.088639163032393 1.000000000000000 0.000940204781955
18 20 2.053958979599019 0.098095609164268 1.000000000000000 0.000495929531914
19 21 2.053952590591575 0.049051985595233 1.000000000000000 0.000315564211418
20 22 2.053949829426102 0.027112558968258 1.000000000000000 0.000356015488760
21 23 2.053947009611829 0.027768093166989 1.000000000000000 0.000330926403045
22 24 2.053941602342841 0.061475038453564 1.000000000000000 0.000279370549588
23 25 2.053938266957279 0.059057340887211 1.000000000000000 0.000191083516801
24 26 2.053937037680203 0.025973040892929 1.000000000000000 0.000145531530668
25 27 2.053936293833510 0.016448354491945 1.000000000000000 0.000148048081747
26 28 2.053934761742347 0.031810662273220 1.000000000000000 0.000131647591616
27 29 2.053932917192129 0.056733331600082 1.000000000000000 0.000085801702915
28 30 2.053932307248521 0.027792261466072 1.000000000000000 0.000056676381906
29 31 2.053932039201662 0.013588132685766 1.000000000000000 0.000049846657077
30 32 2.053931806286017 0.012146339286043 1.000000000000000 0.000042904466157
31 33 2.053931602591578 0.012949321026617 1.000000000000000 0.000034721052773
32 34 2.053931446270137 0.012662454503162 1.000000000000000 0.000033836629483
33 35 2.053931287983334 0.016572482204094 1.000000000000000 0.000038031409567
34 36 2.053931169686199 0.016090077382798 1.000000000000000 0.000030765114849
35 37 2.053931098298808 0.005751701047488 1.000000000000000 0.000023330894720
36 38 2.053931050803019 0.005894388784985 1.000000000000000 0.000019740840109
37 39 2.053931011419588 0.005938054745723 1.000000000000000 0.000018897408373
38 40 2.053930979037684 0.009986542398799 1.000000000000000 0.000026942510779
39 41 2.053930968498528 0.001349760933098 1.000000000000000 0.000009894334525
40 42 2.053930962305785 0.001502005058788 1.000000000000000 0.000010725741030
41 43 2.053930952029420 0.002433058690516 1.000000000000000 0.000014059782788
42 44 2.053930919461024 0.009180737814410 1.000000000000000 0.000021505026415
43 45 2.053930874646717 0.013718233236581 1.000000000000000 0.000025324096628
44 46 2.053930788594550 0.034222296334752 1.000000000000000 0.000039783972627
45 47 2.053930686495676 0.037441880712610 1.000000000000000 0.000022453704746
46 48 2.053930601139935 0.027653034711644 1.000000000000000 0.000015961651289
47 49 2.053930525708947 0.022876072575053 1.000000000000000 0.000021487531171
48 50 2.053930442422972 0.026971817139190 1.000000000000000 0.000022154042785
49 51 2.053930291911042 0.063855151880337 1.000000000000000 0.000040620774748
50 52 2.053930086264600 0.073197243317725 1.000000000000000 0.000029436551170
51 53 2.053929764362720 0.120807233910857 1.000000000000000 0.000043049698764
52 54 2.053929316918580 0.165491044692143 1.000000000000000 0.000069416113369
53 55 2.053928681151921 0.266562160502049 1.000000000000000 0.000056026430300
54 56 2.053928203419021 0.210713748481624 1.000000000000000 0.000063413620258
55 57 2.053927853468612 0.137097605992188 1.000000000000000 0.000038278457145
56 58 2.053927623758542 0.064276269821370 1.000000000000000 0.000046907356623
57 59 2.053927267436331 0.100698681771931 1.000000000000000 0.000053084410716
58 60 2.053926510126234 0.276627860398749 1.000000000000000 0.000050647066610
59 61 2.053925877603152 0.297324249302976 1.000000000000000 0.000059179020707
60 62 2.053925364489546 0.261751727896032 1.000000000000000 0.000051430152945
61 63 2.053924950336384 0.189227054579897 1.000000000000000 0.000053431300802
62 64 2.053924538753646 0.159302144472117 1.000000000000000 0.000058073464505
63 65 2.053924418648738 0.028627088653244 1.000000000000000 0.000017648645035
64 66 2.053924403501043 0.017368905001073 1.000000000000000 0.000010790404848
65 67 2.053924392553426 0.010076402435115 1.000000000000000 0.000011982576488
66 68 2.053924366672926 0.005376909979928 1.000000000000000 0.000011853044831
67 69 2.053924340216991 0.023069896623971 1.000000000000000 0.000006092404307
68 70 2.053924331984672 0.018076765319996 1.000000000000000 0.000009360880951
69 71 2.053924328629746 0.006529848665513 1.000000000000000 0.000004242816295
70 72 2.053924326348072 0.002269512204351 1.000000000000000 0.000005271399788
71 73 2.053924324622051 0.003223940279615 1.000000000000000 0.000003644657012
72 74 2.053924323322777 0.004069615614488 1.000000000000000 0.000001676616849
73 75 2.053924322698632 0.002326677138984 1.000000000000000 0.000001807023744
74 76 2.053924322389379 0.000634195744182 1.000000000000000 0.000001822447571
75 77 2.053924322129812 0.001845805494146 1.000000000000000 0.000001478935399
76 78 2.053924322055889 0.001845805494146 1.000000000000000 0.000000473820448
Convergence criteria met.
After: gradient norm = 4.738204476499137E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.0993,-1.0993}
Count Table 1:
---------------
h: {1.4759,0.7309,0.2842,-0.5192,-1.9718}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-0.6951,-0.0195,-1.6368,-1.1332,-1.4800,-1.5513,0.6188,-1.0715,-0.9944,0.7724,-1.3435,-1.9185,-1.4728,1.3853,-1.9663,-1.4302,-0.2135,0.1798,-1.7990,-1.6513,-1.4241,0.6033,-2.6252,-0.0380,-1.4914,1.3862,-1.9715,-1.4074,-1.3515,-1.2163,-1.7093,0.7931,-0.1129,-1.6905,-0.7194,-0.9613,-1.7752,-0.7970,0.0398,-0.9515,-0.9879,-0.4153,-1.7427,-0.3380,-2.0856,-1.1401,0.6623,-0.9205,-1.0440,-1.8557,0.1317,-0.7160,-0.9849,-0.7552,-1.4360,-0.3085}
Activity(exp=0): {0.0000,2.1304}
Activity(exp=1): {0.0000,-1.5449,-0.6943,-0.8678,-2.5073}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
The Likelihood DID improve.
informationThreshold = 0.1
>>> Information used for optimizeSizeHeuristic: I[0] = 0.24427868788752305, I[1] = 0.663673617721874, I[k-2] = 0.32528768898263566, I[k-1] = 0.11372417254114331
Suggested variations:
key=16;8;3, description = Expands: deltaLeft = 1, deltaRight = 1, deltaFlank = 1.
> Optimizing variation "Expands: deltaLeft = 1, deltaRight = 1, deltaFlank = 1." (component1-2-variation6).
>> Starting new optimization: component1-2-variation6. (2021-05-22 06:29:54.401).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[71,72]},{"h":[73,74,75,76,77]}],"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],"activity":[[64,65],[66,67,68,69,70]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.0550430036531764
gradient = {0.0018,0.0016,-0.0104,0.0070,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0011,-0.0036,0.0005,0.0020,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000}
gradient norm = 0.013429680910078633
Starting Function Value: 2.0550430036531764
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 2 2.050970717503276 1.000000000000000 74.461932989750000 0.042350023684259
2 4 2.049477362180613 0.117989213184233 0.318157225822525 0.010703641993010
3 5 2.049051841887455 0.192560706666097 1.000000000000000 0.004091153834019
4 6 2.048917084134504 0.038616883568061 1.000000000000000 0.003626445953651
5 7 2.048492428953444 0.227078665130234 1.000000000000000 0.004477238623886
6 9 2.048412166781740 0.074765844609897 0.182767182002134 0.005621037983124
7 10 2.048347530425818 0.055730513657593 1.000000000000000 0.003095963080369
8 11 2.048293397526505 0.051926052226722 1.000000000000000 0.002372211901381
9 12 2.048239463956428 0.055768088648875 1.000000000000000 0.003233200705057
10 13 2.048157237158834 0.096350597400779 1.000000000000000 0.003218215212264
11 14 2.048086168520719 0.108522114511058 1.000000000000000 0.002472859963301
12 15 2.048057990470117 0.093685873278863 1.000000000000000 0.002627540074491
13 16 2.048032451226064 0.023858895350572 1.000000000000000 0.001317467020986
14 17 2.048019995369320 0.023254893835553 1.000000000000000 0.001168660941655
15 18 2.048002403893907 0.052503120988920 1.000000000000000 0.001015980602332
16 19 2.047987583252027 0.078630924487093 1.000000000000000 0.001641973077583
17 20 2.047972944645307 0.065502086470327 1.000000000000000 0.000949243014681
18 21 2.047964808424762 0.025225019527166 1.000000000000000 0.000809710531067
19 22 2.047953325012824 0.044243123836450 1.000000000000000 0.000618327908835
20 23 2.047944403219449 0.048167100707144 1.000000000000000 0.000656804436429
21 24 2.047934619921159 0.067117739664459 1.000000000000000 0.000603636405516
22 25 2.047926020927193 0.076066031198701 1.000000000000000 0.001024361409686
23 26 2.047917932834166 0.048595666824440 1.000000000000000 0.000468604265613
24 27 2.047912394721693 0.040185356750093 1.000000000000000 0.000487280530457
25 28 2.047908176253530 0.034346852751507 1.000000000000000 0.000616279076873
26 29 2.047900671446173 0.070611172657215 1.000000000000000 0.000537832030006
27 30 2.047897383767253 0.098772031784637 1.000000000000000 0.000770994402469
28 31 2.047891909663111 0.023803707029750 1.000000000000000 0.000222357823558
29 32 2.047890415333219 0.010998178470302 1.000000000000000 0.000199861872605
30 33 2.047887817293381 0.027973328407134 1.000000000000000 0.000223091964552
31 34 2.047885006122282 0.046899684121157 1.000000000000000 0.000175052745216
32 35 2.047883488825308 0.056955411975645 1.000000000000000 0.000180791746952
33 36 2.047882912959780 0.009138608194704 1.000000000000000 0.000092541831818
34 37 2.047882594738916 0.010329526994539 1.000000000000000 0.000058139278847
35 38 2.047882386867916 0.008681363594041 1.000000000000000 0.000053126448108
36 39 2.047882074685202 0.015455827564496 1.000000000000000 0.000052219186685
37 40 2.047881769384711 0.018537150565466 1.000000000000000 0.000041991199437
38 41 2.047881594325489 0.025255457946806 1.000000000000000 0.000085920326833
39 42 2.047881417933619 0.006830096148772 1.000000000000000 0.000027215324293
40 43 2.047881352098215 0.004527426852954 1.000000000000000 0.000028741965851
41 44 2.047881276455077 0.007290667229344 1.000000000000000 0.000029707749523
42 45 2.047881173689866 0.013392848391273 1.000000000000000 0.000020098578831
43 46 2.047881132980929 0.012114820556326 1.000000000000000 0.000024094680028
44 47 2.047881107824719 0.005144997959754 1.000000000000000 0.000014619058642
45 48 2.047881097775016 0.001680163397077 1.000000000000000 0.000010098878292
46 49 2.047881077681001 0.004390030377479 1.000000000000000 0.000009735672253
47 50 2.047881054405803 0.006765443979091 1.000000000000000 0.000015190873200
48 51 2.047881012422748 0.015841726605237 1.000000000000000 0.000021016975105
49 52 2.047880961989899 0.023554241649121 1.000000000000000 0.000027013604128
50 53 2.047880907077449 0.014928110187998 1.000000000000000 0.000015914301369
51 54 2.047880841063217 0.022810124735021 1.000000000000000 0.000014765921593
52 55 2.047880806640297 0.011868230343642 1.000000000000000 0.000022250988766
53 56 2.047880766684864 0.018118359492121 1.000000000000000 0.000013064286011
54 57 2.047880739522358 0.009359702476168 1.000000000000000 0.000012935279544
55 58 2.047880642085777 0.041604370203923 1.000000000000000 0.000026093021970
56 59 2.047880552571558 0.041314033006359 1.000000000000000 0.000027954382839
57 60 2.047880428251035 0.051453651443342 1.000000000000000 0.000026145340388
58 61 2.047880111400178 0.130442759855402 1.000000000000000 0.000036555799644
59 62 2.047879684576317 0.272777521690516 1.000000000000000 0.000063260253134
60 63 2.047879220481145 0.147379184848276 1.000000000000000 0.000046624078011
61 64 2.047878748804974 0.165750721376234 1.000000000000000 0.000040247845647
62 65 2.047878465840686 0.127141791025063 1.000000000000000 0.000039465991548
63 66 2.047878211457295 0.126531039514077 1.000000000000000 0.000033633166493
64 67 2.047877896915896 0.157509433796623 1.000000000000000 0.000039422661187
65 68 2.047877388009945 0.239341644838317 1.000000000000000 0.000060870221758
66 69 2.047876818549803 0.300994370626788 1.000000000000000 0.000037937614700
67 70 2.047876433652363 0.178054397636454 1.000000000000000 0.000054533732420
68 71 2.047876143484690 0.127531494124660 1.000000000000000 0.000027178481955
69 72 2.047876060871151 0.008534867428629 1.000000000000000 0.000017256014359
70 73 2.047875999962657 0.011496117914699 1.000000000000000 0.000012246532459
71 74 2.047875949478899 0.031254093618341 1.000000000000000 0.000011834633151
72 75 2.047875930142116 0.023945416841727 1.000000000000000 0.000007208769172
73 76 2.047875923537405 0.008830004048928 1.000000000000000 0.000004501419183
74 77 2.047875919863387 0.001982176505997 1.000000000000000 0.000003111611462
75 78 2.047875917624890 0.003055064040166 1.000000000000000 0.000002597732432
76 79 2.047875916511657 0.001861407202385 1.000000000000000 0.000001862378495
77 80 2.047875916214119 0.001861407202385 1.000000000000000 0.000000815180686
Convergence criteria met.
After: gradient norm = 8.151806862877064E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.0853,-1.0853}
Count Table 1:
---------------
h: {1.4696,0.7265,0.2865,-0.4965,-1.9861}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-1.0632,-1.1703,0.0478,-1.1827,-0.6094,-0.0540,-1.6332,-1.0736,-1.5230,-1.5571,0.7416,-1.0319,-1.1253,0.8130,-1.3030,-1.7549,-1.4989,1.4715,-1.9761,-1.3667,-0.1588,0.2381,-1.6781,-1.7714,-1.5308,0.7726,-2.6042,-0.0078,-1.5497,1.5735,-1.9533,-1.4408,-1.3269,-1.2296,-1.6751,0.8613,0.0328,-1.6743,-0.6934,-1.0354,-1.7919,-0.7332,0.1593,-1.0045,-1.0273,-0.2956,-1.7706,-0.2769,-2.2379,-1.1623,0.9216,-0.8917,-1.0908,-1.7793,0.3047,-0.8049,-1.0057,-0.6267,-1.4586,-0.2793,-0.9010,-0.4811,-0.8040,-1.1825}
Activity(exp=0): {-0.0000,2.5435}
Activity(exp=1): {0.0000,-1.3807,-0.6368,-1.1651,-2.7313}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
The Likelihood DID improve.
informationThreshold = 0.1
>>> Information used for optimizeSizeHeuristic: I[0] = 0.24410516065086302, I[1] = 0.2198435483768239, I[k-2] = 0.12524930896156317, I[k-1] = 0.04539883078943491
Suggested variations:
key=18;9;4, description = Expands: deltaLeft = 1, deltaRight = 1, deltaFlank = 1.
> Optimizing variation "Expands: deltaLeft = 1, deltaRight = 1, deltaFlank = 1." (component1-2-variation7).
>> Starting new optimization: component1-2-variation7. (2021-05-22 06:31:23.19).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[79,80]},{"h":[81,82,83,84,85]}],"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]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.0489945978114066
gradient = {-0.0021,0.0005,0.0005,0.0011,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0023,0.0020,-0.0014,0.0017,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000}
gradient norm = 0.0045380529681042754
Starting Function Value: 2.0489945978114066
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.048231734425507 0.327578216029234 72.184749347708890 0.013844655527348
2 5 2.047963375948043 0.127228951899986 0.395307048255262 0.004596935493333
3 6 2.047925497024033 0.023323604623362 1.000000000000000 0.003039887012787
4 7 2.047875883284831 0.033887720264004 1.000000000000000 0.003521226137909
5 8 2.047781808747775 0.075679592611881 1.000000000000000 0.004569979301346
6 9 2.047687809648763 0.098921510780073 1.000000000000000 0.003653676497120
7 11 2.047665251066832 0.031009903099056 0.450301957001138 0.001994938552014
8 12 2.047651462727271 0.018076592795720 1.000000000000000 0.001048767645433
9 13 2.047643300850309 0.013648472174476 1.000000000000000 0.001191646897379
10 14 2.047628629270496 0.031378838884606 1.000000000000000 0.001645565815365
11 15 2.047611780432396 0.047351589813142 1.000000000000000 0.001435666475418
12 16 2.047597139927980 0.055588575504020 1.000000000000000 0.000659858346129
13 17 2.047592860954254 0.030971016839539 1.000000000000000 0.000552957841916
14 18 2.047591357149159 0.009639406998448 1.000000000000000 0.000442166691000
15 19 2.047590585274341 0.004609544203892 1.000000000000000 0.000336298082354
16 20 2.047588670108409 0.016473759003748 1.000000000000000 0.000260616036973
17 21 2.047587701666166 0.013770931854328 1.000000000000000 0.000411049883443
18 22 2.047586472157239 0.016307465911606 1.000000000000000 0.000405262561505
19 23 2.047584703465202 0.023461894212102 1.000000000000000 0.000255587736893
20 24 2.047583328351678 0.018858422335391 1.000000000000000 0.000169184603012
21 25 2.047582124850506 0.020650468812311 1.000000000000000 0.000225034325541
22 26 2.047581177957077 0.018462024545870 1.000000000000000 0.000204304573640
23 27 2.047580218549116 0.030210375674812 1.000000000000000 0.000406779735315
24 28 2.047579397239962 0.011357162238654 1.000000000000000 0.000148496282546
25 29 2.047578881318255 0.010260367834532 1.000000000000000 0.000164710547203
26 30 2.047578507076478 0.009363194474645 1.000000000000000 0.000196849936203
27 31 2.047577688884593 0.022818712567216 1.000000000000000 0.000184520777355
28 32 2.047576990086584 0.030648720770828 1.000000000000000 0.000113825903998
29 33 2.047576672701757 0.008771462381937 1.000000000000000 0.000079652450361
30 34 2.047576348798099 0.011893754318900 1.000000000000000 0.000087745012676
31 35 2.047576078263936 0.013301872054164 1.000000000000000 0.000079390038935
32 36 2.047575854606497 0.014958144653953 1.000000000000000 0.000072124404387
33 37 2.047575760838407 0.007277077650855 1.000000000000000 0.000037040863779
34 38 2.047575723604734 0.002618099344053 1.000000000000000 0.000037440548487
35 39 2.047575676326377 0.003531893875649 1.000000000000000 0.000033573147088
36 40 2.047575615677379 0.006100203104648 1.000000000000000 0.000020078064214
37 41 2.047575573694060 0.006180856345887 1.000000000000000 0.000017032846730
38 42 2.047575541343374 0.006062460405223 1.000000000000000 0.000022850808519
39 43 2.047575507802478 0.006897566844182 1.000000000000000 0.000024413474129
40 44 2.047575474330496 0.007503219365584 1.000000000000000 0.000020010893792
41 45 2.047575451623347 0.005343801127400 1.000000000000000 0.000013803916243
42 46 2.047575435731236 0.003499439274883 1.000000000000000 0.000016550749365
43 47 2.047575415371232 0.004661454253688 1.000000000000000 0.000015684864372
44 48 2.047575391216683 0.007028287667394 1.000000000000000 0.000011768288351
45 49 2.047575375602178 0.005755819515227 1.000000000000000 0.000009268994919
46 50 2.047575363927910 0.004709518577773 1.000000000000000 0.000010792694911
47 51 2.047575346974860 0.006561448455559 1.000000000000000 0.000014622512503
48 52 2.047575319477269 0.016031608357450 1.000000000000000 0.000024503499827
49 53 2.047575281915488 0.013004304985243 1.000000000000000 0.000017104036603
50 54 2.047575233277669 0.016503819564003 1.000000000000000 0.000017461354728
51 55 2.047575154009607 0.029799894678045 1.000000000000000 0.000027416147368
52 56 2.047575004458413 0.062024920959295 1.000000000000000 0.000040405545213
53 57 2.047574750679930 0.144010773173259 1.000000000000000 0.000077529044444
54 58 2.047574414279759 0.157985366577280 1.000000000000000 0.000055485181368
55 59 2.047574038792688 0.155622908772810 1.000000000000000 0.000037741635319
56 60 2.047573685199558 0.156321970483458 1.000000000000000 0.000046755663568
57 61 2.047573395294920 0.152913191565336 1.000000000000000 0.000071854957357
58 62 2.047573113711000 0.079154861460193 1.000000000000000 0.000055844984354
59 63 2.047572554228449 0.221201882085332 1.000000000000000 0.000036536817578
60 64 2.047572225994948 0.159245391323781 1.000000000000000 0.000043230869561
61 65 2.047571692059611 0.379086656919225 1.000000000000000 0.000063603033637
62 66 2.047571287524981 0.270726634206109 1.000000000000000 0.000072111029710
63 67 2.047570958967601 0.018844777124508 1.000000000000000 0.000042916264248
64 68 2.047570677216855 0.050916589443965 1.000000000000000 0.000036071550848
65 69 2.047570613404009 0.042654155163429 1.000000000000000 0.000021181583802
66 70 2.047570569667659 0.045416259489644 1.000000000000000 0.000018929144409
67 71 2.047570539379648 0.030002978448378 1.000000000000000 0.000009790047326
68 72 2.047570530115447 0.007038726668371 1.000000000000000 0.000007526086250
69 73 2.047570525802436 0.002187231042772 1.000000000000000 0.000006343067521
70 74 2.047570519627836 0.002598001621880 1.000000000000000 0.000004833918353
71 75 2.047570512545635 0.004386535926519 1.000000000000000 0.000005974429510
72 76 2.047570509654376 0.003908052916112 1.000000000000000 0.000007202981033
73 77 2.047570508551651 0.001516259064031 1.000000000000000 0.000003633312671
74 78 2.047570507880368 0.001810225458442 1.000000000000000 0.000001833955025
75 79 2.047570507550771 0.000547355107331 1.000000000000000 0.000001918149531
76 80 2.047570506829062 0.001020537371345 1.000000000000000 0.000001854388234
77 81 2.047570506497856 0.001020537371345 1.000000000000000 0.000000813120911
Convergence criteria met.
After: gradient norm = 8.131209114224349E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {1.0831,-1.0831}
Count Table 1:
---------------
h: {1.4686,0.7257,0.2868,-0.4937,-1.9874}
Binding mode 0:
---------------
Mononucleotide: {-3.7733,-0.2140,-0.4430,-2.6655}
Activity(exp=0): {-0.0000,-0.9574}
Activity(exp=1): {-0.0000,-1.2555,-1.7362,-1.7823,-1.3645}
Position Bias(exp=0, s=0): {-1.0620,-2.6363,0.6284,-0.1095,0.2350,0.4877,0.7136,0.6521,0.2201,0.2420,-0.0567,-0.0149,-0.0439,0.4157,0.2419,0.0610,0.0645,0.0028,-0.1904,-0.1312,-0.5385,0.4980,0.7131,0.1107,0.3995,0.1288,-0.7727,-0.9412,0.1258,-0.3947}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.2751,-0.8683,-0.0533,0.4014,-0.5940,-0.5406,0.6041,-0.3725,0.8079,1.1288,-0.6610,0.5727,-3.1203,-4.6243,0.4154,0.0150,-0.1027,0.3758,-0.3411,0.5796}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-0.4759,-0.7487,-0.8500,-1.0113,-0.9198,-1.0686,0.1866,-1.2837,-0.5204,0.0427,-1.6181,-0.9896,-1.4728,-1.5337,0.8633,-0.9422,-1.0464,0.9146,-1.3164,-1.6372,-1.4253,1.5766,-1.8659,-1.3708,-0.1064,0.3147,-1.5727,-1.7209,-1.4606,0.8653,-2.5687,0.0786,-1.5256,1.6460,-1.8812,-1.3245,-1.2405,-1.1653,-1.5913,0.9117,0.0975,-1.5845,-0.6316,-0.9667,-1.8049,-0.6278,0.2505,-0.9031,-0.9913,-0.2342,-1.6606,-0.1993,-2.1313,-1.1650,1.0381,-0.8271,-1.0034,-1.7231,0.3600,-0.7188,-0.9705,-0.5666,-1.3052,-0.2430,-0.7905,-0.4533,-0.7076,-1.1339,-0.4834,-1.0920,-0.5461,-0.9644}
Activity(exp=0): {0.0000,2.7310}
Activity(exp=1): {0.0000,-1.3176,-0.6013,-1.1732,-2.7242}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
The Likelihood DID improve.
> No varitions possible for Binding mode 1.
> Optimizing the full model (component1-4-all).
>> Starting new optimization: component1-4-all. (2021-05-22 06:32:59.376).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[140,141]},{"h":[142,143,144,145,146]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[0,1,2,3],"activity":[[54,55],[56,57,58,59,60]],"positionBias":[[[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],[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1]],[[34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53],[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1]]]},{"mononucleotide":[61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132],"activity":[[133,134],[135,136,137,138,139]]},{}]}
Value and gradient before optimization:
=======================================
value = 2.048460999815119
gradient = {-0.0024,0.0030,0.0043,-0.0049,-0.0001,-0.0000,0.0002,-0.0001,-0.0000,0.0002,0.0001,0.0002,0.0001,0.0000,-0.0001,-0.0000,-0.0000,-0.0001,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0001,0.0000,-0.0001,0.0001,-0.0001,-0.0001,-0.0000,-0.0001,-0.0001,-0.0003,-0.0011,-0.0004,-0.0003,-0.0014,-0.0014,0.0007,-0.0017,0.0025,0.0079,-0.0014,0.0011,-0.0002,-0.0000,-0.0003,-0.0012,-0.0017,-0.0003,-0.0003,-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,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000}
gradient norm = 0.011924781175490461
Starting Function Value: 2.048460999815119
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.047993760638426 0.080673508671584 6.765198244257575 0.029678032587327
2 4 2.047213709094287 0.072136231575812 1.000000000000000 0.026356272002412
3 5 2.042325368623414 1.270008119794783 1.000000000000000 0.081590211445139
4 6 2.039573123503925 0.143955875552527 1.000000000000000 0.022860515395931
5 7 2.037338108460823 0.442943387860437 1.000000000000000 0.024558050731217
6 9 2.034656389725958 0.627652166683177 0.269965104981161 0.030007209698944
7 10 2.033423186181466 0.613824922162415 1.000000000000000 0.027545721110271
8 12 2.033048334894501 0.074645180754057 0.405089973778965 0.017330401753564
9 13 2.032832073943927 0.037259719801430 1.000000000000000 0.007775964773620
10 14 2.032758635410391 0.017461632793174 1.000000000000000 0.005852157258416
11 15 2.032677424755231 0.037945834387347 1.000000000000000 0.006664879052076
12 16 2.032015313170316 0.358524897208273 1.000000000000000 0.012340737392425
13 17 2.030976987278905 0.654902929804948 1.000000000000000 0.021345769074491
14 18 2.030353835320241 0.650003830131121 1.000000000000000 0.041952374291693
15 19 2.028837263999507 0.416252527062058 1.000000000000000 0.021737784558046
16 20 2.028414173562489 0.158232470573651 1.000000000000000 0.008678343826174
17 21 2.028305395593430 0.070633961114734 1.000000000000000 0.004535725011814
18 22 2.028236454235268 0.037345618400351 1.000000000000000 0.003867468197985
19 23 2.028080952842143 0.079049521841629 1.000000000000000 0.004100404284969
20 24 2.027960473133278 0.100208361264643 1.000000000000000 0.003862680590432
21 26 2.027928695435382 0.049435947657457 0.491576187927995 0.003996256890425
22 27 2.027894172015869 0.040297461951482 1.000000000000000 0.002320118665869
23 28 2.027859021710438 0.063259900121002 1.000000000000000 0.001811906571972
24 29 2.027838771993530 0.040908515896936 1.000000000000000 0.002783644555684
25 30 2.027803939913720 0.071733538783857 1.000000000000000 0.003831493060990
26 31 2.027756240284755 0.094467990043819 1.000000000000000 0.003583890566535
27 32 2.027648329403302 0.220157356068414 1.000000000000000 0.002422104457475
28 33 2.027540136065994 0.397358595043064 1.000000000000000 0.006766279942871
29 34 2.027447980630229 0.057196468323420 1.000000000000000 0.002875547914419
30 35 2.027376082046219 0.160625251459236 1.000000000000000 0.002884925399077
31 36 2.027328065763372 0.095113168082595 1.000000000000000 0.003495731279302
32 37 2.027283446331700 0.189484181235853 1.000000000000000 0.002310878917221
33 38 2.027258579855961 0.113669862307903 1.000000000000000 0.002719083337529
34 39 2.027235195409024 0.065203062428060 1.000000000000000 0.001739841716277
35 40 2.027195963170329 0.173858200958257 1.000000000000000 0.001175929731820
36 41 2.027165097452434 0.118833885183942 1.000000000000000 0.001349813688191
37 42 2.027121210647635 0.206965043755533 1.000000000000000 0.001082524469765
38 43 2.027078192826692 0.156324837587812 1.000000000000000 0.002987971477813
39 44 2.027055013832367 0.301834122758437 1.000000000000000 0.003401388562746
40 45 2.027022889191533 0.125270016275602 1.000000000000000 0.001907798561098
41 46 2.027010509035293 0.032218328775503 1.000000000000000 0.001656647645845
42 47 2.026984186277575 0.083266233113845 1.000000000000000 0.000856136601138
43 48 2.026969037556736 0.087528307490128 1.000000000000000 0.000662636670716
44 49 2.026960065181739 0.047455075557386 1.000000000000000 0.000705842263744
45 50 2.026941073454305 0.090102635723320 1.000000000000000 0.000956397180260
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53 58 2.026871362794943 0.099235752092371 1.000000000000000 0.000760800586601
54 59 2.026862210992324 0.100799677602204 1.000000000000000 0.000847155510801
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56 61 2.026838346662595 0.149632682098269 1.000000000000000 0.000603650010850
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59 64 2.026803335493285 0.153335143507893 1.000000000000000 0.000810951698105
60 65 2.026787569686829 0.240601789447613 1.000000000000000 0.000908437308156
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63 68 2.026756553785557 0.165925927756545 1.000000000000000 0.000991020011421
64 69 2.026751754444822 0.104375386710387 1.000000000000000 0.000408329138705
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103 109 2.026589697775691 0.201877928990738 0.480299468742371 0.001618045582297
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107 113 2.026564793798980 0.085428253716382 1.000000000000000 0.000396112135108
108 114 2.026560120637464 0.104780837078006 1.000000000000000 0.000480105457295
109 115 2.026558865759974 0.084732262543126 1.000000000000000 0.001789008248728
110 116 2.026551601141600 0.055004347528971 1.000000000000000 0.001240871031017
111 117 2.026549517457146 0.119786726408595 1.000000000000000 0.000407846694603
112 118 2.026548266322311 0.097702601837241 1.000000000000000 0.000944150136742
113 119 2.026547461405183 0.024956568840559 1.000000000000000 0.000680324652400
114 120 2.026546702524799 0.024981240025747 1.000000000000000 0.000455352001355
115 121 2.026545278203340 0.046794018218205 1.000000000000000 0.000368048930672
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120 127 2.026535200774136 0.030946527888912 1.000000000000000 0.000427966037643
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122 129 2.026533307763913 0.028129732225473 1.000000000000000 0.000338589412563
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124 131 2.026531915878258 0.027462990327039 1.000000000000000 0.000422719210792
125 132 2.026530832736893 0.040969189021509 1.000000000000000 0.000431592252012
126 133 2.026530123537948 0.044334993201767 1.000000000000000 0.000662416683048
127 134 2.026528606951454 0.025419865865741 1.000000000000000 0.000239586399170
128 135 2.026527910561500 0.034622085952896 1.000000000000000 0.000157390044270
129 136 2.026527506329694 0.027177628109141 1.000000000000000 0.000176041809963
130 137 2.026527028818230 0.031960967976781 1.000000000000000 0.000177676286260
131 139 2.026526696554747 0.030476203774943 0.474990574437006 0.000247467330948
132 140 2.026526312706311 0.013523283521447 1.000000000000000 0.000145641043655
133 141 2.026526026682710 0.013018647551546 1.000000000000000 0.000140945360802
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136 144 2.026524760392538 0.030925010370734 1.000000000000000 0.000292717537041
137 145 2.026524129565582 0.023355737970728 1.000000000000000 0.000209402070480
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139 147 2.026522489461570 0.035418019520203 1.000000000000000 0.000218493449780
140 148 2.026521918149825 0.019003981000219 1.000000000000000 0.000214395287087
141 149 2.026521567176459 0.081963417843328 1.000000000000000 0.000461245889334
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150 158 2.026517181960064 0.067343794829826 1.000000000000000 0.000373476656104
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160 168 2.026512510726014 0.038408095588140 1.000000000000000 0.000262620073555
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466 496 2.026376281408861 0.003151256617453 1.000000000000000 0.000007915486702
467 497 2.026376280492371 0.005912972819363 1.000000000000000 0.000011277228103
468 498 2.026376278906051 0.002697160353115 1.000000000000000 0.000007795908728
469 499 2.026376277588211 0.001606408791100 1.000000000000000 0.000006635145268
470 500 2.026376276455578 0.003588149584407 1.000000000000000 0.000006890205898
471 501 2.026376275687687 0.006690793355814 1.000000000000000 0.000024288796962
472 502 2.026376274010878 0.001660583245415 1.000000000000000 0.000011893207251
473 503 2.026376272546633 0.001940828301187 1.000000000000000 0.000005556498302
474 504 2.026376271392293 0.002186939375040 1.000000000000000 0.000008401876587
475 505 2.026376269716107 0.003372089080336 1.000000000000000 0.000009229122713
476 506 2.026376266479504 0.007273815305700 1.000000000000000 0.000013909705455
477 507 2.026376263858648 0.015623905893067 1.000000000000000 0.000019827800944
478 508 2.026376258771845 0.002178102060748 1.000000000000000 0.000008616111824
479 509 2.026376255962901 0.002844322238663 1.000000000000000 0.000006352857281
480 510 2.026376253122802 0.006538786439853 1.000000000000000 0.000010361684161
481 511 2.026376250170609 0.006767421205661 1.000000000000000 0.000007788990080
482 512 2.026376248095775 0.005578226123975 1.000000000000000 0.000005946415500
483 513 2.026376245561715 0.006543810251694 1.000000000000000 0.000006529695834
484 515 2.026376243937723 0.006552299939259 0.333333919427244 0.000014881329561
485 516 2.026376241739890 0.002284294926885 1.000000000000000 0.000011390394490
486 517 2.026376238150541 0.004685109938799 1.000000000000000 0.000005017735778
487 518 2.026376236770019 0.002405923829181 1.000000000000000 0.000004510563304
488 519 2.026376234396106 0.005838784002990 1.000000000000000 0.000006715599482
489 521 2.026376233515426 0.003010456288982 0.190248858008477 0.000009978435161
490 522 2.026376232205907 0.002852473422447 1.000000000000000 0.000006986257758
491 523 2.026376230422773 0.003428796425442 1.000000000000000 0.000004712964249
492 524 2.026376229073329 0.002234413769890 1.000000000000000 0.000004383274884
493 525 2.026376226765427 0.005453458454561 1.000000000000000 0.000005184761717
494 527 2.026376225702002 0.002494698791286 0.477176853317818 0.000007370977886
495 528 2.026376224422525 0.006240508101423 1.000000000000000 0.000008521713042
496 529 2.026376223617715 0.006865246835518 1.000000000000000 0.000007120707737
497 530 2.026376222820588 0.001402362690182 1.000000000000000 0.000004304672666
498 531 2.026376221971393 0.001217009362066 1.000000000000000 0.000005937821078
499 532 2.026376221120654 0.002491914358939 1.000000000000000 0.000014640147750
500 533 2.026376220546855 0.005339480989884 1.000000000000000 0.000016567124556
>>> Maximum iteration count reached.
After: gradient norm = 1.6567124556317208E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.4615,-0.4615}
Count Table 1:
---------------
h: {1.4729,0.5990,0.3968,-0.2491,-2.2197}
Binding mode 0:
---------------
Mononucleotide: {-1.9279,-0.8302,-1.4471,-1.6014}
Activity(exp=0): {-0.0000,-1.8717}
Activity(exp=1): {-0.0000,-0.7080,-1.5028,-1.3993,-0.3247}
Position Bias(exp=0, s=0): {0.6944,-0.4627,-0.2192,0.3335,0.8604,-0.9050,1.0154,0.1526,-1.1057,0.1763,0.0381,0.4687,-0.1264,1.0549,-0.3159,-0.0116,-1.0984,-0.0969,-1.0208,-0.9863,-0.3392,-1.0605,0.7370,0.6118,-0.1051,0.1942,0.1645,-1.9629,0.6044,0.8390}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.5399,0.3518,-1.3318,0.1962,0.2997,0.1574,0.0142,0.1530,0.1752,0.2011,-0.0925,-0.4215,-0.3266,-0.3861,0.0444,-0.1817,0.2980,-0.2909,-3.9527,0.6185}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-0.4687,-0.6748,-0.7861,-0.9753,-0.9009,-0.9776,0.1880,-1.2145,-0.5051,0.0393,-1.4485,-0.9907,-1.3988,-1.3470,0.8028,-0.9620,-1.0517,0.8644,-1.1434,-1.5743,-1.3794,1.5334,-1.7206,-1.3384,-0.1051,0.3135,-1.4686,-1.6447,-1.3658,0.8464,-2.4471,0.0616,-1.4748,1.5711,-1.6608,-1.3404,-1.1995,-1.0812,-1.4283,0.8041,0.0715,-1.4484,-0.5994,-0.9287,-1.7140,-0.5615,0.2622,-0.8917,-0.9725,-0.2014,-1.5361,-0.1950,-2.0671,-1.0340,0.9866,-0.7904,-0.9688,-1.5636,0.3479,-0.7205,-0.9255,-0.5115,-1.2319,-0.2361,-0.7738,-0.3994,-0.6433,-1.0884,-0.4630,-1.0106,-0.5089,-0.9225}
Activity(exp=0): {-0.0000,1.4597}
Activity(exp=1): {0.0000,-0.7841,-0.5715,-1.0777,-1.9313}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {0.0000,0.0000}
Activity(exp=1): {0.0000,0.0000,0.0000,0.0000,0.0000}
==================================
== Starts fiting Binding mode 2 ==
==================================
> Optimizing h (component2-0-h).
>> Starting new optimization: component2-0-h. (2021-05-22 06:45:47.406).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[0,1]},{"h":[2,3,4,5,6]}],"bindingModeInteractions":[],"bindingModes":[{},{},{}]}
Value and gradient before optimization:
=======================================
value = 2.020006774415126
gradient = {-0.0200,0.0200,-0.0281,-0.0121,0.0059,0.0160,0.0183}
gradient norm = 0.04859027899167241
Starting Function Value: 2.020006774415126
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.015280057195985 0.193543792402215 3.983179278212928 0.028330889561149
2 4 2.013761792162142 0.099432772935893 1.000000000000000 0.008242848515787
3 5 2.013587318268593 0.042218797807335 1.000000000000000 0.001803528073073
4 6 2.013577643551425 0.010215508223675 1.000000000000000 0.000263433897423
5 7 2.013577499541930 0.001190409579571 1.000000000000000 0.000005995741856
6 8 2.013577499451778 0.000027462846564 1.000000000000000 0.000000849066397
7 9 2.013577499449983 0.000027462846564 1.000000000000000 0.000000006658727
Convergence criteria met.
After: gradient norm = 6.6587267423618275E-9
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.5057,-0.5057}
Count Table 1:
---------------
h: {1.6616,0.6885,0.3871,-0.3532,-2.3841}
Binding mode 0:
---------------
Mononucleotide: {-1.9279,-0.8302,-1.4471,-1.6014}
Activity(exp=0): {-0.0000,-1.8717}
Activity(exp=1): {-0.0000,-0.7080,-1.5028,-1.3993,-0.3247}
Position Bias(exp=0, s=0): {0.6944,-0.4627,-0.2192,0.3335,0.8604,-0.9050,1.0154,0.1526,-1.1057,0.1763,0.0381,0.4687,-0.1264,1.0549,-0.3159,-0.0116,-1.0984,-0.0969,-1.0208,-0.9863,-0.3392,-1.0605,0.7370,0.6118,-0.1051,0.1942,0.1645,-1.9629,0.6044,0.8390}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.5399,0.3518,-1.3318,0.1962,0.2997,0.1574,0.0142,0.1530,0.1752,0.2011,-0.0925,-0.4215,-0.3266,-0.3861,0.0444,-0.1817,0.2980,-0.2909,-3.9527,0.6185}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-0.4687,-0.6748,-0.7861,-0.9753,-0.9009,-0.9776,0.1880,-1.2145,-0.5051,0.0393,-1.4485,-0.9907,-1.3988,-1.3470,0.8028,-0.9620,-1.0517,0.8644,-1.1434,-1.5743,-1.3794,1.5334,-1.7206,-1.3384,-0.1051,0.3135,-1.4686,-1.6447,-1.3658,0.8464,-2.4471,0.0616,-1.4748,1.5711,-1.6608,-1.3404,-1.1995,-1.0812,-1.4283,0.8041,0.0715,-1.4484,-0.5994,-0.9287,-1.7140,-0.5615,0.2622,-0.8917,-0.9725,-0.2014,-1.5361,-0.1950,-2.0671,-1.0340,0.9866,-0.7904,-0.9688,-1.5636,0.3479,-0.7205,-0.9255,-0.5115,-1.2319,-0.2361,-0.7738,-0.3994,-0.6433,-1.0884,-0.4630,-1.0106,-0.5089,-0.9225}
Activity(exp=0): {-0.0000,1.4597}
Activity(exp=1): {0.0000,-0.7841,-0.5715,-1.0777,-1.9313}
Binding mode 2:
---------------
Mononucleotide: {-0.0008,0.0029,0.0043,0.0015,0.0017,-0.0030,0.0034,-0.0043,0.0049,-0.0046,-0.0006,0.0019,-0.0040,-0.0049,0.0004,0.0040,-0.0034,0.0036,0.0013,-0.0030,0.0007,-0.0044,-0.0041,-0.0042,0.0004,-0.0031,-0.0048,0.0046,0.0002,-0.0016,0.0042,0.0034,0.0044,-0.0001,-0.0015,-0.0043,0.0013,-0.0022,-0.0015,0.0010,0.0026,-0.0027,0.0038,0.0016,0.0006,-0.0033,0.0049,-0.0001}
Activity(exp=0): {-4.2341,-5.9875}
Activity(exp=1): {-4.2933,-5.0017,-5.7883,-5.6907,-4.6221}
> Initial optimization (component2-1-f0).
>> Starting new optimization: component2-1-f0. (2021-05-22 06:45:56.578).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[55,56]},{"h":[57,58,59,60,61]}],"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],"activity":[[48,49],[50,51,52,53,54]]}]}
Value and gradient before optimization:
=======================================
value = 2.020289608676753
gradient = {0.0002,-0.0001,0.0001,0.0002,0.0002,-0.0000,0.0001,0.0002,0.0002,-0.0000,0.0001,0.0002,0.0002,-0.0000,0.0001,0.0002,0.0002,-0.0000,0.0000,0.0002,0.0002,0.0000,0.0000,0.0002,0.0002,0.0000,-0.0000,0.0002,0.0002,0.0000,-0.0000,0.0002,0.0002,0.0001,-0.0000,0.0002,0.0002,0.0001,-0.0000,0.0002,0.0002,0.0001,-0.0001,0.0002,0.0002,0.0001,-0.0001,0.0002,-0.0000,0.0000,-0.0000,0.0001,0.0002,0.0001,0.0001,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000}
gradient norm = 0.0011414054359723353
Starting Function Value: 2.020289608676753
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.020269230648525 0.073171417762510 64.106421308723440 0.004528477835656
2 4 2.020223797191049 0.027680420859289 1.000000000000000 0.002803553019364
3 5 2.020167719674200 0.070732961020170 1.000000000000000 0.002852404695451
4 6 2.020113728418529 0.124389188374084 1.000000000000000 0.003103213141264
5 7 2.020081684224355 0.100064269310408 1.000000000000000 0.002469390914453
6 8 2.020067641288724 0.133003627512763 1.000000000000000 0.003103031195110
7 9 2.020048314785423 0.036500448700500 1.000000000000000 0.000609163002286
8 10 2.020044871639275 0.052636125136881 1.000000000000000 0.000341848744137
9 11 2.020043232889409 0.045497952280483 1.000000000000000 0.000288921044988
10 12 2.020040080544730 0.046296603601290 1.000000000000000 0.000323225472531
11 13 2.020033292055857 0.197528131751949 1.000000000000000 0.001277576751294
12 14 2.020021358266627 0.067516122926890 1.000000000000000 0.000834572907246
13 15 2.020012904139640 0.119435167384347 1.000000000000000 0.000658139991549
14 16 2.020002871392471 0.168746710053584 1.000000000000000 0.000851924346607
15 17 2.019998882684024 0.129245085172529 1.000000000000000 0.000371277718002
16 18 2.019996592652912 0.068184391250947 1.000000000000000 0.000373306526204
17 19 2.019995458047093 0.051409382621663 1.000000000000000 0.000364789316650
18 20 2.019995085496216 0.092648532959749 1.000000000000000 0.000435072876944
19 21 2.019994348897584 0.029876750864050 1.000000000000000 0.000153703921120
20 22 2.019994034265710 0.003491260907672 1.000000000000000 0.000154114659134
21 23 2.019988447688707 0.061753810834094 1.000000000000000 0.000968640271545
22 29 2.019755313653600 1.141971023202591 7.395353208879815 0.013517969028210
23 32 2.019752728221101 0.049767503262815 0.005426957542567 0.014240728709811
24 33 2.019655922478800 0.682663860077030 1.000000000000000 0.016799658423241
25 35 2.019437446000052 0.304973696801929 0.469492877623887 0.016241706057742
26 36 2.019056522943222 0.193872808023384 1.000000000000000 0.006585460100144
27 37 2.018872203246112 0.350945916144033 1.000000000000000 0.009781639585287
28 38 2.018723479793622 0.236245387866701 1.000000000000000 0.005423561205439
29 40 2.017924350792406 0.456688801041310 5.000000000000000 0.010084194938887
30 42 2.017609532997356 0.236198309149974 0.184193391416617 0.017642603765787
31 43 2.016843261288647 0.503125586987815 1.000000000000000 0.012271868608095
32 45 2.016162981434208 0.386004077076839 0.293942145444222 0.015202205856554
33 46 2.015656417373463 0.763405179826222 1.000000000000000 0.011502108453697
34 47 2.015363038001671 0.223112278788375 1.000000000000000 0.005574884636821
35 49 2.015279822093808 0.165829983989862 0.296339817128718 0.005425512029822
36 50 2.015189688306097 0.104919776621249 1.000000000000000 0.004433568155343
37 51 2.015046112964440 0.080276801861988 1.000000000000000 0.003922354964413
38 53 2.014143455058912 0.662708546737186 0.501919052611679 0.012692484195934
39 54 2.013623681973036 0.414752100200295 1.000000000000000 0.018078325463162
40 55 2.012986648851487 0.375438370908783 1.000000000000000 0.012786547284984
41 56 2.012510654675058 0.367270768294414 1.000000000000000 0.009659160955559
42 57 2.012227044466170 0.232054850510641 1.000000000000000 0.007065959776876
43 59 2.012028217748101 0.326213346975539 0.414996887243674 0.007120181746464
44 60 2.011777288797578 0.342098313755751 1.000000000000000 0.005340714745453
45 61 2.011393446752078 0.351588742743051 1.000000000000000 0.003478280366824
46 62 2.010988004912098 0.414372383067146 1.000000000000000 0.005557064458921
47 63 2.010364421994238 0.545677470197674 1.000000000000000 0.007254920893847
48 64 2.009454277927080 0.701019408695890 1.000000000000000 0.010293609598897
49 65 2.008698245678895 0.726260291791066 1.000000000000000 0.007221331980792
50 66 2.008090757806078 0.359126153128213 1.000000000000000 0.003554975879737
51 67 2.007941533728717 0.120169714870326 1.000000000000000 0.002876220404250
52 69 2.007858111083324 0.123748257366871 0.487939777193833 0.006248972477731
53 70 2.007646988801215 0.244244917762740 1.000000000000000 0.004341303953784
54 71 2.007471393264506 0.139999802486211 1.000000000000000 0.002528273619170
55 72 2.007364157349166 0.144742307002188 1.000000000000000 0.001910518538330
56 73 2.007314481076431 0.071427681754474 1.000000000000000 0.002405450427844
57 74 2.007169551401892 0.234221725884858 1.000000000000000 0.003068879696103
58 75 2.007050743267337 0.177237981144659 1.000000000000000 0.002543748179998
59 76 2.006931740627725 0.274795944015970 1.000000000000000 0.007073261537764
60 77 2.006884032200759 0.195195449042360 1.000000000000000 0.003828166482234
61 78 2.006825875976054 0.081047186139134 1.000000000000000 0.001722050872250
62 79 2.006802296911772 0.068738498246180 1.000000000000000 0.002171199680726
63 80 2.006774640063707 0.091268251391103 1.000000000000000 0.001995094223418
64 81 2.006726577080279 0.153950897060653 1.000000000000000 0.001048765473116
65 82 2.006690956206530 0.171617070703596 1.000000000000000 0.000999807127704
66 83 2.006641383782560 0.183829598321150 1.000000000000000 0.001182487844929
67 84 2.006609132294393 0.198756584010013 1.000000000000000 0.002226299234002
68 85 2.006602534901341 0.106581752352021 1.000000000000000 0.002876731982971
69 86 2.006586156521799 0.051454205273502 1.000000000000000 0.000939361909280
70 87 2.006574033940923 0.038927340059657 1.000000000000000 0.001666646935927
71 88 2.006556558007024 0.087299918196599 1.000000000000000 0.002327261666012
72 89 2.006537464548326 0.099328309688097 1.000000000000000 0.001763100566372
73 90 2.006514814363169 0.130258424343071 1.000000000000000 0.000896716661262
74 91 2.006499163618133 0.096415583198134 1.000000000000000 0.000793095935412
75 92 2.006490850464765 0.078347051637314 1.000000000000000 0.000566436574153
76 93 2.006482316007165 0.055795217649063 1.000000000000000 0.001721378006491
77 94 2.006476604373719 0.068238425658982 1.000000000000000 0.000597221067765
78 95 2.006473876024068 0.037809093773500 1.000000000000000 0.000371457667480
79 96 2.006471176090626 0.021833147818420 1.000000000000000 0.000316646172870
80 97 2.006462960860915 0.057349002051684 1.000000000000000 0.000271079864494
81 98 2.006451456749483 0.117104089249904 1.000000000000000 0.000676089524872
82 99 2.006443659000292 0.098398446874212 1.000000000000000 0.000882515703190
83 100 2.006431599914333 0.119854249251792 1.000000000000000 0.000998315500050
84 101 2.006413193402620 0.196898195737728 1.000000000000000 0.001424496840458
85 102 2.006401061707716 0.115640251980018 1.000000000000000 0.000620959789252
86 103 2.006394513713333 0.100942135790769 1.000000000000000 0.001049625945814
87 104 2.006389526795797 0.040103325714749 1.000000000000000 0.000538167079128
88 105 2.006386133891613 0.054482404786501 1.000000000000000 0.000326435049808
89 106 2.006381819707358 0.062617614182305 1.000000000000000 0.000304635157756
90 107 2.006377515958420 0.063529504753759 1.000000000000000 0.000325404739003
91 108 2.006375138263757 0.040797107090049 1.000000000000000 0.000152064293171
92 109 2.006374240902638 0.026737813820834 1.000000000000000 0.000141634576945
93 110 2.006372391149938 0.038787046960989 1.000000000000000 0.000167258351413
94 111 2.006370224110680 0.057613507265276 1.000000000000000 0.000152519633273
95 112 2.006367640895522 0.067921474210737 1.000000000000000 0.000236590924181
96 113 2.006363275476018 0.137630898390175 1.000000000000000 0.000373335491216
97 114 2.006360367025987 0.089502661078790 1.000000000000000 0.000338083343597
98 115 2.006356941947505 0.093804428238393 1.000000000000000 0.000665650241584
99 116 2.006355172433367 0.047326060485684 1.000000000000000 0.000215542610604
100 117 2.006354702701885 0.032773066500887 1.000000000000000 0.000454978826943
101 118 2.006354374183244 0.009930181878102 1.000000000000000 0.000275880912976
102 119 2.006354048201897 0.015516347366065 1.000000000000000 0.000132512485642
103 120 2.006353751671052 0.018094459666896 1.000000000000000 0.000170716443454
104 121 2.006353418123140 0.022179380012510 1.000000000000000 0.000276543443249
105 122 2.006353063008679 0.020221072858855 1.000000000000000 0.000325116204234
106 123 2.006352473947874 0.025109389430109 1.000000000000000 0.000330043644661
107 124 2.006351501873964 0.042581513252034 1.000000000000000 0.000322210891691
108 125 2.006350603932709 0.044342360958700 1.000000000000000 0.000285924982172
109 126 2.006349924366499 0.040948873402196 1.000000000000000 0.000415687524711
110 127 2.006349346860875 0.025969163687493 1.000000000000000 0.000189559830873
111 128 2.006348968304784 0.015161839659489 1.000000000000000 0.000131471048259
112 129 2.006348610350368 0.017104636002688 1.000000000000000 0.000126850045601
113 130 2.006348195800467 0.024410826668356 1.000000000000000 0.000139476131449
114 131 2.006347724293299 0.030749866612996 1.000000000000000 0.000168959523742
115 132 2.006347546366380 0.058503162785172 1.000000000000000 0.000380791311737
116 133 2.006347125260776 0.010989974944227 1.000000000000000 0.000105285576545
117 134 2.006346979721780 0.008266315602297 1.000000000000000 0.000087186874067
118 135 2.006346795280995 0.015953373928528 1.000000000000000 0.000122453458311
119 136 2.006346560749017 0.020520161487104 1.000000000000000 0.000155011591523
120 137 2.006346047947709 0.046920552758091 1.000000000000000 0.000214854766793
121 138 2.006345311961161 0.065390536494547 1.000000000000000 0.000262331781209
122 139 2.006344091436478 0.102613431669086 1.000000000000000 0.000262767420131
123 140 2.006342288112597 0.150524845873781 1.000000000000000 0.000246670203432
124 141 2.006340991753422 0.123760034277205 1.000000000000000 0.000131384144749
125 142 2.006340393179870 0.020415955467657 1.000000000000000 0.000103289724885
126 143 2.006340003654145 0.012086979438209 1.000000000000000 0.000139663523254
127 144 2.006339316051035 0.025376978902774 1.000000000000000 0.000208203378113
128 145 2.006338222439851 0.075575949503481 1.000000000000000 0.000325712123142
129 146 2.006336699874486 0.155648851920495 1.000000000000000 0.000336992920934
130 147 2.006334535918110 0.223445855348532 1.000000000000000 0.000335562151575
131 148 2.006331205042835 0.410767180217997 1.000000000000000 0.000188727879502
132 149 2.006328709815505 0.277027797477695 1.000000000000000 0.000295463558894
133 150 2.006326556035637 0.227475026867254 1.000000000000000 0.000431504663815
134 151 2.006323924896563 0.225808853267698 1.000000000000000 0.000457379252845
135 152 2.006316348451263 0.673699351259362 1.000000000000000 0.000483965537761
136 153 2.006315591623981 1.262356214419814 1.000000000000000 0.001015497280460
137 154 2.006304513287029 0.143516959769017 1.000000000000000 0.000405614982692
138 155 2.006301651510781 0.166743959568086 1.000000000000000 0.000232202725897
139 156 2.006298917680953 0.308875509168496 1.000000000000000 0.000521778909988
140 157 2.006296882798546 0.229158752369337 1.000000000000000 0.000421232532048
141 158 2.006293143616946 0.593276536855633 1.000000000000000 0.000453018561535
142 159 2.006286885127412 0.746627188020878 1.000000000000000 0.000340415153622
143 160 2.006280497474630 1.028841495760910 1.000000000000000 0.000443115020508
144 161 2.006279684111182 0.503024556954430 1.000000000000000 0.000706697982523
145 162 2.006273273853613 0.091868051388650 1.000000000000000 0.000845935341026
146 163 2.006269226114934 0.081118047265301 1.000000000000000 0.000620515500454
147 164 2.006264640724358 0.196957352672551 1.000000000000000 0.000416352168270
148 165 2.006262069901768 0.378808671492479 1.000000000000000 0.000360569251569
149 166 2.006259396399070 0.558868203085652 1.000000000000000 0.000248039859717
150 167 2.006257075865101 0.445199588196204 1.000000000000000 0.000186113565791
151 168 2.006255651178438 0.210328121556744 1.000000000000000 0.000135618765993
152 169 2.006254798584365 0.030975297266398 1.000000000000000 0.000132537184178
153 170 2.006254743928711 0.083185348799323 1.000000000000000 0.000324568683306
154 171 2.006254014888961 0.037222502243344 1.000000000000000 0.000095421425043
155 172 2.006253788828580 0.015441801910986 1.000000000000000 0.000103605931642
156 173 2.006253104230509 0.084283844525717 1.000000000000000 0.000180582820842
157 174 2.006252280111810 0.105853597483919 1.000000000000000 0.000267837266675
158 175 2.006251293437308 0.079757439872958 1.000000000000000 0.000177344847035
159 176 2.006249886746240 0.269206777222911 1.000000000000000 0.000169482046704
160 177 2.006249136298858 0.099864411012038 1.000000000000000 0.000159307003544
161 178 2.006248413420607 0.166216542627355 1.000000000000000 0.000117706683114
162 179 2.006248355454726 0.029516039008344 1.000000000000000 0.000094807603978
163 180 2.006248195064313 0.081582398098739 1.000000000000000 0.000076526383030
164 181 2.006248128820468 0.023599591473063 1.000000000000000 0.000055535337213
165 182 2.006248085298762 0.017166160982362 1.000000000000000 0.000037749604833
166 183 2.006247948874683 0.027072084954484 1.000000000000000 0.000062174257444
167 184 2.006247799669392 0.019575664346741 1.000000000000000 0.000105045652965
168 185 2.006247455802926 0.036740770872866 1.000000000000000 0.000122606698759
169 186 2.006246882005667 0.066642390780721 1.000000000000000 0.000184867766826
170 187 2.006246009758530 0.090389304833319 1.000000000000000 0.000202320521003
171 189 2.006245607976557 0.057581992963889 0.467619940669385 0.000143151521223
172 190 2.006245154053137 0.108769658718564 1.000000000000000 0.000177922956230
173 191 2.006244796314285 0.039902976288097 1.000000000000000 0.000065932210113
174 192 2.006244668676435 0.025959005243866 1.000000000000000 0.000046257440180
175 193 2.006244509606227 0.019702000095386 1.000000000000000 0.000039743984286
176 194 2.006244356485729 0.043953619436288 1.000000000000000 0.000082525176786
177 196 2.006244309629252 0.014239078877045 0.221570468791015 0.000073364244958
178 197 2.006244117978255 0.030930700956808 1.000000000000000 0.000058498740349
179 198 2.006243593807094 0.120472557812796 1.000000000000000 0.000104137437951
180 199 2.006243381749857 0.195349973781580 1.000000000000000 0.000260717589453
181 200 2.006242222754812 0.049902357683394 1.000000000000000 0.000206547252294
182 201 2.006239925035671 0.147937272639493 1.000000000000000 0.000243012409236
183 202 2.006234648345474 0.487496812956678 1.000000000000000 0.000400566273723
184 203 2.006225289334024 1.119566651865400 1.000000000000000 0.000902376050943
185 204 2.006219615150170 1.248374045634112 1.000000000000000 0.002027788957183
186 206 2.006213470379337 1.030310092693189 0.478811654592620 0.000428114768394
187 207 2.006209845752678 0.174590618377938 1.000000000000000 0.000453941478244
188 208 2.006208353322426 0.200691682971467 1.000000000000000 0.000300643991332
189 209 2.006207892698475 0.036405057655409 1.000000000000000 0.000188172066855
190 210 2.006207273063267 0.140170741137283 1.000000000000000 0.000071960323884
191 211 2.006207192552434 0.088644700345010 1.000000000000000 0.000172301961295
192 212 2.006207008398792 0.057000365888541 1.000000000000000 0.000135376986193
193 213 2.006206934046310 0.014814236692568 1.000000000000000 0.000042269878116
194 214 2.006206886433112 0.022965609321861 1.000000000000000 0.000062537154835
195 215 2.006206819177336 0.011037726823218 1.000000000000000 0.000051567907222
196 216 2.006206700854854 0.023612817388205 1.000000000000000 0.000056889462333
197 217 2.006206596101458 0.016736273415226 1.000000000000000 0.000081587957105
198 218 2.006206351286153 0.032709773070256 1.000000000000000 0.000126337564663
199 219 2.006205959805201 0.047498861328427 1.000000000000000 0.000157484762846
200 220 2.006205249088608 0.089576168153657 1.000000000000000 0.000163213146645
201 222 2.006205224164983 0.008515893819679 0.013186571718398 0.000199227186098
202 223 2.006204704174865 0.074910128567246 1.000000000000000 0.000119937052295
203 224 2.006204508571106 0.022158974390763 1.000000000000000 0.000034000715341
204 225 2.006204477801807 0.018058025874870 1.000000000000000 0.000037961834890
205 227 2.006204471999880 0.003087764190017 0.470617742556713 0.000022094798042
206 228 2.006204468499891 0.004042712846976 1.000000000000000 0.000015287849211
207 229 2.006204465204906 0.005856810753548 1.000000000000000 0.000006060419015
208 230 2.006204464783301 0.001240433896621 1.000000000000000 0.000002392188213
209 231 2.006204464659781 0.000722267300824 1.000000000000000 0.000000986414042
210 232 2.006204464634176 0.000301124629028 1.000000000000000 0.000000921512000
211 233 2.006204464625915 0.000277009812553 1.000000000000000 0.000001200587264
212 234 2.006204464618374 0.000277009812553 1.000000000000000 0.000000379403787
Convergence criteria met.
After: gradient norm = 3.794037871529463E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.4699,-0.4699}
Count Table 1:
---------------
h: {2.6956,0.8050,0.0958,-0.7857,-2.8107}
Binding mode 0:
---------------
Mononucleotide: {-1.9279,-0.8302,-1.4471,-1.6014}
Activity(exp=0): {-0.0000,-1.8717}
Activity(exp=1): {-0.0000,-0.7080,-1.5028,-1.3993,-0.3247}
Position Bias(exp=0, s=0): {0.6944,-0.4627,-0.2192,0.3335,0.8604,-0.9050,1.0154,0.1526,-1.1057,0.1763,0.0381,0.4687,-0.1264,1.0549,-0.3159,-0.0116,-1.0984,-0.0969,-1.0208,-0.9863,-0.3392,-1.0605,0.7370,0.6118,-0.1051,0.1942,0.1645,-1.9629,0.6044,0.8390}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.5399,0.3518,-1.3318,0.1962,0.2997,0.1574,0.0142,0.1530,0.1752,0.2011,-0.0925,-0.4215,-0.3266,-0.3861,0.0444,-0.1817,0.2980,-0.2909,-3.9527,0.6185}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-0.4687,-0.6748,-0.7861,-0.9753,-0.9009,-0.9776,0.1880,-1.2145,-0.5051,0.0393,-1.4485,-0.9907,-1.3988,-1.3470,0.8028,-0.9620,-1.0517,0.8644,-1.1434,-1.5743,-1.3794,1.5334,-1.7206,-1.3384,-0.1051,0.3135,-1.4686,-1.6447,-1.3658,0.8464,-2.4471,0.0616,-1.4748,1.5711,-1.6608,-1.3404,-1.1995,-1.0812,-1.4283,0.8041,0.0715,-1.4484,-0.5994,-0.9287,-1.7140,-0.5615,0.2622,-0.8917,-0.9725,-0.2014,-1.5361,-0.1950,-2.0671,-1.0340,0.9866,-0.7904,-0.9688,-1.5636,0.3479,-0.7205,-0.9255,-0.5115,-1.2319,-0.2361,-0.7738,-0.3994,-0.6433,-1.0884,-0.4630,-1.0106,-0.5089,-0.9225}
Activity(exp=0): {-0.0000,1.4597}
Activity(exp=1): {0.0000,-0.7841,-0.5715,-1.0777,-1.9313}
Binding mode 2:
---------------
Mononucleotide: {-0.3353,-0.7482,-0.3424,-0.6489,-0.4815,-0.6628,-0.3625,-0.5680,-0.4849,-0.8027,-0.2599,-0.5274,-0.6403,-0.5846,-0.2900,-0.5598,-0.4097,-0.7434,-0.3305,-0.5912,0.4932,-2.2134,0.4720,-0.8266,-1.6912,0.0250,-0.8976,0.4891,-0.3511,-0.8836,1.5570,-2.3970,-0.2725,-1.4099,-0.1647,-0.2276,-0.5974,-0.7291,-0.4638,-0.2845,-0.3738,-0.5178,-0.3843,-0.7989,-0.4976,-0.4765,-0.2965,-0.8041}
Activity(exp=0): {-0.0000,-3.4742}
Activity(exp=1): {-0.0000,2.1727,0.2978,-0.4993,-0.5718}
Suggested variations:
key=12;5;0, description = Initial model.
> Optimizing variation "Initial model." (component2-2-variation0).
>> Starting new optimization: component2-2-variation0. (2021-05-22 06:51:08.025).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[55,56]},{"h":[57,58,59,60,61]}],"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],"activity":[[48,49],[50,51,52,53,54]]}]}
Value and gradient before optimization:
=======================================
value = 2.0062044646183743
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}
gradient norm = 3.7940378715331656E-7
Already at minimum!
After: gradient norm = 3.7940378715331656E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.4699,-0.4699}
Count Table 1:
---------------
h: {2.6956,0.8050,0.0958,-0.7857,-2.8107}
Binding mode 0:
---------------
Mononucleotide: {-1.9279,-0.8302,-1.4471,-1.6014}
Activity(exp=0): {-0.0000,-1.8717}
Activity(exp=1): {-0.0000,-0.7080,-1.5028,-1.3993,-0.3247}
Position Bias(exp=0, s=0): {0.6944,-0.4627,-0.2192,0.3335,0.8604,-0.9050,1.0154,0.1526,-1.1057,0.1763,0.0381,0.4687,-0.1264,1.0549,-0.3159,-0.0116,-1.0984,-0.0969,-1.0208,-0.9863,-0.3392,-1.0605,0.7370,0.6118,-0.1051,0.1942,0.1645,-1.9629,0.6044,0.8390}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.5399,0.3518,-1.3318,0.1962,0.2997,0.1574,0.0142,0.1530,0.1752,0.2011,-0.0925,-0.4215,-0.3266,-0.3861,0.0444,-0.1817,0.2980,-0.2909,-3.9527,0.6185}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-0.4687,-0.6748,-0.7861,-0.9753,-0.9009,-0.9776,0.1880,-1.2145,-0.5051,0.0393,-1.4485,-0.9907,-1.3988,-1.3470,0.8028,-0.9620,-1.0517,0.8644,-1.1434,-1.5743,-1.3794,1.5334,-1.7206,-1.3384,-0.1051,0.3135,-1.4686,-1.6447,-1.3658,0.8464,-2.4471,0.0616,-1.4748,1.5711,-1.6608,-1.3404,-1.1995,-1.0812,-1.4283,0.8041,0.0715,-1.4484,-0.5994,-0.9287,-1.7140,-0.5615,0.2622,-0.8917,-0.9725,-0.2014,-1.5361,-0.1950,-2.0671,-1.0340,0.9866,-0.7904,-0.9688,-1.5636,0.3479,-0.7205,-0.9255,-0.5115,-1.2319,-0.2361,-0.7738,-0.3994,-0.6433,-1.0884,-0.4630,-1.0106,-0.5089,-0.9225}
Activity(exp=0): {-0.0000,1.4597}
Activity(exp=1): {0.0000,-0.7841,-0.5715,-1.0777,-1.9313}
Binding mode 2:
---------------
Mononucleotide: {-0.3353,-0.7482,-0.3424,-0.6489,-0.4815,-0.6628,-0.3625,-0.5680,-0.4849,-0.8027,-0.2599,-0.5274,-0.6403,-0.5846,-0.2900,-0.5598,-0.4097,-0.7434,-0.3305,-0.5912,0.4932,-2.2134,0.4720,-0.8266,-1.6912,0.0250,-0.8976,0.4891,-0.3511,-0.8836,1.5570,-2.3970,-0.2725,-1.4099,-0.1647,-0.2276,-0.5974,-0.7291,-0.4638,-0.2845,-0.3738,-0.5178,-0.3843,-0.7989,-0.4976,-0.4765,-0.2965,-0.8041}
Activity(exp=0): {-0.0000,-3.4742}
Activity(exp=1): {-0.0000,2.1727,0.2978,-0.4993,-0.5718}
The Likelihood DID NOT improve. Discarding fit component2-2-variation0.
Suggested variations:
key=12;6;0, description = Increases flank length.
> Optimizing variation "Increases flank length." (component2-2-variation1).
>> Starting new optimization: component2-2-variation1. (2021-05-22 06:51:09.431).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[55,56]},{"h":[57,58,59,60,61]}],"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],"activity":[[48,49],[50,51,52,53,54]]}]}
Value and gradient before optimization:
=======================================
value = 2.0079883208355676
gradient = {0.0029,0.0016,0.0027,0.0043,0.0049,0.0019,0.0026,0.0021,0.0026,0.0017,0.0053,0.0020,0.0022,0.0044,0.0028,0.0021,0.0026,0.0018,0.0048,0.0023,0.0066,0.0002,0.0036,0.0011,0.0006,0.0033,0.0013,0.0064,0.0014,0.0010,0.0090,0.0002,0.0030,0.0012,0.0037,0.0037,0.0022,0.0026,0.0027,0.0041,0.0031,0.0027,0.0032,0.0026,0.0029,0.0029,0.0031,0.0026,-0.0000,0.0000,-0.0000,0.0057,0.0041,0.0015,0.0002,-0.0000,0.0000,-0.0084,-0.0011,0.0033,0.0038,0.0024}
gradient norm = 0.02610815046155599
Starting Function Value: 2.0079883208355676
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.007606852407808 0.032989111128982 1.263556036937898 0.005333061537854
2 4 2.007583617320840 0.005205343954584 1.000000000000000 0.004035694679635
3 5 2.007513635196009 0.022892016715717 1.000000000000000 0.005882770609412
4 6 2.007407490222154 0.046738523688559 1.000000000000000 0.009547460538339
5 7 2.007270469941307 0.074269948691080 1.000000000000000 0.009955674712072
6 8 2.007189859688887 0.083300923408681 1.000000000000000 0.007125424196930
7 9 2.007130584069206 0.029417356371767 1.000000000000000 0.001858396531765
8 10 2.007122455777118 0.009249502041849 1.000000000000000 0.001334618056650
9 11 2.007113387207368 0.016775611114255 1.000000000000000 0.002283809935316
10 12 2.007104787394312 0.019124362973640 1.000000000000000 0.002802241291369
11 13 2.007086344014025 0.048918467324165 1.000000000000000 0.002849621754939
12 14 2.007082587744314 0.066354708800129 1.000000000000000 0.002865274544176
13 15 2.007066063226135 0.013106017793965 1.000000000000000 0.000952975280740
14 16 2.007062284746349 0.008791632949983 1.000000000000000 0.000440411838871
15 17 2.007059353013713 0.012914357064201 1.000000000000000 0.000869135062614
16 18 2.007056602700039 0.015159190188789 1.000000000000000 0.001176580412579
17 19 2.007051231773236 0.031501204368709 1.000000000000000 0.001188335365922
18 20 2.007041016352239 0.069676282689749 1.000000000000000 0.001378379594970
19 21 2.007037547196036 0.056859739013755 1.000000000000000 0.002145978303006
20 22 2.007033002278960 0.012293751372695 1.000000000000000 0.000832747727270
21 23 2.007031370695476 0.007920510445351 1.000000000000000 0.000376174659908
22 24 2.007029929008196 0.012547110968720 1.000000000000000 0.000714028246987
23 25 2.007027062962046 0.030586360682568 1.000000000000000 0.001289887559930
24 26 2.007023126814936 0.047249367087153 1.000000000000000 0.001481351941507
25 27 2.007015606968707 0.070711765506327 1.000000000000000 0.001333228148530
26 28 2.007004888390082 0.157258287588516 1.000000000000000 0.000918920585920
27 29 2.006998911865527 0.034417525228094 1.000000000000000 0.000392929032665
28 30 2.006995669991202 0.020883211929468 1.000000000000000 0.000362024224120
29 31 2.006992940420886 0.068110039817178 1.000000000000000 0.001557616887023
30 32 2.006988482960231 0.021114183875480 1.000000000000000 0.000792624159217
31 33 2.006984062613926 0.046684329739335 1.000000000000000 0.000287216136021
32 34 2.006982220874285 0.040392727484139 1.000000000000000 0.000270328885423
33 35 2.006980610166982 0.035925337723718 1.000000000000000 0.000228963968636
34 36 2.006976563548254 0.063543653810515 1.000000000000000 0.000456122787743
35 37 2.006974316102331 0.059405813785596 1.000000000000000 0.000187622619613
36 38 2.006973098504734 0.025026403802421 1.000000000000000 0.000309958628357
37 39 2.006972009453288 0.016238396984623 1.000000000000000 0.000212366306105
38 40 2.006970164335522 0.028232878790025 1.000000000000000 0.000270516913873
39 41 2.006968484658109 0.029704434282908 1.000000000000000 0.000437001930516
40 42 2.006967108864636 0.033975951526222 1.000000000000000 0.000410244714249
41 43 2.006965311791829 0.040295631743706 1.000000000000000 0.000242239174705
42 44 2.006964230518959 0.033380286713100 1.000000000000000 0.000103839573957
43 45 2.006963975651015 0.009147490449501 1.000000000000000 0.000167415146064
44 46 2.006963642547419 0.010523027585370 1.000000000000000 0.000184393189868
45 47 2.006962670244573 0.028552271255768 1.000000000000000 0.000209159881684
46 48 2.006961202490476 0.056877535497271 1.000000000000000 0.000102253456048
47 49 2.006960555867749 0.030188697716890 1.000000000000000 0.000074707818302
48 50 2.006960242474529 0.014880276408386 1.000000000000000 0.000063955222440
49 51 2.006960093710218 0.009999925344131 1.000000000000000 0.000034854765316
50 52 2.006960043428546 0.004597078289830 1.000000000000000 0.000020201886291
51 53 2.006960004249815 0.004034810887475 1.000000000000000 0.000027697687960
52 54 2.006959975813046 0.004336124160467 1.000000000000000 0.000023623567835
53 55 2.006959924545543 0.007033136729772 1.000000000000000 0.000034369048282
54 56 2.006959836898044 0.014054671774674 1.000000000000000 0.000024859268446
55 57 2.006959752883770 0.014667343576142 1.000000000000000 0.000028090991092
56 58 2.006959656612981 0.019858515509061 1.000000000000000 0.000038236314998
57 59 2.006959605641971 0.008438934616748 1.000000000000000 0.000018835603578
58 60 2.006959583682746 0.003298907372530 1.000000000000000 0.000015075422027
59 61 2.006959558008292 0.004423045197224 1.000000000000000 0.000020975640269
60 62 2.006959519375011 0.010217885288207 1.000000000000000 0.000019222332702
61 63 2.006959489007384 0.010549303693227 1.000000000000000 0.000024281718782
62 64 2.006959471646935 0.008243607253437 1.000000000000000 0.000006166040811
63 65 2.006959468494587 0.001539495800978 1.000000000000000 0.000004194196443
64 66 2.006959465962032 0.000941647624106 1.000000000000000 0.000005829524078
65 67 2.006959463266557 0.001674058237213 1.000000000000000 0.000004424451060
66 68 2.006959461263346 0.001486479122778 1.000000000000000 0.000006152298948
67 69 2.006959459711152 0.001799225646762 1.000000000000000 0.000003215253541
68 70 2.006959459159123 0.000774289394863 1.000000000000000 0.000002544190072
69 71 2.006959458306316 0.001110708396880 1.000000000000000 0.000004485883438
70 72 2.006959456845477 0.001893987777022 1.000000000000000 0.000007430586514
71 73 2.006959454204104 0.003350113284289 1.000000000000000 0.000010062805431
72 74 2.006959448260410 0.007653473035411 1.000000000000000 0.000012282928244
73 75 2.006959438232590 0.014516218812424 1.000000000000000 0.000011210198690
74 77 2.006959435701348 0.005144844499732 0.231703903604513 0.000015177086315
75 78 2.006959429874187 0.007548404429125 1.000000000000000 0.000005922497144
76 79 2.006959427789722 0.001942647642791 1.000000000000000 0.000002833258384
77 80 2.006959427071449 0.000662908965655 1.000000000000000 0.000003750742467
78 81 2.006959425385598 0.001383306423147 1.000000000000000 0.000004998892367
79 82 2.006959422720505 0.003586326265380 1.000000000000000 0.000005508970588
80 83 2.006959419979509 0.006681498723851 1.000000000000000 0.000008445964463
81 84 2.006959418919284 0.003751874273624 1.000000000000000 0.000005513427441
82 85 2.006959418286051 0.002221029110025 1.000000000000000 0.000004836773288
83 86 2.006959417551572 0.001871075535683 1.000000000000000 0.000003793964894
84 87 2.006959416416065 0.002389039818391 1.000000000000000 0.000003547403813
85 88 2.006959415021755 0.002801057875003 1.000000000000000 0.000003662943656
86 89 2.006959413725598 0.002584806545387 1.000000000000000 0.000002566795951
87 90 2.006959412725988 0.002347456645886 1.000000000000000 0.000004759812789
88 91 2.006959412367592 0.000708398216819 1.000000000000000 0.000002141326661
89 92 2.006959412223666 0.000370962149602 1.000000000000000 0.000001375271773
90 93 2.006959412148837 0.000370962149602 1.000000000000000 0.000000699471811
Convergence criteria met.
After: gradient norm = 6.99471810695327E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.4684,-0.4684}
Count Table 1:
---------------
h: {2.6063,0.8004,0.1245,-0.7529,-2.7783}
Binding mode 0:
---------------
Mononucleotide: {-1.9279,-0.8302,-1.4471,-1.6014}
Activity(exp=0): {-0.0000,-1.8717}
Activity(exp=1): {-0.0000,-0.7080,-1.5028,-1.3993,-0.3247}
Position Bias(exp=0, s=0): {0.6944,-0.4627,-0.2192,0.3335,0.8604,-0.9050,1.0154,0.1526,-1.1057,0.1763,0.0381,0.4687,-0.1264,1.0549,-0.3159,-0.0116,-1.0984,-0.0969,-1.0208,-0.9863,-0.3392,-1.0605,0.7370,0.6118,-0.1051,0.1942,0.1645,-1.9629,0.6044,0.8390}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.5399,0.3518,-1.3318,0.1962,0.2997,0.1574,0.0142,0.1530,0.1752,0.2011,-0.0925,-0.4215,-0.3266,-0.3861,0.0444,-0.1817,0.2980,-0.2909,-3.9527,0.6185}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-0.4687,-0.6748,-0.7861,-0.9753,-0.9009,-0.9776,0.1880,-1.2145,-0.5051,0.0393,-1.4485,-0.9907,-1.3988,-1.3470,0.8028,-0.9620,-1.0517,0.8644,-1.1434,-1.5743,-1.3794,1.5334,-1.7206,-1.3384,-0.1051,0.3135,-1.4686,-1.6447,-1.3658,0.8464,-2.4471,0.0616,-1.4748,1.5711,-1.6608,-1.3404,-1.1995,-1.0812,-1.4283,0.8041,0.0715,-1.4484,-0.5994,-0.9287,-1.7140,-0.5615,0.2622,-0.8917,-0.9725,-0.2014,-1.5361,-0.1950,-2.0671,-1.0340,0.9866,-0.7904,-0.9688,-1.5636,0.3479,-0.7205,-0.9255,-0.5115,-1.2319,-0.2361,-0.7738,-0.3994,-0.6433,-1.0884,-0.4630,-1.0106,-0.5089,-0.9225}
Activity(exp=0): {-0.0000,1.4597}
Activity(exp=1): {0.0000,-0.7841,-0.5715,-1.0777,-1.9313}
Binding mode 2:
---------------
Mononucleotide: {-0.3285,-0.6873,-0.2900,-0.8233,-0.5618,-0.6493,-0.3535,-0.5646,-0.4926,-0.8273,-0.3220,-0.4872,-0.5735,-0.7191,-0.2944,-0.5422,-0.3532,-0.6984,-0.4658,-0.6118,0.2304,-1.5900,0.2299,-0.9994,-1.6624,-0.0748,-0.8607,0.4688,-0.5048,-1.1645,1.8465,-2.3063,-0.2525,-1.4485,-0.2462,-0.1819,-0.5575,-0.7861,-0.5313,-0.2542,-0.3662,-0.5567,-0.3261,-0.8801,-0.5464,-0.4890,-0.2603,-0.8334}
Activity(exp=0): {-0.0000,-3.5684}
Activity(exp=1): {-0.0000,2.1017,0.2777,-0.4514,-0.4888}
The Likelihood DID NOT improve. Discarding fit component2-2-variation1.
Suggested variations:
key=12;5;-1, description = Heuristic shift (-1).
> Optimizing variation "Heuristic shift (-1)." (component2-2-variation2).
>> Starting new optimization: component2-2-variation2. (2021-05-22 06:53:17.497).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[55,56]},{"h":[57,58,59,60,61]}],"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],"activity":[[48,49],[50,51,52,53,54]]}]}
Value and gradient before optimization:
=======================================
value = 2.03516874673187
gradient = {0.0385,0.0210,0.0325,0.0227,0.0295,0.0201,0.0425,0.0225,0.0246,0.0324,0.0339,0.0237,0.0319,0.0214,0.0367,0.0247,0.0572,0.0027,0.0428,0.0119,0.0061,0.0321,0.0129,0.0635,0.0144,0.0070,0.0914,0.0019,0.0308,0.0092,0.0345,0.0402,0.0238,0.0238,0.0279,0.0392,0.0286,0.0282,0.0334,0.0244,0.0267,0.0306,0.0349,0.0224,0.0238,0.0310,0.0228,0.0371,-0.0000,0.0001,-0.0000,0.0482,0.0434,0.0196,0.0034,-0.0020,0.0020,-0.0647,-0.0187,0.0226,0.0352,0.0256}
gradient norm = 0.24894787591963988
Starting Function Value: 2.03516874673187
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.008102834534833 0.237800493992083 0.955222024343943 0.010603590015108
2 4 2.008025986632786 0.009545736368220 1.000000000000000 0.006885953898683
3 5 2.007921780685825 0.019897228944096 1.000000000000000 0.008158300346885
4 6 2.007737735711924 0.045163033741547 1.000000000000000 0.013104751144276
5 7 2.007422005417981 0.092558716394827 1.000000000000000 0.017294507502693
6 8 2.006963739093010 0.147311881571268 1.000000000000000 0.018132255629022
7 9 2.006843951775772 0.226948960721270 1.000000000000000 0.017656001258079
8 10 2.006396706869359 0.053859007608713 1.000000000000000 0.005836199014199
9 11 2.006313743005833 0.027255995257407 1.000000000000000 0.002426828962972
10 12 2.006266012742965 0.042851733282925 1.000000000000000 0.003598752800892
11 13 2.006207826418570 0.062872480897767 1.000000000000000 0.005151121542420
12 14 2.006133691534138 0.086855647823523 1.000000000000000 0.004386611667016
13 16 2.006109436580767 0.036808973645344 0.353360315939088 0.004219457860181
14 17 2.006070696112854 0.049350632922364 1.000000000000000 0.001990283955865
15 18 2.006052833028306 0.024965034601721 1.000000000000000 0.001510861644864
16 19 2.006038129076267 0.029789711560846 1.000000000000000 0.002281124059080
17 20 2.006024795481564 0.033341477554193 1.000000000000000 0.002270606264660
18 21 2.005999990195939 0.069150959576301 1.000000000000000 0.001422226445820
19 22 2.005986742965939 0.061483722467055 1.000000000000000 0.000695006369324
20 23 2.005983491766454 0.026910030123482 1.000000000000000 0.001180450575254
21 24 2.005981515582087 0.005804238669201 1.000000000000000 0.000710643107347
22 25 2.005978720237243 0.011122725955792 1.000000000000000 0.000465601783876
23 26 2.005975275352639 0.019251384375354 1.000000000000000 0.000648133112117
24 27 2.005971130332386 0.030222443626958 1.000000000000000 0.000890216286367
25 28 2.005966731143016 0.032451688471450 1.000000000000000 0.000804845570033
26 29 2.005962852908486 0.059984049289939 1.000000000000000 0.001123638839017
27 30 2.005957885118196 0.024606193102761 1.000000000000000 0.000478297601051
28 31 2.005954853556178 0.017399926694707 1.000000000000000 0.000582351105337
29 32 2.005951153312282 0.033041426203955 1.000000000000000 0.000707385358655
30 33 2.005945284424167 0.050453191511769 1.000000000000000 0.000613161698814
31 34 2.005932855865440 0.124861557015089 1.000000000000000 0.000588452016775
32 35 2.005925000004407 0.085095830868256 1.000000000000000 0.000606692723032
33 36 2.005914647941817 0.098835136013144 1.000000000000000 0.000704787780411
34 37 2.005903049114350 0.132336929358507 1.000000000000000 0.000429924455351
35 38 2.005897409207697 0.073298049144385 1.000000000000000 0.000494190646521
36 39 2.005893922462933 0.032704832220981 1.000000000000000 0.000838090357033
37 40 2.005892204855159 0.046598123975456 1.000000000000000 0.000316056753833
38 41 2.005891047305672 0.016309651946554 1.000000000000000 0.000333436413913
39 42 2.005889174528231 0.016771054578967 1.000000000000000 0.000231920350616
40 43 2.005887360845474 0.022482538528938 1.000000000000000 0.000163789229592
41 44 2.005886088436275 0.027753555934078 1.000000000000000 0.000131428108079
42 45 2.005885003615732 0.023513751267525 1.000000000000000 0.000096457731743
43 46 2.005883870099321 0.029359143526943 1.000000000000000 0.000097328251135
44 47 2.005883029866828 0.027153454303941 1.000000000000000 0.000084752393992
45 48 2.005882277398960 0.034087165314336 1.000000000000000 0.000130901210118
46 49 2.005881864006183 0.019343687285492 1.000000000000000 0.000060141266788
47 50 2.005881601384989 0.013404747343830 1.000000000000000 0.000067079331156
48 51 2.005881407865671 0.010027764065250 1.000000000000000 0.000064994910577
49 52 2.005881133365339 0.017914601322804 1.000000000000000 0.000068345774258
50 53 2.005880986596158 0.015356976014141 1.000000000000000 0.000065725416764
51 54 2.005880912897048 0.007426568241572 1.000000000000000 0.000074881797281
52 55 2.005880807525490 0.011587045678451 1.000000000000000 0.000075386293812
53 56 2.005880682359418 0.013699117053600 1.000000000000000 0.000062221802183
54 57 2.005880477235581 0.025230194032082 1.000000000000000 0.000042731350433
55 58 2.005880330209411 0.020600699035542 1.000000000000000 0.000043620685860
56 59 2.005880191267300 0.017715841848189 1.000000000000000 0.000037269171075
57 60 2.005879989415837 0.027333463765314 1.000000000000000 0.000043155903351
58 61 2.005879842465268 0.024152770801490 1.000000000000000 0.000045719378979
59 62 2.005879684313204 0.023240167879965 1.000000000000000 0.000074926834202
60 63 2.005879444400398 0.040611105922926 1.000000000000000 0.000048054523539
61 64 2.005879251921811 0.031630366200608 1.000000000000000 0.000039230728155
62 65 2.005879035095461 0.040195343198705 1.000000000000000 0.000044734744091
63 66 2.005878886376586 0.028145336463750 1.000000000000000 0.000058598035452
64 67 2.005878720075571 0.031737344544302 1.000000000000000 0.000052723838517
65 68 2.005878563522245 0.035133947972534 1.000000000000000 0.000046364345810
66 69 2.005878460188968 0.023154685929490 1.000000000000000 0.000035469893385
67 70 2.005878374188450 0.021049708193751 1.000000000000000 0.000051765846222
68 71 2.005878275968144 0.021620216525417 1.000000000000000 0.000059156397042
69 72 2.005878098412241 0.045171250882420 1.000000000000000 0.000033402382515
70 73 2.005878005651756 0.030393122722289 1.000000000000000 0.000037023066772
71 74 2.005877964125864 0.012668531728252 1.000000000000000 0.000029012304269
72 75 2.005877945879341 0.003071381037738 1.000000000000000 0.000028384178988
73 76 2.005877910918674 0.005906275749261 1.000000000000000 0.000030208903950
74 77 2.005877828100464 0.022438479081421 1.000000000000000 0.000024113309441
75 78 2.005877759592183 0.023952578104911 1.000000000000000 0.000019495124729
76 79 2.005877693076585 0.029823676081773 1.000000000000000 0.000013803218644
77 80 2.005877680072376 0.013781455855599 1.000000000000000 0.000031244311770
78 81 2.005877669508931 0.003767977163567 1.000000000000000 0.000005850903898
79 82 2.005877668440618 0.001021797508709 1.000000000000000 0.000004259243629
80 83 2.005877666896514 0.000738241433964 1.000000000000000 0.000004112881167
81 84 2.005877663328115 0.001867069469682 1.000000000000000 0.000006337955546
82 85 2.005877657615361 0.003553478258410 1.000000000000000 0.000009161136559
83 86 2.005877646724726 0.007523516787213 1.000000000000000 0.000009869117360
84 87 2.005877631504392 0.013023829864633 1.000000000000000 0.000021839450344
85 88 2.005877622802752 0.007698815257947 1.000000000000000 0.000013569882494
86 89 2.005877617441477 0.004464680960170 1.000000000000000 0.000007533766081
87 90 2.005877614257813 0.002027724428742 1.000000000000000 0.000005730593331
88 91 2.005877607359941 0.005290421724509 1.000000000000000 0.000008307505122
89 92 2.005877601166584 0.006234490882646 1.000000000000000 0.000009536901580
90 93 2.005877594993673 0.007311627369342 1.000000000000000 0.000007930887581
91 94 2.005877590677966 0.007326654969753 1.000000000000000 0.000006200766339
92 95 2.005877587039390 0.002093263188164 1.000000000000000 0.000006094904639
93 96 2.005877574777095 0.009284967442305 1.000000000000000 0.000015570380641
94 97 2.005877555586683 0.017719391177692 1.000000000000000 0.000027632549303
95 98 2.005877501883923 0.055837105109646 1.000000000000000 0.000049530548591
96 99 2.005877395271803 0.121869881459644 1.000000000000000 0.000073491946294
97 100 2.005877214692856 0.227479619613386 1.000000000000000 0.000085030076862
98 101 2.005877039759970 0.261576579874651 1.000000000000000 0.000063455407498
99 102 2.005876957527054 0.119152167998550 1.000000000000000 0.000022804349693
100 103 2.005876937931166 0.023586681883402 1.000000000000000 0.000006475630114
101 104 2.005876934149010 0.022830793148987 1.000000000000000 0.000004981575977
102 105 2.005876932271347 0.003678766582770 1.000000000000000 0.000005993602591
103 106 2.005876922021877 0.006666969060116 1.000000000000000 0.000012376098205
104 107 2.005876912993425 0.010032757091017 1.000000000000000 0.000019559862207
105 109 2.005876906316465 0.016058404989132 0.438344172506624 0.000021228956860
106 110 2.005876899298199 0.025973106555518 1.000000000000000 0.000008692874186
107 111 2.005876897282083 0.011701300006332 1.000000000000000 0.000004175713779
108 112 2.005876896294561 0.001125548816807 1.000000000000000 0.000002894661143
109 113 2.005876895801436 0.003555279924674 1.000000000000000 0.000008989314534
110 114 2.005876895598205 0.001079481985812 1.000000000000000 0.000001562827296
111 115 2.005876895573752 0.001079481985812 1.000000000000000 0.000000583169096
Convergence criteria met.
After: gradient norm = 5.831690964526393E-7
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.4657,-0.4657}
Count Table 1:
---------------
h: {2.7906,0.7852,0.0719,-0.8092,-2.8385}
Binding mode 0:
---------------
Mononucleotide: {-1.9279,-0.8302,-1.4471,-1.6014}
Activity(exp=0): {-0.0000,-1.8717}
Activity(exp=1): {-0.0000,-0.7080,-1.5028,-1.3993,-0.3247}
Position Bias(exp=0, s=0): {0.6944,-0.4627,-0.2192,0.3335,0.8604,-0.9050,1.0154,0.1526,-1.1057,0.1763,0.0381,0.4687,-0.1264,1.0549,-0.3159,-0.0116,-1.0984,-0.0969,-1.0208,-0.9863,-0.3392,-1.0605,0.7370,0.6118,-0.1051,0.1942,0.1645,-1.9629,0.6044,0.8390}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {0.5399,0.3518,-1.3318,0.1962,0.2997,0.1574,0.0142,0.1530,0.1752,0.2011,-0.0925,-0.4215,-0.3266,-0.3861,0.0444,-0.1817,0.2980,-0.2909,-3.9527,0.6185}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-0.4687,-0.6748,-0.7861,-0.9753,-0.9009,-0.9776,0.1880,-1.2145,-0.5051,0.0393,-1.4485,-0.9907,-1.3988,-1.3470,0.8028,-0.9620,-1.0517,0.8644,-1.1434,-1.5743,-1.3794,1.5334,-1.7206,-1.3384,-0.1051,0.3135,-1.4686,-1.6447,-1.3658,0.8464,-2.4471,0.0616,-1.4748,1.5711,-1.6608,-1.3404,-1.1995,-1.0812,-1.4283,0.8041,0.0715,-1.4484,-0.5994,-0.9287,-1.7140,-0.5615,0.2622,-0.8917,-0.9725,-0.2014,-1.5361,-0.1950,-2.0671,-1.0340,0.9866,-0.7904,-0.9688,-1.5636,0.3479,-0.7205,-0.9255,-0.5115,-1.2319,-0.2361,-0.7738,-0.3994,-0.6433,-1.0884,-0.4630,-1.0106,-0.5089,-0.9225}
Activity(exp=0): {-0.0000,1.4597}
Activity(exp=1): {0.0000,-0.7841,-0.5715,-1.0777,-1.9313}
Binding mode 2:
---------------
Mononucleotide: {-0.5118,-0.5836,-0.3239,-0.6502,-0.4488,-0.7081,-0.4641,-0.4485,-0.4945,-0.7590,-0.2254,-0.5906,-0.3506,-0.6718,-0.4621,-0.5850,0.1641,-1.5735,0.1868,-0.8469,-1.4004,-0.1114,-0.9926,0.4349,-0.3476,-1.0403,1.8427,-2.5242,-0.3151,-1.1872,-0.2727,-0.2946,-0.5541,-0.7324,-0.6554,-0.1276,-0.2747,-0.5497,-0.3125,-0.9327,-0.5925,-0.4883,-0.2971,-0.6916,-0.5399,-0.7143,-0.0762,-0.7381}
Activity(exp=0): {-0.0000,-4.0544}
Activity(exp=1): {-0.0000,2.4284,0.3888,-0.4202,-0.4120}
The Likelihood DID improve.
informationThreshold = 0.1
>>> Information used for optimizeSizeHeuristic: I[0] = 0.011231737428286148, I[1] = 0.008027035797174564, I[k-2] = 0.015888550658411604, I[k-1] = 0.05784028557939824
> No varitions possible for Binding mode 2.
> Optimizing the full model (component2-4-all).
>> Starting new optimization: component2-4-all. (2021-05-22 06:55:50.269).
>>> Packing before optimization
Packing: {"enrichmentModel":[{},{}],"countTable":[{"h":[195,196]},{"h":[197,198,199,200,201]}],"bindingModeInteractions":[],"bindingModes":[{"mononucleotide":[0,1,2,3],"activity":[[54,55],[56,57,58,59,60]],"positionBias":[[[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],[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1]],[[34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53],[-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1]]]},{"mononucleotide":[61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132],"activity":[[133,134],[135,136,137,138,139]]},{"mononucleotide":[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],"activity":[[188,189],[190,191,192,193,194]]}]}
Value and gradient before optimization:
=======================================
value = 2.0191188325453386
gradient = {0.0005,0.0024,0.0024,0.0004,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0002,0.0002,0.0001,0.0003,0.0004,0.0003,0.0004,0.0004,0.0004,0.0003,0.0003,0.0002,0.0003,0.0003,0.0003,0.0003,0.0003,0.0004,0.0000,0.0002,-0.0000,0.0001,-0.0000,0.0003,0.0012,0.0025,0.0016,-0.0027,-0.0024,-0.0003,-0.0003,-0.0003,-0.0001,-0.0036,-0.0017,-0.0040,-0.0015,-0.0000,-0.0002,0.0000,0.0000,-0.0056,-0.0001,-0.0003,-0.0052,-0.0001,-0.0000,-0.0000,-0.0056,-0.0000,-0.0000,-0.0022,-0.0031,-0.0002,-0.0002,-0.0000,-0.0041,-0.0000,-0.0015,0.0000,-0.0057,0.0000,-0.0000,-0.0001,-0.0001,-0.0001,-0.0055,-0.0037,-0.0001,-0.0013,-0.0006,-0.0001,-0.0010,-0.0040,-0.0006,-0.0004,-0.0024,-0.0001,-0.0028,-0.0000,-0.0000,-0.0052,-0.0004,-0.0006,-0.0001,-0.0043,-0.0007,-0.0009,-0.0019,-0.0004,-0.0025,-0.0013,-0.0020,-0.0014,-0.0009,-0.0020,-0.0006,-0.0022,-0.0009,-0.0000,-0.0001,0.0000,-0.0003,-0.0012,-0.0025,-0.0016,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-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 = 0.01976875063756595
Starting Function Value: 2.0191188325453386
Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm
1 3 2.018728639893818 0.037129408156206 1.878186883780620 0.008311283781485
2 4 2.018630538737417 0.017045777562224 1.000000000000000 0.005567828676817
3 5 2.018521442375718 0.035191000309164 1.000000000000000 0.004090154728592
4 6 2.018473953983817 0.035590179513908 1.000000000000000 0.010132061132651
5 7 2.018397379888180 0.024959336540623 1.000000000000000 0.006836286895798
6 8 2.018221024290556 0.097399715157968 1.000000000000000 0.006634780037283
7 9 2.018131636437116 0.060360309212516 1.000000000000000 0.006579712460907
8 10 2.018007988633305 0.098088786809447 1.000000000000000 0.005354358748128
9 11 2.017921595629503 0.086559530407674 1.000000000000000 0.003418424420769
10 12 2.017848400929426 0.074741620893459 1.000000000000000 0.004349179845512
11 13 2.017750754767356 0.131002952156935 1.000000000000000 0.003637333917104
12 14 2.017619255680449 0.144053320483723 1.000000000000000 0.004130745000292
13 15 2.017455372633454 0.227097729686242 1.000000000000000 0.007104713651777
14 16 2.017388339969594 0.065228335443302 1.000000000000000 0.002796573794501
15 17 2.017343522804258 0.094687976038745 1.000000000000000 0.004974293127131
16 18 2.017311672169889 0.034097607043120 1.000000000000000 0.002700358837231
17 19 2.017253595045631 0.149477811506619 1.000000000000000 0.002358550287842
18 20 2.017197261221726 0.148897191192561 1.000000000000000 0.002052040489720
19 21 2.017173753944917 0.302248689608035 1.000000000000000 0.009621773711159
20 22 2.017088576133872 0.108116024938419 1.000000000000000 0.009200279012544
21 23 2.017065290226181 0.054835679668581 1.000000000000000 0.001743202012258
22 24 2.017045336214153 0.032526378621630 1.000000000000000 0.001612151864758
23 25 2.017017318041845 0.059725047924110 1.000000000000000 0.001746075212293
24 26 2.016936286682915 0.150738965926594 1.000000000000000 0.002755772374482
25 27 2.016862015484904 0.172092035991556 1.000000000000000 0.004404247632399
26 28 2.016817540311236 0.079889056433449 1.000000000000000 0.001499475421039
27 29 2.016792622610891 0.083742065807223 1.000000000000000 0.002485824039908
28 30 2.016763392588531 0.057788528945287 1.000000000000000 0.001994023110254
29 31 2.016707651346631 0.161421855686741 1.000000000000000 0.002969042395351
30 32 2.016640818087949 0.166878479832622 1.000000000000000 0.001638381835218
31 33 2.016597974146649 0.171689639026950 1.000000000000000 0.003799497490915
32 34 2.016578336551557 0.089383283554744 1.000000000000000 0.004587474897868
33 35 2.016563870047861 0.051422172471654 1.000000000000000 0.001375772670404
34 36 2.016552966837441 0.016298144599703 1.000000000000000 0.001917583035021
35 37 2.016528361601849 0.052609012167921 1.000000000000000 0.003197767505430
36 38 2.016505836243585 0.071923246269418 1.000000000000000 0.002981159126597
37 39 2.016453893862432 0.166932292088541 1.000000000000000 0.004166876985745
38 40 2.016386138361170 0.239343399454776 1.000000000000000 0.003517376642483
39 41 2.016326006510207 0.258570212480460 1.000000000000000 0.004950369692666
40 42 2.016278750334756 0.167456323889043 1.000000000000000 0.002279299913802
41 43 2.016270219534328 0.189572801050493 1.000000000000000 0.004215307606098
42 44 2.016260784066151 0.069411751287881 1.000000000000000 0.001415168609872
43 45 2.016251960056880 0.018728016046402 1.000000000000000 0.000955756852448
44 46 2.016234283082421 0.089676827635624 1.000000000000000 0.001003694310653
45 47 2.016206258756834 0.144111690917670 1.000000000000000 0.000884974342688
46 48 2.016172960599111 0.318821025981167 1.000000000000000 0.004296029331104
47 49 2.016163204002472 0.031056226386962 1.000000000000000 0.001168488481885
48 50 2.016158893978880 0.055486597745135 1.000000000000000 0.000797886241904
49 51 2.016152067737065 0.053477231181189 1.000000000000000 0.000618467691503
50 52 2.016138395011744 0.146351974655642 1.000000000000000 0.000562601610074
51 53 2.016124731719659 0.113335059955939 1.000000000000000 0.000651619902133
52 54 2.016109530454784 0.153475706483841 1.000000000000000 0.000607417148064
53 55 2.016100767974551 0.066827262108254 1.000000000000000 0.000636877886671
54 56 2.016093466131995 0.111166045700117 1.000000000000000 0.002015394091937
55 57 2.016088769665198 0.054007285204002 1.000000000000000 0.000558926098580
56 58 2.016086279745690 0.034887388544075 1.000000000000000 0.000768695595547
57 59 2.016084421200415 0.030479075934895 1.000000000000000 0.000759787620444
58 60 2.016080234356802 0.047327049403672 1.000000000000000 0.000857939390918
59 61 2.016070052552977 0.134107637570808 1.000000000000000 0.000899811095146
60 62 2.016061060837997 0.120633845338474 1.000000000000000 0.001195775426426
61 63 2.016050891279121 0.149029680539791 1.000000000000000 0.000557971919411
62 64 2.016047586691002 0.079578688118833 1.000000000000000 0.000907913605142
63 65 2.016045457436134 0.041502239764796 1.000000000000000 0.000990907838219
64 66 2.016044156500508 0.082934200735705 1.000000000000000 0.000365891408557
65 67 2.016043085736966 0.017348632907822 1.000000000000000 0.000251526067504
66 68 2.016041346541738 0.044403133161970 1.000000000000000 0.000404133238030
67 69 2.016040500080873 0.022059729907545 1.000000000000000 0.000427436964522
68 70 2.016037648546270 0.069167278562964 1.000000000000000 0.000418211042596
69 71 2.016033939177215 0.094514350851336 1.000000000000000 0.000417491342833
70 72 2.016029633507741 0.112868953557830 1.000000000000000 0.000354190157899
71 73 2.016024331650867 0.127673620155830 1.000000000000000 0.000569606176943
72 74 2.016017986956054 0.170462272595909 1.000000000000000 0.000383159803119
73 75 2.016012314677518 0.123951619421617 1.000000000000000 0.000750154355966
74 76 2.016007807039168 0.132444459114875 1.000000000000000 0.000391481745703
75 77 2.016003971947762 0.066627156441342 1.000000000000000 0.001045546108467
76 78 2.016001110744945 0.081072123023092 1.000000000000000 0.000487051242740
77 79 2.015998209761265 0.037631800917010 1.000000000000000 0.000476427340495
78 80 2.015990156237418 0.139829667931586 1.000000000000000 0.000620786921460
79 81 2.015979536472059 0.211907386444796 1.000000000000000 0.001155182737717
80 82 2.015974363723883 0.073901414498776 1.000000000000000 0.000738352464494
81 83 2.015966203130216 0.222467976569608 1.000000000000000 0.000408895025175
82 84 2.015962660511693 0.080378754286025 1.000000000000000 0.000635202101949
83 85 2.015959312039522 0.230632906508663 1.000000000000000 0.000491846695978
84 86 2.015957989033110 0.067727583621162 1.000000000000000 0.001272357586168
85 87 2.015956990679599 0.011213217889868 1.000000000000000 0.000853599979390
86 88 2.015954664267773 0.027360459502957 1.000000000000000 0.000421135206072
87 89 2.015953566297892 0.021873813286874 1.000000000000000 0.000569554154799
88 90 2.015951138681283 0.040671949782382 1.000000000000000 0.000660529866744
89 91 2.015946498112518 0.065561053564290 1.000000000000000 0.000968375226554
90 92 2.015942555092952 0.072846832290434 1.000000000000000 0.000821822404218
91 93 2.015938952060923 0.082784227038442 1.000000000000000 0.000524713633843
92 94 2.015935911631037 0.100162461556872 1.000000000000000 0.000203965792486
93 95 2.015934691733378 0.059617968708447 1.000000000000000 0.000226262142581
94 96 2.015933090361678 0.061022578866283 1.000000000000000 0.000259562563227
95 97 2.015930769073267 0.077919132995973 1.000000000000000 0.000204620675964
96 98 2.015928558693849 0.060830502323705 1.000000000000000 0.000197769473356
97 99 2.015925732960131 0.083081149354219 1.000000000000000 0.000394937551843
98 100 2.015923625002505 0.055995561247996 1.000000000000000 0.000224751474645
99 101 2.015922387055900 0.035768182920298 1.000000000000000 0.000342555006797
100 102 2.015921214935410 0.035106746244452 1.000000000000000 0.000213491229153
101 103 2.015920663362851 0.048126489054237 1.000000000000000 0.000219470259307
102 104 2.015920100530708 0.018023706225994 1.000000000000000 0.000214973448225
103 105 2.015919618821874 0.028456045684334 1.000000000000000 0.000213223239658
104 107 2.015919458313783 0.009269680194200 0.338785752080870 0.000272070299566
105 108 2.015919181219895 0.008003658025341 1.000000000000000 0.000174774997758
106 109 2.015918839702439 0.011885416696258 1.000000000000000 0.000183023524090
107 110 2.015918456489914 0.017068734750126 1.000000000000000 0.000215399612811
108 111 2.015917982881559 0.020300326246589 1.000000000000000 0.000256608380129
109 112 2.015917531423155 0.026201305094215 1.000000000000000 0.000284743501117
110 113 2.015917104511584 0.008354019594299 1.000000000000000 0.000211599500952
111 114 2.015916550774748 0.029534129159011 1.000000000000000 0.000213395728275
112 115 2.015916212277203 0.019560265515114 1.000000000000000 0.000188160816939
113 116 2.015915789431861 0.023444757131783 1.000000000000000 0.000156396668854
114 117 2.015915192039439 0.026307250160858 1.000000000000000 0.000224532216258
115 118 2.015914401636898 0.037342501351805 1.000000000000000 0.000232884267196
116 119 2.015913583696098 0.038277837912954 1.000000000000000 0.000235182327935
117 120 2.015912841232007 0.068742658044947 1.000000000000000 0.000504197874146
118 121 2.015912415445289 0.010281757745610 1.000000000000000 0.000180502558557
119 122 2.015912250923428 0.005308293172405 1.000000000000000 0.000127456261166
120 123 2.015911990156674 0.009528181850840 1.000000000000000 0.000136008950674
121 124 2.015911543457213 0.024854607693656 1.000000000000000 0.000189505866565
122 125 2.015910874441357 0.040441743564626 1.000000000000000 0.000275873685529
123 126 2.015910493483138 0.106311540555302 1.000000000000000 0.000294722806358
124 127 2.015909674604351 0.042635501687148 1.000000000000000 0.000337274892585
125 128 2.015909136727155 0.024039288458186 1.000000000000000 0.000186616147097
126 129 2.015908827480472 0.010328059104450 1.000000000000000 0.000132876553482
127 130 2.015908209374124 0.029741203857506 1.000000000000000 0.000161138505083
128 131 2.015907461650238 0.052605651256712 1.000000000000000 0.000150605429996
129 132 2.015906644333972 0.061463249562036 1.000000000000000 0.000163898070929
130 134 2.015906160900529 0.052921315010129 0.471918052261915 0.000547856196641
131 135 2.015905619434089 0.027958170804459 1.000000000000000 0.000344292217420
132 136 2.015905224894414 0.028014460174782 1.000000000000000 0.000114917193865
133 137 2.015905088442057 0.013304478250111 1.000000000000000 0.000099084464676
134 138 2.015904912118756 0.015480021224729 1.000000000000000 0.000131103992141
135 139 2.015904664792712 0.024980262062734 1.000000000000000 0.000157631453169
136 141 2.015904511696653 0.015831216684601 0.155717359364846 0.000200715884710
137 142 2.015904142057343 0.025118608879353 1.000000000000000 0.000127398825651
138 143 2.015903566781407 0.031598330794616 1.000000000000000 0.000163314367710
139 144 2.015903184042817 0.049514879942068 1.000000000000000 0.000309960082861
140 145 2.015902686499083 0.024309399003547 1.000000000000000 0.000247652775385
141 146 2.015902136804344 0.032484565166528 1.000000000000000 0.000310038206597
142 147 2.015901529756186 0.047490021719732 1.000000000000000 0.000234784354251
143 149 2.015901308012704 0.024417618257021 0.279643693508284 0.000221536070193
144 150 2.015900961673107 0.077201202298087 1.000000000000000 0.000614753407313
145 151 2.015900294337940 0.014849437248987 1.000000000000000 0.000246752438558
146 152 2.015899927159493 0.030112267813080 1.000000000000000 0.000152716887696
147 153 2.015899603422887 0.031634481482943 1.000000000000000 0.000142965692573
148 154 2.015899032956487 0.087170037960813 1.000000000000000 0.000215512483222
149 155 2.015898497022322 0.067559747682087 1.000000000000000 0.000184505106401
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399 424 2.015643044101998 0.009694680579741 1.000000000000000 0.000054532745895
400 425 2.015643021905917 0.007035070399725 1.000000000000000 0.000041272294756
401 426 2.015642981743002 0.016636939690713 1.000000000000000 0.000036952887621
402 427 2.015642961199319 0.009364076327181 1.000000000000000 0.000044668325250
403 428 2.015642929066754 0.024162955466660 1.000000000000000 0.000093580966287
404 429 2.015642891595440 0.006446938828813 1.000000000000000 0.000040156026468
405 430 2.015642869393447 0.004211133002620 1.000000000000000 0.000030260549803
406 431 2.015642848356370 0.005160628696183 1.000000000000000 0.000046454034597
407 432 2.015642820676892 0.007594545267568 1.000000000000000 0.000057821244823
408 433 2.015642778371596 0.021527025951041 1.000000000000000 0.000095962782782
409 434 2.015642750075647 0.015002289842671 1.000000000000000 0.000044523099666
410 435 2.015642734496264 0.009706082770390 1.000000000000000 0.000028314677653
411 436 2.015642720620637 0.008823775594495 1.000000000000000 0.000024318579041
412 437 2.015642702217671 0.009169656072034 1.000000000000000 0.000055464526901
413 438 2.015642678940622 0.010719471114606 1.000000000000000 0.000054956691360
414 440 2.015642668187406 0.006034530997574 0.440677261561981 0.000079888315204
415 441 2.015642652990044 0.005485457640752 1.000000000000000 0.000045136566599
416 442 2.015642643798031 0.005304365725326 1.000000000000000 0.000027644382175
417 443 2.015642635047631 0.005251801716191 1.000000000000000 0.000036801699511
418 444 2.015642622416117 0.007416660188345 1.000000000000000 0.000054859178911
419 445 2.015642606543817 0.009982682452432 1.000000000000000 0.000057328810797
420 446 2.015642580404545 0.013323013940691 1.000000000000000 0.000045221616922
421 447 2.015642564738610 0.023416884022397 1.000000000000000 0.000123420394995
422 448 2.015642543677512 0.015030234844797 1.000000000000000 0.000137536053362
423 449 2.015642526997233 0.005314125447165 1.000000000000000 0.000052270602348
424 450 2.015642517593719 0.006018316681087 1.000000000000000 0.000029648866921
425 451 2.015642504234767 0.007150327927075 1.000000000000000 0.000034255097694
426 452 2.015642481213287 0.010444390467725 1.000000000000000 0.000047180805348
427 453 2.015642446558936 0.017858391894798 1.000000000000000 0.000063387242106
428 455 2.015642424002956 0.014914782040357 0.293906653576258 0.000061846245180
429 456 2.015642398169127 0.016480268843997 1.000000000000000 0.000092200230400
430 457 2.015642364342855 0.028014049612427 1.000000000000000 0.000029647666919
431 458 2.015642351526097 0.007019668297438 1.000000000000000 0.000040432786308
432 459 2.015642335946001 0.006935094020919 1.000000000000000 0.000054989645527
433 460 2.015642311828986 0.009399299986277 1.000000000000000 0.000057481959605
434 461 2.015642268974375 0.021681129034661 1.000000000000000 0.000096731954984
435 462 2.015642230475772 0.032209252456604 1.000000000000000 0.000058333614901
436 463 2.015642203828060 0.007134504559443 1.000000000000000 0.000034340752789
437 464 2.015642179776034 0.007456292619646 1.000000000000000 0.000031451754784
438 465 2.015642151651064 0.009482520644515 1.000000000000000 0.000034392749329
439 467 2.015642126091658 0.021570890674814 0.498337426683503 0.000069806698946
440 468 2.015642092219613 0.017051120135175 1.000000000000000 0.000031528935244
441 469 2.015642077986179 0.005777620858525 1.000000000000000 0.000020751103101
442 470 2.015642062334128 0.011091103106641 1.000000000000000 0.000024750878745
443 472 2.015642055768214 0.008697451963995 0.272954324764895 0.000030136049281
444 473 2.015642047344255 0.008446238600458 1.000000000000000 0.000076726753714
445 474 2.015642036537943 0.005496740932432 1.000000000000000 0.000023595594057
446 475 2.015642030931421 0.003498353173753 1.000000000000000 0.000023827988847
447 476 2.015642023364519 0.003932083000283 1.000000000000000 0.000024581056407
448 477 2.015642013266822 0.015983355719094 1.000000000000000 0.000062484604580
449 478 2.015641990543775 0.008658539447105 1.000000000000000 0.000033463679991
450 479 2.015641975326518 0.004555836903225 1.000000000000000 0.000022468984853
451 480 2.015641949054075 0.013105317298282 1.000000000000000 0.000028934600893
452 481 2.015641931532093 0.008310294880665 1.000000000000000 0.000026884310601
453 483 2.015641917028464 0.010103054177366 0.399059465742093 0.000047072764252
454 484 2.015641895064504 0.011589877580071 1.000000000000000 0.000022246717255
455 485 2.015641883112534 0.005394048684708 1.000000000000000 0.000024605557862
456 486 2.015641866438654 0.008510160231641 1.000000000000000 0.000030096520883
457 487 2.015641847132881 0.010133588793570 1.000000000000000 0.000021458690374
458 489 2.015641836556616 0.007169605359817 0.351950895136540 0.000055188387168
459 490 2.015641825604135 0.006871457145435 1.000000000000000 0.000019002830565
460 491 2.015641819963564 0.003394049750478 1.000000000000000 0.000022491965858
461 492 2.015641814059988 0.002566485216610 1.000000000000000 0.000026737919251
462 493 2.015641796582285 0.006728520873255 1.000000000000000 0.000023577202628
463 495 2.015641793840881 0.003298244530976 0.133888884277548 0.000057269801888
464 496 2.015641782194298 0.007084300773324 1.000000000000000 0.000028636849235
465 497 2.015641774671172 0.006727299724708 1.000000000000000 0.000016996649670
466 498 2.015641766553908 0.007126019112933 1.000000000000000 0.000024199857206
467 499 2.015641755734031 0.008695181678539 1.000000000000000 0.000030951967402
468 500 2.015641736765922 0.012135974116753 1.000000000000000 0.000025964820871
469 501 2.015641732175799 0.018236601744029 1.000000000000000 0.000056341545600
470 502 2.015641708740349 0.007697564625775 1.000000000000000 0.000032275154662
471 503 2.015641703339000 0.007992167100487 1.000000000000000 0.000015292936033
472 504 2.015641698591868 0.006904209650547 1.000000000000000 0.000025768983426
473 505 2.015641693921311 0.006928469859551 1.000000000000000 0.000018109231218
474 506 2.015641688420157 0.006652204892467 1.000000000000000 0.000021549618233
475 507 2.015641675731810 0.011245522270108 1.000000000000000 0.000023311764976
476 508 2.015641658256641 0.016335814066758 1.000000000000000 0.000039167871334
477 509 2.015641636944677 0.015945594188168 1.000000000000000 0.000023146474238
478 510 2.015641617831619 0.006178510832946 1.000000000000000 0.000028276505984
479 511 2.015641596412647 0.011672030976151 1.000000000000000 0.000041560922516
480 512 2.015641582350692 0.007238454833699 1.000000000000000 0.000022864991007
481 513 2.015641564975608 0.011472457742013 1.000000000000000 0.000028122179450
482 514 2.015641546763754 0.012050846454705 1.000000000000000 0.000029000860656
483 515 2.015641523417962 0.023494406920412 1.000000000000000 0.000064902105823
484 516 2.015641503207999 0.010070580087504 1.000000000000000 0.000035401991654
485 517 2.015641486480597 0.009096428411108 1.000000000000000 0.000031814172523
486 518 2.015641465567765 0.012598003088133 1.000000000000000 0.000033013801093
487 519 2.015641460424582 0.036974544322458 1.000000000000000 0.000086116272872
488 520 2.015641426742751 0.010837946360897 1.000000000000000 0.000022649072497
489 521 2.015641420296017 0.004829847138164 1.000000000000000 0.000016637614301
490 522 2.015641413362749 0.007060682045003 1.000000000000000 0.000022625046979
491 523 2.015641406999886 0.007624441362182 1.000000000000000 0.000025090489789
492 524 2.015641399192004 0.007113689858801 1.000000000000000 0.000018711805128
493 525 2.015641390360418 0.009002318744569 1.000000000000000 0.000016424363675
494 527 2.015641386400453 0.002882945827404 0.392456780822055 0.000040577544704
495 528 2.015641381005888 0.003251756388850 1.000000000000000 0.000024023069866
496 529 2.015641375284316 0.003222520375218 1.000000000000000 0.000012778091039
497 530 2.015641371619520 0.002800990794480 1.000000000000000 0.000015315110015
498 531 2.015641365008672 0.005602541776263 1.000000000000000 0.000015999584607
499 532 2.015641351654848 0.010046396447120 1.000000000000000 0.000017738859748
500 534 2.015641343008741 0.011344259946883 0.421821625083910 0.000030931192182
>>> Maximum iteration count reached.
After: gradient norm = 3.0931192182084936E-5
>>> Parameters after optimization
Count Table 0:
---------------
h: {0.6227,-0.6227}
Count Table 1:
---------------
h: {2.8590,1.2331,0.4377,-0.7612,-3.7686}
Binding mode 0:
---------------
Mononucleotide: {-3.1819,-1.8586,-3.9216,-2.1708}
Activity(exp=0): {-0.0000,-0.5875}
Activity(exp=1): {-0.0000,-1.5102,-2.4665,-2.9131,-3.6557}
Position Bias(exp=0, s=0): {-1.1989,-0.1109,-0.1645,-0.1730,0.8986,-0.3011,0.3583,0.3991,-0.0611,0.4818,-0.3062,0.5433,0.1552,0.6957,-0.6806,0.4288,-0.5763,0.5128,-0.0870,-0.0503,0.5725,-1.4682,-0.0507,0.1678,0.1012,-0.3571,0.1313,-0.5716,-0.5057,0.6293}
Position Bias(exp=0, s=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}
Position Bias(exp=1, s=0): {2.5690,-1.8466,-1.8630,-1.0634,-1.4456,0.7450,-1.1020,0.2963,-0.2572,-1.5588,-1.7127,-1.7155,-1.3795,-1.1650,0.7949,-1.0453,2.1082,-1.9256,-2.6003,3.6218}
Position Bias(exp=1, s=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}
Binding mode 1:
---------------
Mononucleotide: {-0.4240,-0.6499,-0.7222,-0.9134,-0.8511,-0.9348,0.2465,-1.1701,-0.4613,0.0402,-1.3071,-0.9813,-1.3682,-1.2301,0.8309,-0.9420,-1.0222,0.8288,-0.9507,-1.5653,-1.3766,1.4734,-1.5757,-1.2305,-0.1043,0.3476,-1.3948,-1.5580,-1.3517,0.8414,-2.2785,0.0793,-1.5114,1.6419,-1.6076,-1.2324,-1.1736,-1.0190,-1.3743,0.8574,0.1195,-1.4325,-0.5008,-0.8957,-1.6706,-0.5025,0.3170,-0.8535,-0.9097,-0.1664,-1.4612,-0.1722,-1.9965,-0.9899,1.0302,-0.7534,-0.9297,-1.4847,0.3924,-0.6875,-0.8672,-0.4485,-1.1808,-0.2130,-0.7222,-0.3579,-0.6126,-1.0168,-0.4167,-0.9514,-0.4697,-0.8717}
Activity(exp=0): {-0.0000,1.1914}
Activity(exp=1): {-0.0000,-0.8056,-0.6138,-1.0754,-1.4061}
Binding mode 2:
---------------
Mononucleotide: {-0.3584,-0.4000,-0.2160,-0.3434,-0.2806,-0.4824,-0.3003,-0.2546,-0.2563,-0.3800,-0.1919,-0.4896,-0.2318,-0.4536,-0.2350,-0.3973,-0.0570,-0.9739,0.0937,-0.3806,-0.7190,0.0019,-0.9191,0.3184,0.4333,-0.7836,1.5906,-2.5581,-0.2341,-0.9863,0.0258,-0.1232,-0.4627,-0.5170,-0.2857,-0.0524,-0.1938,-0.3090,-0.1672,-0.6479,-0.3979,-0.3578,-0.1173,-0.4448,-0.2918,-0.5256,0.0012,-0.5013}
Activity(exp=0): {-0.0000,-2.3493}
Activity(exp=1): {-0.0000,0.5027,-0.4814,-0.3307,1.3409}
> Optimization done.
Probound Model
±
Optimized model:
{"metadata":{"timeStamp":"2021-05-22 07:14:02.872","logLikelihoodPerRead":2.0156413430087405,"logLikelihood":751933.9567868841,"gradientCalls":2572,"fitSteps":2463,"regularization":0.02071501962685406,"functionCalls":0,"fitter":"proBound","fitName":"component2-4-all","fitTime":3415.206,"dataLoops":2572},"optimizerSetting":{"output":{"outputPath":"jobs/133d27f6506e","baseName":"fit"},"nThreads":20,"likelihoodThreshold":2.0E-4,"lbfgsSettings":{"memory":100,"convergence":1.0E-7,"MCSearch":true,"maxIters":500},"lambdaL2":1.0E-6,"fixedLibrarySize":false,"expBound":40,"nRetries":3,"hkSettings":{"epsilon":1.0E-7,"kickFinal":false,"fdDelta":1.0E-4,"kickAll":false,"maxIters":200,"evCutoff":1.0E-9}},"modelSettings":{"enrichmentModel":[{"variationsOptimized":false,"bindingSaturation":false,"cumulativeEnrichment":true,"concentration":1,"modelType":"SELEX","bindingModeInteractions":[],"componentName":"SELEX enrichment model 0","freezingLevel":0,"includeComponent":true,"bindingModes":[0,1,2],"variationDescription":[],"modifications":[]},{"variationsOptimized":false,"bindingSaturation":false,"cumulativeEnrichment":true,"concentration":1,"modelType":"SELEX","bindingModeInteractions":[],"componentName":"SELEX enrichment model 1","freezingLevel":0,"includeComponent":true,"bindingModes":[0,1,2],"variationDescription":[],"modifications":[]}],"letterOrder":"ACGT","countTable":[{"leftFlank":"ACACTCTTTCCCTACACGACGCTCTTCCGATCTTGACGTC","variationsOptimized":true,"transliterate":{"in":[],"out":[]},"variableRegionLength":30,"countTableFile":"jobs/133d27f6506e/countTable.0.tsv.gz","modeledColumns":[0,1],"inputFileType":"tsv.gz","nColumns":2,"rightFlank":"GACGTCAGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG","componentName":"Count table 0","freezingLevel":0,"includeComponent":true,"variationDescription":[]},{"leftFlank":"CGGAGTCGGCAAGCAGAAGACGGCATACGATAGC","variationsOptimized":true,"transliterate":{"in":[],"out":[]},"variableRegionLength":20,"countTableFile":"jobs/133d27f6506e/countTable.1.tsv.gz","modeledColumns":[0,1,2,3,4],"inputFileType":"tsv.gz","nColumns":5,"rightFlank":"TCGCTAGATCGGAAGAGCGTCG","componentName":"Count table 1","freezingLevel":0,"includeComponent":true,"variationDescription":[]}],"bindingModeInteractions":[],"bindingModes":[{"variationsOptimized":true,"fitLogActivity":true,"flankLength":0,"singleStrand":true,"variationName":"1;0;0","size":1,"dinucleotideDistance":0,"componentName":"Binding mode 0","freezingLevel":0,"positionBias":true,"includeComponent":true,"variationDescription":[{"variationName":"1;0;0","descriptionString":"Initial 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