Status
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Terminal Output
Builder file created | |
Configuration file | |
ProBound run | |
Sequence logos |
Terminal output
Pipeline Output:
> Converts the configuration file to work on run server, checks input OK > Builds configuration file OK > Runs ProBound OK > Runs Model Viewer OK
Configuration Builder File
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ProBound builder configuration file:
[{"function": "optimizerSetting", "nThreads": 20, "lambdaL2": 1e-06}, {"function": "addTable", "leftFlank": "GTTCAGAGTTCTACAGTCCGACGATC", "countTableFile": "/public_html/public/jobs/95360d4ae086/countTable.0.tsv.gz", "modeledColumns": [0, 1, 2, 3], "nColumns": 4, "rightFlank": "CCCGGGTCGTATGCCGTCTTCTGCTTG", "inputFileType": "tsv.gz", "variableRegionLength": 30}, {"function": "addTable", "leftFlank": "GTTCAGAGTTCTACAGTCCGACGATCTGG", "countTableFile": "/public_html/public/jobs/95360d4ae086/countTable.1.tsv.gz", "modeledColumns": [0, 1, 2, 3], "nColumns": 4, "rightFlank": "CCAGCTGTCGTATGCCGTCTTCTGCTTG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "GTTCAGAGTTCTACAGTCCGACGATCTGG", "countTableFile": "/public_html/public/jobs/95360d4ae086/countTable.2.tsv.gz", "modeledColumns": [0, 1, 2], "nColumns": 3, "rightFlank": "CCAGCTGTCGTATGCCGTCTTCTGCTTG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "TGGGCCTGG", "countTableFile": "/public_html/public/jobs/95360d4ae086/countTable.3.tsv.gz", "modeledColumns": [0, 1], "nColumns": 2, "rightFlank": "CCAGG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addTable", "leftFlank": "GTTCAGAGTTCTACAGTCCGACGATCTGG", "countTableFile": "/public_html/public/jobs/95360d4ae086/countTable.4.tsv.gz", "modeledColumns": [0, 1], "nColumns": 2, "rightFlank": "CCACGTCTCGTATGCCGTCTTCTGCTTG", "inputFileType": "tsv.gz", "variableRegionLength": 16}, {"function": "addSELEX", "bindingModes": [0, 1, 2, 3, 4], "bindingModeInteractions": [-1]}, {"function": "addSELEX", "bindingModes": [0, 1, 2, 3], "bindingModeInteractions": []}, {"function": "addSELEX", "bindingModes": [0, 3], "bindingModeInteractions": []}, {"function": "addSELEX", "bindingModes": [0, 2], "bindingModeInteractions": []}, {"function": "addSELEX", "bindingModes": [0, 4], "bindingModeInteractions": []}, {"function": "addNS"}, {"function": "addBindingMode", "flankLength": 7, "size": 13}, {"function": "addBindingMode", "flankLength": 5, "size": 8}, {"function": "addBindingMode", "flankLength": 5, "size": 8}, {"function": "addBindingMode", "flankLength": 5, "size": 8}, {"function": "bindingModeSeed", "index": 1, "mononucleotideIUPAC": "NATGATTTATGAN"}, {"function": "bindingModeSeed", "index": 2, "mononucleotideIUPAC": "NTTGAYRN"}, {"function": "bindingModeSeed", "index": 3, "mononucleotideIUPAC": "NTTATGGN"}, {"function": "bindingModeSeed", "index": 4, "mononucleotideIUPAC": "NNTGAYRN"}, {"function": "addInteraction", "bindingModes": [1, 4], "positionBias": false, "maxOverlap": 7}, {"function": "interactionConstraints", "index": 0, "experimentSpecificInteraction": true}, {"function": "output", "outputPath": "/public_html/public/jobs/95360d4ae086", "baseName": "fit", "storeHessian": false, "printTrajectory": false}]
Configuration File
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ProBound configuration file:
{ "modelSeeding": {"bindingModes": [ {"seedScale": 1}, { "mononucleotideIUPAC": "NATGATTTATGAN", "seedScale": 1 }, { "mononucleotideIUPAC": "NTTGAYRN", "seedScale": 1 }, { "mononucleotideIUPAC": "NTTATGGN", "seedScale": 1 }, { "mononucleotideIUPAC": "NNTGAYRN", "seedScale": 1 } ]}, "optimizerSetting": { "nThreads": 20, "likelihoodThreshold": 0, "lambdaL2": 1.0E-6, "patternSearchSettings": {}, "pseudocount": 0, "minimizerType": "lbfgs", "nRetries": 3, "hkSettings": {}, "output": { "storeHessian": false, "outputPath": "/public_html/public/jobs/95360d4ae086", "printTrajectory": false, "baseName": "fit", "printPSAM": false, "verbose": true }, "lbfgsSettings": {}, "sgdSettings": {}, "fixedLibrarySize": false, "expBound": 40, "slbfgs_plsSettings": {}, "slbfgsSettings": {} }, "modelSettings": { "enrichmentModel": [ { "r0KUsed": 1, "round": 1, "bindingSaturation": false, "concentration": 1, "modelType": "SELEX", "bindingModeInteractions": [-1], "r0KsTested": [1], "bindingModes": [ 0, 1, 2, 3, 4 ], "modifications": [] }, { "r0KUsed": 1, "round": 1, "bindingSaturation": false, "concentration": 1, "modelType": "SELEX", "bindingModeInteractions": [], "r0KsTested": [1], "bindingModes": [ 0, 1, 2, 3 ], "modifications": [] }, { "r0KUsed": 1, "round": 1, "bindingSaturation": false, "concentration": 1, "modelType": "SELEX", "bindingModeInteractions": [], "r0KsTested": [1], "bindingModes": [ 0, 3 ], "modifications": [] }, { "r0KUsed": 1, "round": 1, "bindingSaturation": false, "concentration": 1, "modelType": "SELEX", "bindingModeInteractions": [], "r0KsTested": [1], "bindingModes": [ 0, 2 ], "modifications": [] }, { "r0KUsed": 1, "round": 1, "bindingSaturation": false, "concentration": 1, "modelType": "SELEX", "bindingModeInteractions": [], "r0KsTested": [1], "bindingModes": [ 0, 4 ], "modifications": [] } ], "countTable": [ { "leftFlank": "GTTCAGAGTTCTACAGTCCGACGATC", "transliterate": { "in": [], "out": [] }, "variableRegionLength": 30, "modeledColumns": [ 0, 1, 2, 3 ], "inputFileType": "tsv.gz", "nColumns": 4, "rightFlank": "CCCGGGTCGTATGCCGTCTTCTGCTTG", "countTableFile": "/public_html/public/jobs/95360d4ae086/countTable.0.tsv.gz" }, { "leftFlank": "GTTCAGAGTTCTACAGTCCGACGATCTGG", "transliterate": { "in": [], "out": [] }, "variableRegionLength": 16, "modeledColumns": [ 0, 1, 2, 3 ], "inputFileType": "tsv.gz", "nColumns": 4, "rightFlank": "CCAGCTGTCGTATGCCGTCTTCTGCTTG", "countTableFile": "/public_html/public/jobs/95360d4ae086/countTable.1.tsv.gz" }, { "leftFlank": "GTTCAGAGTTCTACAGTCCGACGATCTGG", "transliterate": { "in": [], "out": [] }, "variableRegionLength": 16, "modeledColumns": [ 0, 1, 2 ], "inputFileType": "tsv.gz", "nColumns": 3, "rightFlank": "CCAGCTGTCGTATGCCGTCTTCTGCTTG", "countTableFile": "/public_html/public/jobs/95360d4ae086/countTable.2.tsv.gz" }, { "leftFlank": "TGGGCCTGG", "transliterate": { "in": [], "out": [] }, "variableRegionLength": 16, "modeledColumns": [ 0, 1 ], "inputFileType": "tsv.gz", "nColumns": 2, "rightFlank": "CCAGG", "countTableFile": "/public_html/public/jobs/95360d4ae086/countTable.3.tsv.gz" }, { "leftFlank": "GTTCAGAGTTCTACAGTCCGACGATCTGG", "transliterate": { "in": [], "out": [] }, "variableRegionLength": 16, "modeledColumns": [ 0, 1 ], "inputFileType": "tsv.gz", "nColumns": 2, "rightFlank": "CCACGTCTCGTATGCCGTCTTCTGCTTG", "countTableFile": "/public_html/public/jobs/95360d4ae086/countTable.4.tsv.gz" } ], "bindingModeInteractions": [{ "fitLogActivity": true, "maxSpacing": -1, "positionBias": false, "bindingModes": [ 1, 4 ], "maxOverlap": 7 }], "bindingModes": [ { "size": 0, "fitLogActivity": true, "flankLength": 0, "dinucleotideDistance": 0, "positionBias": false, "singleStrand": false, "modifications": [] }, { "size": 13, "fitLogActivity": true, "flankLength": 7, "dinucleotideDistance": 0, "positionBias": false, "singleStrand": false, "modifications": [] }, { "size": 8, "fitLogActivity": true, "flankLength": 5, "dinucleotideDistance": 0, "positionBias": false, "singleStrand": false, "modifications": [] }, { "size": 8, "fitLogActivity": true, "flankLength": 5, "dinucleotideDistance": 0, "positionBias": false, "singleStrand": false, "modifications": [] }, { "size": 8, "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 }, { "fitDelta": [false], "roundSpecificGamma": true, "fitRho": false, "roundSpecificDelta": true, "fitGamma": false, "trySaturation": false, "roundSpecificRho": true }, { "fitDelta": [false], "roundSpecificGamma": true, "fitRho": false, "roundSpecificDelta": true, "fitGamma": false, "trySaturation": false, "roundSpecificRho": true }, { "fitDelta": [false], "roundSpecificGamma": true, "fitRho": false, "roundSpecificDelta": true, "fitGamma": false, "trySaturation": false, "roundSpecificRho": true } ], "nShifts": 0, "countTable": [ {}, {}, {}, {}, {} ], "addBindingModesSequentially": true, "bindingModeInteractions": [{ "experimentSpecificInteraction": true, "experimentSpecificActivity": true, "roundSpecificActivity": true }], "flankLengths": [0], "singleModeLengthSweep": false, "bindingModes": [ { "maxFlankLength": -1, "positionBiasBinWidth": 1, "optimizeSizeHeuristic": false, "maxSize": -1, "optimizeFlankLength": false, "symmetryString": "null", "roundSpecificActivity": true, "informationThreshold": 0.1, "optimizeMotifShift": false, "fittingStages": [], "optimizeMotifShiftHeuristic": false, "experimentSpecificPositionBias": true, "minSize": -1, "experimentSpecificActivity": true, "optimizeSize": false }, { "maxFlankLength": -1, "positionBiasBinWidth": 1, "optimizeSizeHeuristic": false, "maxSize": -1, "optimizeFlankLength": false, "symmetryString": "null", "roundSpecificActivity": true, "informationThreshold": 0.1, "optimizeMotifShift": false, "fittingStages": [], "optimizeMotifShiftHeuristic": false, "experimentSpecificPositionBias": true, "minSize": -1, "experimentSpecificActivity": true, "optimizeSize": false }, { "maxFlankLength": -1, "positionBiasBinWidth": 1, "optimizeSizeHeuristic": false, "maxSize": -1, "optimizeFlankLength": false, "symmetryString": "null", "roundSpecificActivity": true, "informationThreshold": 0.1, "optimizeMotifShift": false, "fittingStages": [], "optimizeMotifShiftHeuristic": false, "experimentSpecificPositionBias": true, "minSize": -1, "experimentSpecificActivity": true, "optimizeSize": false }, { "maxFlankLength": -1, "positionBiasBinWidth": 1, "optimizeSizeHeuristic": false, "maxSize": -1, "optimizeFlankLength": false, "symmetryString": "null", "roundSpecificActivity": true, "informationThreshold": 0.1, "optimizeMotifShift": false, "fittingStages": [], "optimizeMotifShiftHeuristic": false, "experimentSpecificPositionBias": true, "minSize": -1, "experimentSpecificActivity": true, "optimizeSize": false }, { "maxFlankLength": -1, "positionBiasBinWidth": 1, "optimizeSizeHeuristic": false, "maxSize": -1, "optimizeFlankLength": false, "symmetryString": "null", "roundSpecificActivity": true, "informationThreshold": 0.1, "optimizeMotifShift": false, "fittingStages": [], "optimizeMotifShiftHeuristic": false, "experimentSpecificPositionBias": true, "minSize": -1, "experimentSpecificActivity": true, "optimizeSize": false } ] } }
Probound Text Output
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Output from ProBound:
> Reading configuration JSON object and validating general schema. > Validating configuration schema. {"enrichmentModel":[{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"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,"bindingModeInteractions":[{"experimentSpecificInteraction":true,"experimentSpecificActivity":true,"roundSpecificActivity":true}],"flankLengths":[0],"singleModeLengthSweep":false,"bindingModes":[{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false}]} Entry=bindingModes, aEntry=[{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false},{"maxFlankLength":-1,"positionBiasBinWidth":1,"optimizeSizeHeuristic":false,"maxSize":-1,"optimizeFlankLength":false,"symmetryString":"null","roundSpecificActivity":true,"informationThreshold":0.1,"optimizeMotifShift":false,"fittingStages":[],"optimizeMotifShiftHeuristic":false,"experimentSpecificPositionBias":true,"minSize":-1,"experimentSpecificActivity":true,"optimizeSize":false}] Entry=bindingModeInteractions, aEntry=[{"experimentSpecificInteraction":true,"experimentSpecificActivity":true,"roundSpecificActivity":true}] Entry=countTable, aEntry=[{},{},{},{},{}] Entry=enrichmentModel, aEntry=[{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true},{"fitDelta":[false],"roundSpecificGamma":true,"fitRho":false,"roundSpecificDelta":true,"fitGamma":false,"trySaturation":false,"roundSpecificRho":true}] > Builds likelihood object. >> Creating CombinedLikelihood object. Alphabet ======== Letter Complement: C-G,A-T Letter Order: ACGT Optimizer settings: =================== lambdaL2 = 1.0E-6 pseudocount = 0.0 expBound = 40.0 fixedLibrarySize = false >> Determining fitting order. Summary of experiments ====================== Experiment 0: ------------- Count table: Count table 0 Enrichment model: SELEX enrichment model 0 Concentration: 1.0 Binding modes: Binding mode 0 Binding mode 1 Binding mode 2 Binding mode 3 Binding mode 4 Binding mode interactions: Binding mode interaction 0 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 3 Binding mode interactions: NONE Experiment 2: ------------- Count table: Count table 2 Enrichment model: SELEX enrichment model 2 Concentration: 1.0 Binding modes: Binding mode 0 Binding mode 3 Binding mode interactions: NONE Experiment 3: ------------- Count table: Count table 3 Enrichment model: SELEX enrichment model 3 Concentration: 1.0 Binding modes: Binding mode 0 Binding mode 2 Binding mode interactions: NONE Experiment 4: ------------- Count table: Count table 4 Enrichment model: SELEX enrichment model 4 Concentration: 1.0 Binding modes: Binding mode 0 Binding mode 4 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 07:15:13.236). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[0,1,2,3]},{"h":[4,5,6,7]},{"h":[8,9,10]},{"h":[11,12]},{"h":[13,14]}],"bindingModeInteractions":[{}],"bindingModes":[{},{},{},{},{}]} Value and gradient before optimization: ======================================= value = 33.5190647680196 gradient = {0.7492,-0.2492,-0.2500,-0.2500,0.7485,-0.2485,-0.2500,-0.2500,0.6652,-0.3319,-0.3333,0.4985,-0.4985,0.4985,-0.4985} gradient norm = 1.7757579408116433 Starting Function Value: 33.5190647680196 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 24.724530287194536 5.000000000000001 2.815699079861446 1.718899031429035 2 6 14.808615706844755 17.238941763050715 0.086652558693423 1.608875483185539 3 8 11.569907253965678 5.858776958438730 0.423019013542229 1.319534370451339 4 9 9.053155589258200 6.659933348249434 1.000000000000000 1.084172901211286 5 10 7.064829985765493 2.477301282771641 1.000000000000000 0.565383031184155 6 11 5.988598467317167 4.427693084026856 1.000000000000000 0.652424464135747 7 12 5.492497452852487 2.358917509063844 1.000000000000000 0.394934832287524 8 14 5.289176612975783 1.074702105658214 0.477338581992685 0.133923695743116 9 15 5.266101938202641 0.425465394854886 1.000000000000000 0.062111071450719 10 16 5.260425501843010 0.297636696961352 1.000000000000000 0.031466296209898 11 17 5.258905128206733 0.095130377458612 1.000000000000000 0.005932999402124 12 18 5.258845270041054 0.017249945453733 1.000000000000000 0.001657693482835 13 19 5.258840275185509 0.006309421892579 1.000000000000000 0.000218356936022 14 20 5.258840203300408 0.000794523137402 1.000000000000000 0.000036099218216 15 21 5.258840200904013 0.000128844948309 1.000000000000000 0.000003863165533 16 22 5.258840200877246 0.000128844948309 1.000000000000000 0.000000377774682 Convergence criteria met. After: gradient norm = 3.7777468203046986E-7 >>> Parameters after optimization Count Table 0: --------------- h: {-10.6842,-3.5614,3.5614,10.6842} Count Table 1: --------------- h: {-9.7831,-3.2610,3.2610,9.7831} Count Table 2: --------------- h: {-6.5221,0.0000,6.5221} Count Table 3: --------------- h: {-3.2610,3.2610} Count Table 4: --------------- h: {-3.2610,3.2610} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-7.1229,-7.1229,-7.1229,-7.1229} Activity(exp=1): {-6.5221,-6.5221,-6.5221,-6.5221} Activity(exp=2): {-6.5221,-6.5221,-6.5221} Activity(exp=3): {-6.5221,-6.5221} Activity(exp=4): {-6.5221,-6.5221} Binding mode 1: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=0, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} > Initial optimization (component0-1-f0). >> Starting new optimization: component0-1-f0. (2021-05-22 07:15:17.077). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[15,16,17,18]},{"h":[19,20,21,22]},{"h":[23,24,25]},{"h":[26,27]},{"h":[28,29]}],"bindingModeInteractions":[{}],"bindingModes":[{"mononucleotide":[],"activity":[[0,1,2,3],[4,5,6,7],[8,9,10],[11,12],[13,14]]},{},{},{},{}]} Value and gradient before optimization: ======================================= value = 5.258840200877299 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} gradient norm = 1.0508558587174843E-4 Starting Function Value: 5.258840200877299 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 5.258840185850437 0.000281877696794 2.682363089624208 0.000095352392971 2 5 5.258840117276647 0.000982932238824 5.000000000000000 0.000103553176034 3 6 5.258831702144668 0.164186718259613 1.000000000000000 0.001791091732887 4 7 5.258819168578869 0.284482876597563 1.000000000000000 0.003201360567622 5 8 5.258774631506808 1.102245991455320 1.000000000000000 0.006293547025440 6 9 5.258675841393114 2.612931538787008 1.000000000000000 0.010317786599107 7 10 5.258452809328825 6.266260022310130 1.000000000000000 0.015160886241525 8 11 5.258089794439004 11.036688913550213 1.000000000000000 0.017332931080597 9 13 5.258023226372461 3.012220535091698 0.226329083838411 0.018093716023094 10 14 5.257698971769224 10.205114815451880 1.000000000000000 0.010961049547347 11 15 5.257587990900769 2.530854790775075 1.000000000000000 0.002952369197704 12 16 5.257575746776673 1.124690069613388 1.000000000000000 0.000335534482697 13 17 5.257575379181535 0.487058571494216 1.000000000000000 0.000090128006027 14 18 5.257575376730845 0.054624340346018 1.000000000000000 0.000075556680542 15 19 5.257575372037372 0.015638931226227 1.000000000000000 0.000002767823055 16 20 5.257575372028012 0.000686381685266 1.000000000000000 0.000000523819420 17 21 5.257575372027906 0.000686381685266 1.000000000000000 0.000000083855629 Convergence criteria met. After: gradient norm = 8.385562902127627E-8 >>> Parameters after optimization Count Table 0: --------------- h: {-0.0000,-0.0000,0.0000,0.0000} Count Table 1: --------------- h: {-0.0000,-0.0000,0.0000,0.0000} Count Table 2: --------------- h: {-0.0000,0.0000,0.0000} Count Table 3: --------------- h: {-0.0000,0.0000} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=1): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=0, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=0, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Suggested variations: key=0;0;0, description = Initial model. > Optimizing variation "Initial model." (component0-2-variation0). >> Starting new optimization: component0-2-variation0. (2021-05-22 07:15:21.104). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[15,16,17,18]},{"h":[19,20,21,22]},{"h":[23,24,25]},{"h":[26,27]},{"h":[28,29]}],"bindingModeInteractions":[{}],"bindingModes":[{"mononucleotide":[],"activity":[[0,1,2,3],[4,5,6,7],[8,9,10],[11,12],[13,14]]},{},{},{},{}]} Value and gradient before optimization: ======================================= value = 5.257575372027906 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} gradient norm = 8.385562902168628E-8 Already at minimum! After: gradient norm = 8.385562902168628E-8 >>> Parameters after optimization Count Table 0: --------------- h: {-0.0000,-0.0000,0.0000,0.0000} Count Table 1: --------------- h: {-0.0000,-0.0000,0.0000,0.0000} Count Table 2: --------------- h: {-0.0000,0.0000,0.0000} Count Table 3: --------------- h: {-0.0000,0.0000} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=1): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=0, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=0, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} The Likelihood DID NOT improve. Discarding fit component0-2-variation0. > No varitions possible for Binding mode 0. > Optimizing the full model (component0-4-all). >> Starting new optimization: component0-4-all. (2021-05-22 07:15:21.266). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[15,16,17,18]},{"h":[19,20,21,22]},{"h":[23,24,25]},{"h":[26,27]},{"h":[28,29]}],"bindingModeInteractions":[{}],"bindingModes":[{"mononucleotide":[],"activity":[[0,1,2,3],[4,5,6,7],[8,9,10],[11,12],[13,14]]},{},{},{},{}]} Value and gradient before optimization: ======================================= value = 5.257575372027905 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} gradient norm = 8.385562902106475E-8 Already at minimum! After: gradient norm = 8.385562902106475E-8 >>> Parameters after optimization Count Table 0: --------------- h: {-0.0000,-0.0000,0.0000,0.0000} Count Table 1: --------------- h: {-0.0000,-0.0000,0.0000,0.0000} Count Table 2: --------------- h: {-0.0000,0.0000,0.0000} Count Table 3: --------------- h: {-0.0000,0.0000} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=1): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} ================================== == Starts fiting Binding mode 1 == ================================== > Optimizing h (component1-0-h). >> Starting new optimization: component1-0-h. (2021-05-22 07:15:23.987). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[0,1,2,3]},{"h":[4,5,6,7]},{"h":[8,9,10]},{"h":[11,12]},{"h":[13,14]}],"bindingModeInteractions":[{}],"bindingModes":[{},{},{},{},{}]} Value and gradient before optimization: ======================================= value = 7.179905587574487 gradient = {-0.2407,-0.2177,-0.1136,0.5721,-0.2269,-0.1956,-0.0905,0.5131,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000} gradient norm = 0.898170625561755 Starting Function Value: 7.179905587574487 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 2 6.371811549495428 1.000000000000000 1.113374198109136 0.718477476095855 2 3 4.734346338242012 5.407374096840854 1.000000000000000 0.253820742841365 3 4 4.623935561355221 1.144153922671467 1.000000000000000 0.104485081749095 4 5 4.602255027063590 0.393684468272018 1.000000000000000 0.036514428592046 5 6 4.599629481910919 0.153221202391060 1.000000000000000 0.003056011927478 6 7 4.599607520993157 0.013926707152032 1.000000000000000 0.000474365137864 7 8 4.599606873637706 0.002330768438465 1.000000000000000 0.000103082681464 8 9 4.599606839676333 0.000662682694066 1.000000000000000 0.000006159548032 9 10 4.599606839604645 0.000037739463913 1.000000000000000 0.000002515841848 10 11 4.599606839591776 0.000037739463913 1.000000000000000 0.000000127441746 Convergence criteria met. After: gradient norm = 1.2744174596755667E-7 >>> Parameters after optimization Count Table 0: --------------- h: {2.6871,1.1385,-0.7363,-3.0893} Count Table 1: --------------- h: {2.2894,1.1041,-0.5461,-2.8474} Count Table 2: --------------- h: {-0.0000,-0.0000,0.0000} Count Table 3: --------------- h: {-0.0000,0.0000} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=1): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {4.0414,4.0414,4.0414,4.0414} Activity(exp=1): {4.0160,4.0160,4.0160,4.0160} Activity(exp=2): {4.0160,4.0160,4.0160} Activity(exp=3): {4.0160,4.0160} Activity(exp=4): {4.0160,4.0160} Binding mode 2: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} > Initial optimization (component1-1-f0). >> Starting new optimization: component1-1-f0. (2021-05-22 07:15:32.994). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[67,68,69,70]},{"h":[71,72,73,74]},{"h":[75,76,77]},{"h":[78,79]},{"h":[80,81]}],"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],"activity":[[52,53,54,55],[56,57,58,59],[60,61,62],[63,64],[65,66]]},{},{},{}]} Value and gradient before optimization: ======================================= value = 4.59960683959178 gradient = {-0.0320,0.0119,-0.0163,-0.0088,0.0090,0.0158,-0.0466,-0.0234,-0.0014,0.0183,0.0248,-0.0869,-0.0238,0.0147,-0.0388,0.0027,-0.1019,0.0205,0.0247,0.0115,0.0026,0.0129,0.0172,-0.0778,0.0035,0.0254,0.0195,-0.0935,0.0005,0.0208,0.0076,-0.0740,-0.0937,0.0238,0.0126,0.0121,0.0146,0.0003,0.0241,-0.0842,-0.0041,0.0055,0.0156,-0.0622,0.0081,0.0206,-0.0637,-0.0102,0.0049,-0.0526,-0.0005,0.0031,0.0000,-0.0089,-0.0079,-0.0020,0.0000,-0.0082,-0.0167,-0.0014,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-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 = 0.2807754832361925 Starting Function Value: 4.59960683959178 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 4.585220328491374 0.096246642468549 0.342788627266239 0.262144114137500 2 4 4.571392825334806 0.076483652225355 1.000000000000000 0.264730500761795 3 5 4.454294928703026 1.296608053720558 1.000000000000000 0.528902402682481 4 6 4.418233147031716 0.174871743823965 1.000000000000000 0.177358435630455 5 7 4.402239707182408 0.382893405030854 1.000000000000000 0.076671705104793 6 8 4.397706815866339 0.201543080278423 1.000000000000000 0.094081917081382 7 9 4.382992251999465 0.436248745277553 1.000000000000000 0.091584287140324 8 10 4.359729614030497 1.006874464840633 1.000000000000000 0.029727029599423 9 11 4.355494616558189 0.341302896971599 1.000000000000000 0.025146330918814 10 12 4.352130529784157 0.330661573307207 1.000000000000000 0.025333851712631 11 13 4.347000494901533 0.777276221729967 1.000000000000000 0.033134383910591 12 14 4.344731177728834 0.466775918055848 1.000000000000000 0.030199975084737 13 15 4.342763015104795 0.158755170532617 1.000000000000000 0.018986473881987 14 16 4.341750872559274 0.146776028126144 1.000000000000000 0.017322381274369 15 17 4.340262899230308 0.269429368352579 1.000000000000000 0.015928382552438 16 18 4.338024704798380 0.585371036490120 1.000000000000000 0.020678669518708 17 19 4.336400795084735 0.495285505708018 1.000000000000000 0.018769538827268 18 20 4.335297422730525 0.522731521455624 1.000000000000000 0.017416993364388 19 21 4.334608238611507 0.389180776058969 1.000000000000000 0.013051118495601 20 22 4.334099358568778 0.130087750992597 1.000000000000000 0.010268598637658 21 23 4.333113607371740 0.371625922426176 1.000000000000000 0.018876473727269 22 24 4.332402141292755 0.298119586666261 1.000000000000000 0.017803986324901 23 25 4.330960761343996 0.664170999728336 1.000000000000000 0.011812428338343 24 26 4.330278008931260 0.254015553830982 1.000000000000000 0.008616043088886 25 27 4.329920081495432 0.112755839249704 1.000000000000000 0.006705527262480 26 28 4.329670242187741 0.126302281943518 1.000000000000000 0.006681930719145 27 29 4.329288399113212 0.181273002957343 1.000000000000000 0.009652015680920 28 30 4.328955205692085 0.206838065654458 1.000000000000000 0.006384096012374 29 31 4.328753468873677 0.158977357191451 1.000000000000000 0.005245852753854 30 32 4.328493809311702 0.213538103132960 1.000000000000000 0.003882252577588 31 33 4.328370382301996 0.117757000914932 1.000000000000000 0.004755677745339 32 35 4.328322821209649 0.062131720419336 0.470673184473747 0.004506157785086 33 36 4.328279408706489 0.040772663645822 1.000000000000000 0.002374304082216 34 37 4.328246382252760 0.036143938426673 1.000000000000000 0.002489182167952 35 38 4.328219712497656 0.040699303796533 1.000000000000000 0.003274925439362 36 39 4.328188609230717 0.047620175483501 1.000000000000000 0.003272834320608 37 40 4.328132648116360 0.094488220670320 1.000000000000000 0.002471518859321 38 41 4.328066706473061 0.136283061759893 1.000000000000000 0.002454757133217 39 42 4.328000058086950 0.203120375938646 1.000000000000000 0.002907856452009 40 43 4.327938241678906 0.111393299610635 1.000000000000000 0.001711292706403 41 44 4.327887169505016 0.097944530500441 1.000000000000000 0.001192615293627 42 45 4.327854475242822 0.079118734226882 1.000000000000000 0.001237328140958 43 46 4.327841678090008 0.139552151376603 1.000000000000000 0.003893171691722 44 47 4.327812807548557 0.032649656619644 1.000000000000000 0.001680842973272 45 48 4.327804828007072 0.020192511901707 1.000000000000000 0.000829898290896 46 49 4.327798759185852 0.018108982875609 1.000000000000000 0.000644627851374 47 50 4.327792635189402 0.028721733123927 1.000000000000000 0.000745012156141 48 51 4.327783460092036 0.045038617535444 1.000000000000000 0.000784243565960 49 52 4.327779188089998 0.044963076842748 1.000000000000000 0.001324731379940 50 53 4.327775846348211 0.024550633070176 1.000000000000000 0.000479204309106 51 54 4.327774750403020 0.011624391655361 1.000000000000000 0.000282270088032 52 55 4.327773677465797 0.007795333203138 1.000000000000000 0.000277512534691 53 56 4.327772528458246 0.011732087495439 1.000000000000000 0.000293158609687 54 57 4.327770778112432 0.020601890163460 1.000000000000000 0.000292861262552 55 58 4.327769485740583 0.050004934763884 1.000000000000000 0.000738483321469 56 59 4.327767402493947 0.010357622530141 1.000000000000000 0.000309707817919 57 60 4.327766712602823 0.006497950995006 1.000000000000000 0.000236302601617 58 61 4.327766255372580 0.010210615946478 1.000000000000000 0.000151101586778 59 62 4.327766023527947 0.007668879817877 1.000000000000000 0.000110352906693 60 63 4.327765883075994 0.005272235380749 1.000000000000000 0.000093457181680 61 64 4.327765788557989 0.003097268099350 1.000000000000000 0.000135837523769 62 65 4.327765636402919 0.005556914815344 1.000000000000000 0.000147518612868 63 66 4.327765415953544 0.009312706094948 1.000000000000000 0.000212402748383 64 67 4.327765263032549 0.008499303873574 1.000000000000000 0.000089203426274 65 68 4.327765175098885 0.004999590660504 1.000000000000000 0.000083852864862 66 69 4.327765030889220 0.007412773907897 1.000000000000000 0.000172250704622 67 70 4.327764782342713 0.014744044124366 1.000000000000000 0.000322681963339 68 71 4.327764525270216 0.015813174697309 1.000000000000000 0.000402503335029 69 72 4.327764107249338 0.025324998004226 1.000000000000000 0.000336745193194 70 73 4.327763448490032 0.039427437087184 1.000000000000000 0.000214590149788 71 74 4.327762511543608 0.059366308921120 1.000000000000000 0.000292663451098 72 75 4.327761609795682 0.058238669524979 1.000000000000000 0.000605184230677 73 76 4.327760572249302 0.062910020652168 1.000000000000000 0.000827999381992 74 77 4.327758886156325 0.095928424979536 1.000000000000000 0.000883778463743 75 78 4.327753880770946 0.293135443289308 1.000000000000000 0.001076007709655 76 79 4.327744223148477 0.604147987853931 1.000000000000000 0.000799722765652 77 80 4.327729756981562 0.966719236408216 1.000000000000000 0.000697178434938 78 81 4.327709972407397 1.283280925697541 1.000000000000000 0.001390330788054 79 82 4.327686766532854 1.400789927652055 1.000000000000000 0.002307436184983 80 83 4.327659359016474 1.591667952791110 1.000000000000000 0.002904258719851 81 84 4.327622978278692 2.171079325719652 1.000000000000000 0.002358117031862 82 85 4.327592097176026 3.171669038167698 1.000000000000000 0.002578584452844 83 86 4.327565536764620 1.095380618342105 1.000000000000000 0.000844023483775 84 87 4.327554938612847 0.029569325456883 1.000000000000000 0.001298327683806 85 88 4.327544232711822 0.278041258948696 1.000000000000000 0.001572226270577 86 89 4.327532599018017 0.722363336620085 1.000000000000000 0.001184898408415 87 90 4.327521184937787 1.171334814868767 1.000000000000000 0.000454653138137 88 91 4.327517482582386 0.472385409168820 1.000000000000000 0.000542279505015 89 92 4.327515058179725 0.215842653800347 1.000000000000000 0.000822015948979 90 93 4.327512490143279 0.104106547128509 1.000000000000000 0.000858536229912 91 94 4.327509283395542 0.101799065580414 1.000000000000000 0.000401014379167 92 95 4.327508322334181 0.017549012430496 1.000000000000000 0.000156426293481 93 96 4.327507987678525 0.021814291295471 1.000000000000000 0.000203696319046 94 97 4.327507673938785 0.011663555835485 1.000000000000000 0.000267640298882 95 98 4.327507363516786 0.029506101965360 1.000000000000000 0.000246603283195 96 99 4.327507182943874 0.061381017881679 1.000000000000000 0.000109596735043 97 100 4.327507139795645 0.007733136147464 1.000000000000000 0.000035872793900 98 101 4.327507125812858 0.003762758633661 1.000000000000000 0.000045261514870 99 102 4.327507113290675 0.001319520592652 1.000000000000000 0.000056359849519 100 103 4.327507097954371 0.002818122316205 1.000000000000000 0.000051490885948 101 104 4.327507082645912 0.004211359505908 1.000000000000000 0.000031495749140 102 105 4.327507077422561 0.001668114089796 1.000000000000000 0.000019101885888 103 106 4.327507076282396 0.000658238668414 1.000000000000000 0.000007767581095 104 107 4.327507075977792 0.000698762965202 1.000000000000000 0.000007112415724 105 108 4.327507075949031 0.001516177236876 1.000000000000000 0.000022152658385 106 109 4.327507075578326 0.002232562808774 1.000000000000000 0.000005246078562 107 110 4.327507075478773 0.000439616226643 1.000000000000000 0.000003766001120 108 111 4.327507075303315 0.000946433700774 1.000000000000000 0.000007272889092 109 112 4.327507075244024 0.000701900330211 1.000000000000000 0.000003192503871 110 113 4.327507075195907 0.000199962555338 1.000000000000000 0.000002561457016 111 114 4.327507075168356 0.000379984359940 1.000000000000000 0.000001213044334 112 115 4.327507075158843 0.000379984359940 1.000000000000000 0.000000628780078 Convergence criteria met. After: gradient norm = 6.287800776085914E-7 >>> Parameters after optimization Count Table 0: --------------- h: {2.9702,0.6016,-1.1394,-2.4324} Count Table 1: --------------- h: {2.3146,1.6854,-1.3784,-2.6217} Count Table 2: --------------- h: {-0.0000,-0.0000,0.0000} Count Table 3: --------------- h: {-0.0000,0.0000} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=1): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {-0.5572,-0.7732,-0.5802,-0.5718,-0.1347,-1.1806,-0.5298,-0.6371,-0.4298,-1.2692,-1.5186,0.7353,-0.4204,-1.6366,0.4921,-0.9174,1.1525,-1.3427,-1.3708,-0.9213,-1.1909,-0.8108,-1.0806,0.6001,-0.4051,-1.9655,-1.0675,0.9558,-0.8223,-2.0037,-0.2070,0.5506,1.2336,-1.4862,-0.8134,-1.4163,-1.5423,-0.0573,-1.6777,0.7950,-0.7272,-1.4026,0.0008,-0.3533,-0.0969,-1.4440,-0.2279,-0.7134,-0.9428,-0.3431,-0.5980,-0.5983} Activity(exp=0): {0.0000,2.3740,-0.3724,-2.5337} Activity(exp=1): {0.0000,0.1649,1.0118,-3.1267} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Suggested variations: key=13;7;0, description = Initial model. > Optimizing variation "Initial model." (component1-2-variation0). >> Starting new optimization: component1-2-variation0. (2021-05-22 07:18:02.474). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[67,68,69,70]},{"h":[71,72,73,74]},{"h":[75,76,77]},{"h":[78,79]},{"h":[80,81]}],"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],"activity":[[52,53,54,55],[56,57,58,59],[60,61,62],[63,64],[65,66]]},{},{},{}]} Value and gradient before optimization: ======================================= value = 4.327507075158843 gradient = {-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000} gradient norm = 6.28780077607947E-7 Already at minimum! After: gradient norm = 6.28780077607947E-7 >>> Parameters after optimization Count Table 0: --------------- h: {2.9702,0.6016,-1.1394,-2.4324} Count Table 1: --------------- h: {2.3146,1.6854,-1.3784,-2.6217} Count Table 2: --------------- h: {-0.0000,-0.0000,0.0000} Count Table 3: --------------- h: {-0.0000,0.0000} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=1): {-0.0000,-0.0000,-0.0000,-0.0000} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {-0.5572,-0.7732,-0.5802,-0.5718,-0.1347,-1.1806,-0.5298,-0.6371,-0.4298,-1.2692,-1.5186,0.7353,-0.4204,-1.6366,0.4921,-0.9174,1.1525,-1.3427,-1.3708,-0.9213,-1.1909,-0.8108,-1.0806,0.6001,-0.4051,-1.9655,-1.0675,0.9558,-0.8223,-2.0037,-0.2070,0.5506,1.2336,-1.4862,-0.8134,-1.4163,-1.5423,-0.0573,-1.6777,0.7950,-0.7272,-1.4026,0.0008,-0.3533,-0.0969,-1.4440,-0.2279,-0.7134,-0.9428,-0.3431,-0.5980,-0.5983} Activity(exp=0): {0.0000,2.3740,-0.3724,-2.5337} Activity(exp=1): {0.0000,0.1649,1.0118,-3.1267} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} The Likelihood DID NOT improve. Discarding fit component1-2-variation0. > No varitions possible for Binding mode 1. > Optimizing the full model (component1-4-all). >> Starting new optimization: component1-4-all. (2021-05-22 07:18:03.809). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[82,83,84,85]},{"h":[86,87,88,89]},{"h":[90,91,92]},{"h":[93,94]},{"h":[95,96]}],"bindingModeInteractions":[{}],"bindingModes":[{"mononucleotide":[],"activity":[[0,1,2,3],[4,5,6,7],[8,9,10],[11,12],[13,14]]},{"mononucleotide":[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],"activity":[[67,68,69,70],[71,72,73,74],[75,76,77],[78,79],[80,81]]},{},{},{}]} Value and gradient before optimization: ======================================= value = 4.327507075158843 gradient = {-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000} gradient norm = 1.6719728541766727E-5 Starting Function Value: 4.327507075158843 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 4.327507065567155 0.001184648660213 70.853342938781180 0.000069192948702 2 5 4.327507062642200 0.000348897170009 0.323158707864179 0.000103331121462 3 6 4.327507058927418 0.000223790807391 1.000000000000000 0.000084460931873 4 7 4.327507049941021 0.001236826294011 1.000000000000000 0.000027159756938 5 8 4.327507048324417 0.000228757591786 1.000000000000000 0.000028957635836 6 9 4.327507036091389 0.001987018729880 1.000000000000000 0.000055939272868 7 10 4.327507028995169 0.001516260476556 1.000000000000000 0.000086371736569 8 11 4.327507021600794 0.000954708112981 1.000000000000000 0.000043088497237 9 12 4.327507017388685 0.000323927043913 1.000000000000000 0.000029056966511 10 13 4.327507013949832 0.000316438325452 1.000000000000000 0.000042624520480 11 14 4.327507007265833 0.000844654314982 1.000000000000000 0.000061854069373 12 15 4.327506995998497 0.001920336506452 1.000000000000000 0.000070654885230 13 16 4.327506994045457 0.004194301360992 1.000000000000000 0.000143598285367 14 17 4.327506977450010 0.000318502473985 1.000000000000000 0.000047568362863 15 18 4.327506970730386 0.000524699610812 1.000000000000000 0.000037506018075 16 19 4.327506961483081 0.001447775373037 1.000000000000000 0.000067060812379 17 20 4.327506947382709 0.002598317970890 1.000000000000000 0.000093553632767 18 21 4.327506919199165 0.005328463818211 1.000000000000000 0.000103558576653 19 22 4.327506862369199 0.010637931238720 1.000000000000000 0.000117177256108 20 23 4.327506857082946 0.021622354298243 1.000000000000000 0.000210752266726 21 24 4.327506772378117 0.002207412126750 1.000000000000000 0.000072340962594 22 25 4.327506748492906 0.001381608731545 1.000000000000000 0.000048133048350 23 26 4.327506720484701 0.002915805487457 1.000000000000000 0.000080703248542 24 27 4.327506678173748 0.008029330921672 1.000000000000000 0.000118216776743 25 28 4.327506599141876 0.016801740132345 1.000000000000000 0.000136707705898 26 30 4.327506551227615 0.015237167163230 0.475874830509453 0.000225990751182 27 31 4.327506459123808 0.019178128832839 1.000000000000000 0.000110481883052 28 32 4.327506391885891 0.012554355432671 1.000000000000000 0.000096628870682 29 33 4.327506319733296 0.011709736004492 1.000000000000000 0.000129832826829 30 34 4.327506153463650 0.028100675096052 1.000000000000000 0.000170075585160 31 35 4.327505854778138 0.069243446659645 1.000000000000000 0.000299641816425 32 36 4.327505420778026 0.095763392614840 1.000000000000000 0.000228607059545 33 37 4.327504938626604 0.074211845660113 1.000000000000000 0.000179305725507 34 38 4.327504119886578 0.139964408910772 1.000000000000000 0.000227065051687 35 39 4.327503530454749 0.165530257953853 1.000000000000000 0.000492967208108 36 40 4.327502659283067 0.132997076740760 1.000000000000000 0.000346676794793 37 41 4.327501292501743 0.229971707805832 1.000000000000000 0.000286126320444 38 42 4.327499927315101 0.272504873777186 1.000000000000000 0.000363813669308 39 43 4.327498017402765 0.425715745429624 1.000000000000000 0.000556644165254 40 44 4.327495392997100 0.565463211338841 1.000000000000000 0.000448202426129 41 45 4.327491803274887 0.664500786906111 1.000000000000000 0.000458105665588 42 46 4.327486121600686 1.127860674221650 1.000000000000000 0.000403746901454 43 47 4.327482770764377 0.744089936705294 1.000000000000000 0.000278106087985 44 48 4.327481780736561 0.233204820216974 1.000000000000000 0.000324100750477 45 49 4.327481457977386 0.065593572614814 1.000000000000000 0.000119870682399 46 50 4.327481382771407 0.048821062638636 1.000000000000000 0.000085905784506 47 51 4.327481280949358 0.012963370611806 1.000000000000000 0.000075385431672 48 52 4.327481158163863 0.038400489987125 1.000000000000000 0.000073468992863 49 53 4.327481087795147 0.071176956688724 1.000000000000000 0.000134937533531 50 54 4.327481002118438 0.034193917610015 1.000000000000000 0.000043397226646 51 55 4.327480981047549 0.002139123341140 1.000000000000000 0.000031514962131 52 56 4.327480956883135 0.004298256615477 1.000000000000000 0.000022693849356 53 57 4.327480947574510 0.002317705447007 1.000000000000000 0.000023136730913 54 58 4.327480943586693 0.002611760826163 1.000000000000000 0.000011320691079 55 59 4.327480942129165 0.001214265051434 1.000000000000000 0.000007922820603 56 60 4.327480940000193 0.001706866601996 1.000000000000000 0.000007848766745 57 61 4.327480938675621 0.000961228542146 1.000000000000000 0.000012257587192 58 62 4.327480937574454 0.000487855788421 1.000000000000000 0.000004944748991 59 63 4.327480937155145 0.000531035661710 1.000000000000000 0.000003262694070 60 64 4.327480936914646 0.000199382227070 1.000000000000000 0.000003146941356 61 65 4.327480936762821 0.000317359397148 1.000000000000000 0.000006213402315 62 66 4.327480936535246 0.000138373772632 1.000000000000000 0.000002089678014 63 67 4.327480936454324 0.000195522813552 1.000000000000000 0.000001704608433 64 68 4.327480936373932 0.000131241967638 1.000000000000000 0.000001684702269 65 69 4.327480936291222 0.000210099140930 1.000000000000000 0.000001321327404 66 70 4.327480936290189 0.000986530286243 1.000000000000000 0.000003417101147 67 71 4.327480936265271 0.000986530286243 1.000000000000000 0.000000633748618 Convergence criteria met. After: gradient norm = 6.337486181131282E-7 >>> Parameters after optimization Count Table 0: --------------- h: {0.9212,0.6331,-0.0825,-1.4717} Count Table 1: --------------- h: {0.7784,1.0554,-0.1517,-1.6822} Count Table 2: --------------- h: {-0.0000,0.0000,-0.0000} Count Table 3: --------------- h: {0.0000,-0.0000} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-2.0840,-1.0262,0.0959} Activity(exp=1): {-0.0000,-0.9063,-1.8588,0.2872} Activity(exp=2): {0.0000,0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,0.0000} Binding mode 1: --------------- Mononucleotide: {-0.6239,-0.8398,-0.6469,-0.6385,-0.2015,-1.2473,-0.5965,-0.7038,-0.4966,-1.3359,-1.5851,0.6684,-0.4872,-1.7029,0.4252,-0.9842,1.0855,-1.4092,-1.4374,-0.9881,-1.2578,-0.8771,-1.1473,0.5331,-0.4718,-2.0319,-1.1341,0.8887,-0.8891,-2.0699,-0.2738,0.4837,1.1661,-1.5522,-0.8802,-1.4828,-1.6088,-0.1242,-1.7441,0.7280,-0.7939,-1.4692,-0.0659,-0.4201,-0.1637,-1.5106,-0.2947,-0.7801,-1.0095,-0.4098,-0.6647,-0.6650} Activity(exp=0): {0.0000,1.1629,-0.5280,-1.5676} Activity(exp=1): {0.0000,0.1279,0.0250,-1.9694} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} ================================== == Starts fiting Binding mode 2 == ================================== > Optimizing h (component2-0-h). >> Starting new optimization: component2-0-h. (2021-05-22 07:19:32.572). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[0,1,2,3]},{"h":[4,5,6,7]},{"h":[8,9,10]},{"h":[11,12]},{"h":[13,14]}],"bindingModeInteractions":[{}],"bindingModes":[{},{},{},{},{}]} Value and gradient before optimization: ======================================= value = 4.74300285003531 gradient = {-0.1195,-0.0827,0.0010,0.2013,-0.1104,0.0334,-0.0241,0.1011,-0.0000,0.0000,-0.0000,-0.2423,0.2423,-0.0000,0.0000} gradient norm = 0.45077878657736964 Starting Function Value: 4.74300285003531 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 2 4.459737642997841 1.000000000000000 2.218383006868413 0.174977264618199 2 3 4.380250253499773 0.665280833860161 1.000000000000000 0.101886852320864 3 4 4.346276963215534 0.669998934186253 1.000000000000000 0.019245356175562 4 5 4.344836513601894 0.138589607746642 1.000000000000000 0.007081776041067 5 6 4.344664377377103 0.069957639562382 1.000000000000000 0.003274261642817 6 7 4.344640847916474 0.016023953893013 1.000000000000000 0.000332083413237 7 8 4.344640630800064 0.001556038375237 1.000000000000000 0.000061897341607 8 9 4.344640626291134 0.000172537327982 1.000000000000000 0.000004266275700 9 10 4.344640626262411 0.000013577486110 1.000000000000000 0.000000775589354 10 11 4.344640626260928 0.000013577486110 1.000000000000000 0.000000213648429 Convergence criteria met. After: gradient norm = 2.136484291976449E-7 >>> Parameters after optimization Count Table 0: --------------- h: {1.9085,1.0455,-0.4102,-2.5438} Count Table 1: --------------- h: {1.6904,1.1228,-0.3772,-2.4361} Count Table 2: --------------- h: {0.0000,-0.0000,0.0000} Count Table 3: --------------- h: {0.5311,-0.5311} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-2.0840,-1.0262,0.0959} Activity(exp=1): {-0.0000,-0.9063,-1.8588,0.2872} Activity(exp=2): {0.0000,0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,0.0000} Binding mode 1: --------------- Mononucleotide: {-0.6239,-0.8398,-0.6469,-0.6385,-0.2015,-1.2473,-0.5965,-0.7038,-0.4966,-1.3359,-1.5851,0.6684,-0.4872,-1.7029,0.4252,-0.9842,1.0855,-1.4092,-1.4374,-0.9881,-1.2578,-0.8771,-1.1473,0.5331,-0.4718,-2.0319,-1.1341,0.8887,-0.8891,-2.0699,-0.2738,0.4837,1.1661,-1.5522,-0.8802,-1.4828,-1.6088,-0.1242,-1.7441,0.7280,-0.7939,-1.4692,-0.0659,-0.4201,-0.1637,-1.5106,-0.2947,-0.7801,-1.0095,-0.4098,-0.6647,-0.6650} Activity(exp=0): {0.0000,1.1629,-0.5280,-1.5676} Activity(exp=1): {0.0000,0.1279,0.0250,-1.9694} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.2803,-1.6173,-0.7405,0.3695} Activity(exp=1): {0.2319,-0.6592,-1.5806,0.5114} Activity(exp=2): {0.2233,0.2233,0.2233} Activity(exp=3): {0.2233,0.2233} Activity(exp=4): {0.2233,0.2233} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} > Initial optimization (component2-1-f0). >> Starting new optimization: component2-1-f0. (2021-05-22 07:19:46.371). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[47,48,49,50]},{"h":[51,52,53,54]},{"h":[55,56,57]},{"h":[58,59]},{"h":[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],"activity":[[32,33,34,35],[36,37,38,39],[40,41,42],[43,44],[45,46]]},{},{}]} Value and gradient before optimization: ======================================= value = 4.344640626260927 gradient = {0.0055,0.0149,0.0136,0.0052,0.0039,0.0104,0.0082,0.0165,0.0076,0.0115,0.0150,0.0051,0.0055,0.0090,0.0179,0.0067,0.0055,0.0150,0.0140,0.0046,0.0058,0.0138,0.0074,0.0121,0.0066,0.0108,0.0177,0.0039,0.0068,0.0149,0.0131,0.0044,0.0000,0.0049,0.0116,0.0089,0.0000,0.0047,0.0069,0.0044,0.0000,0.0000,0.0000,0.0000,-0.0023,0.0000,0.0000,-0.0000,0.0000,0.0000,-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 = 0.06344555936947728 Starting Function Value: 4.344640626260927 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 4.341826720795345 0.112150780436244 1.767669503599616 0.060168631895314 2 4 4.339491457107683 0.052570567642542 1.000000000000000 0.045100811116459 3 5 4.330012672044783 0.398274805416094 1.000000000000000 0.060647053902642 4 6 4.323764911208339 0.339330503556386 1.000000000000000 0.077546206980164 5 7 4.311855009571737 0.794743197662943 1.000000000000000 0.090142801699090 6 8 4.303124174039800 0.588343982959797 1.000000000000000 0.060329244046174 7 9 4.296069347685180 0.590875428763781 1.000000000000000 0.022137450766597 8 10 4.293009651232248 0.445303751304196 1.000000000000000 0.022872278263159 9 11 4.288000920402066 0.737552020109057 1.000000000000000 0.016418507563978 10 12 4.284209036723306 1.005068165505191 1.000000000000000 0.032343136343305 11 13 4.282135875755840 0.302424339574869 1.000000000000000 0.017759587616022 12 14 4.281372079426341 0.082729446894696 1.000000000000000 0.010373630499101 13 15 4.280273078214087 0.160653678352403 1.000000000000000 0.013893999675281 14 16 4.278770242279935 0.395508605446083 1.000000000000000 0.027782616428216 15 17 4.277336346669403 0.402765600981475 1.000000000000000 0.024906446751388 16 18 4.276063519846809 0.580153883260067 1.000000000000000 0.025954518932535 17 19 4.274879514700918 0.248424787134108 1.000000000000000 0.008446031568724 18 20 4.274368468551322 0.261062655963749 1.000000000000000 0.008503518690509 19 21 4.273302041358278 0.575681264354550 1.000000000000000 0.009659100944846 20 23 4.272870097617734 0.361067712124193 0.466691009886969 0.013285704077233 21 24 4.272418438897325 0.351030203071808 1.000000000000000 0.009545149647554 22 25 4.272258264185916 0.064025974888119 1.000000000000000 0.005323712016787 23 26 4.272145805741697 0.097043593790830 1.000000000000000 0.005196245049549 24 27 4.271828478148762 0.417869129027423 1.000000000000000 0.005683026307207 25 28 4.271692491819304 0.369182926558130 1.000000000000000 0.008125338468498 26 29 4.271514298900085 0.216893458801242 1.000000000000000 0.003020153490938 27 30 4.271444187567210 0.154490716241910 1.000000000000000 0.002041484035024 28 31 4.271395739669655 0.108537628363934 1.000000000000000 0.002975163532341 29 32 4.271309891347133 0.192529405928435 1.000000000000000 0.003417769637202 30 33 4.271234465412446 0.202329469641575 1.000000000000000 0.004971853259102 31 34 4.271167989048315 0.091832332153661 1.000000000000000 0.001641236129531 32 35 4.271140091843718 0.063994554424979 1.000000000000000 0.001634523646166 33 36 4.271112998524107 0.041948524328951 1.000000000000000 0.002082005389642 34 37 4.271083174732715 0.095323222124701 1.000000000000000 0.002397098005561 35 38 4.271056525503496 0.150502332276087 1.000000000000000 0.001617539151930 36 39 4.271039758286321 0.160700394530438 1.000000000000000 0.001423124046929 37 40 4.271029060146922 0.115054330855154 1.000000000000000 0.001273367892557 38 41 4.271020259879719 0.058559994429925 1.000000000000000 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4.270827071040171 0.023221137809177 1.000000000000000 0.000063949816985 128 134 4.270827000433957 0.057114032303964 1.000000000000000 0.000103999661925 129 135 4.270826856644137 0.094757205654107 1.000000000000000 0.000111088989707 130 136 4.270826771970854 0.214350221124541 1.000000000000000 0.000289377380613 131 137 4.270826564706384 0.025889619214880 1.000000000000000 0.000070046851839 132 138 4.270826527074037 0.014567173046925 1.000000000000000 0.000029728574751 133 139 4.270826520359839 0.009649756762323 1.000000000000000 0.000043097838005 134 140 4.270826516329300 0.003590674877915 1.000000000000000 0.000010702174288 135 141 4.270826515257524 0.001807898841710 1.000000000000000 0.000009055735341 136 142 4.270826513830044 0.003212178163094 1.000000000000000 0.000007735294544 137 144 4.270826513496460 0.000790540792350 0.236941408658695 0.000010218580034 138 145 4.270826512888670 0.001071921788470 1.000000000000000 0.000008730839068 139 146 4.270826511004517 0.003129108085751 1.000000000000000 0.000009191734241 140 147 4.270826508197618 0.003626948422071 1.000000000000000 0.000016360559479 141 148 4.270826503859647 0.005663238425756 1.000000000000000 0.000017734512840 142 149 4.270826496983410 0.005320730184857 1.000000000000000 0.000020201577345 143 150 4.270826480142620 0.010136913198876 1.000000000000000 0.000030696644226 144 151 4.270826453512886 0.026246447360906 1.000000000000000 0.000048082647134 145 152 4.270826437854109 0.030978906288467 1.000000000000000 0.000123957208256 146 153 4.270826399557869 0.007607436907316 1.000000000000000 0.000044103750772 147 154 4.270826377394417 0.012666290369176 1.000000000000000 0.000024719469816 148 155 4.270826370633685 0.010611930453582 1.000000000000000 0.000016005817947 149 156 4.270826366485911 0.008386584900585 1.000000000000000 0.000007622039130 150 157 4.270826364317384 0.006558156829352 1.000000000000000 0.000008182130204 151 158 4.270826361376332 0.004331638602872 1.000000000000000 0.000011501970208 152 159 4.270826354276813 0.011115013731672 1.000000000000000 0.000017254499189 153 161 4.270826348515475 0.006130608070832 0.484600720152093 0.000039690473830 154 162 4.270826334562816 0.010726679473884 1.000000000000000 0.000032132088443 155 163 4.270826294176652 0.028868852416492 1.000000000000000 0.000033254194293 156 164 4.270826247325403 0.032018368973020 1.000000000000000 0.000049830589484 157 165 4.270826178883755 0.065999757063838 1.000000000000000 0.000050791746219 158 166 4.270826134433961 0.059744486637383 1.000000000000000 0.000075524076697 159 167 4.270826098201237 0.010975420346503 1.000000000000000 0.000023985944213 160 168 4.270826086195139 0.006078580447186 1.000000000000000 0.000016734991231 161 169 4.270826082489090 0.004959120244941 1.000000000000000 0.000012626481621 162 170 4.270826079976987 0.005280760353919 1.000000000000000 0.000014380845710 163 171 4.270826078817318 0.006133499696793 1.000000000000000 0.000004584318470 164 172 4.270826078412313 0.000572524229482 1.000000000000000 0.000005430817386 165 173 4.270826076781123 0.002085105345519 1.000000000000000 0.000010127498686 166 174 4.270826074191760 0.003004747287024 1.000000000000000 0.000014603559666 167 175 4.270826065691064 0.008802696575286 1.000000000000000 0.000023414802155 168 176 4.270826047328622 0.018548496760286 1.000000000000000 0.000035481124512 169 177 4.270826004224091 0.042743718311223 1.000000000000000 0.000048928108377 170 178 4.270825922325623 0.093144035628590 1.000000000000000 0.000083855460980 171 179 4.270825799082790 0.128359625894037 1.000000000000000 0.000073985553179 172 180 4.270825651498218 0.158126652204015 1.000000000000000 0.000078991082153 173 181 4.270825573885751 0.080321347088634 1.000000000000000 0.000055958426892 174 182 4.270825549329464 0.011154661362052 1.000000000000000 0.000022948015076 175 183 4.270825542245729 0.012436140889118 1.000000000000000 0.000012949002319 176 184 4.270825537259180 0.003580325661390 1.000000000000000 0.000009984618546 177 185 4.270825533166666 0.010210529288118 1.000000000000000 0.000010477203866 178 186 4.270825530584540 0.009666576028840 1.000000000000000 0.000008246004295 179 187 4.270825529185681 0.006956878625406 1.000000000000000 0.000007464377936 180 188 4.270825528583756 0.002463589052969 1.000000000000000 0.000003293302507 181 189 4.270825528413250 0.002907253054636 1.000000000000000 0.000001513874972 182 190 4.270825528370200 0.002907253054636 1.000000000000000 0.000001200203724 Convergence criteria met. After: gradient norm = 1.2002037239130418E-6 >>> Parameters after optimization Count Table 0: --------------- h: {1.4049,0.7816,-0.2718,-1.9148} Count Table 1: --------------- h: {0.7888,1.0610,-0.1540,-1.6958} Count Table 2: --------------- h: {-0.0000,-0.0000,0.0000} Count Table 3: --------------- h: {0.1085,-0.1085} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-2.0840,-1.0262,0.0959} Activity(exp=1): {-0.0000,-0.9063,-1.8588,0.2872} Activity(exp=2): {0.0000,0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,0.0000} Binding mode 1: --------------- Mononucleotide: {-0.6239,-0.8398,-0.6469,-0.6385,-0.2015,-1.2473,-0.5965,-0.7038,-0.4966,-1.3359,-1.5851,0.6684,-0.4872,-1.7029,0.4252,-0.9842,1.0855,-1.4092,-1.4374,-0.9881,-1.2578,-0.8771,-1.1473,0.5331,-0.4718,-2.0319,-1.1341,0.8887,-0.8891,-2.0699,-0.2738,0.4837,1.1661,-1.5522,-0.8802,-1.4828,-1.6088,-0.1242,-1.7441,0.7280,-0.7939,-1.4692,-0.0659,-0.4201,-0.1637,-1.5106,-0.2947,-0.7801,-1.0095,-0.4098,-0.6647,-0.6650} Activity(exp=0): {0.0000,1.1629,-0.5280,-1.5676} Activity(exp=1): {0.0000,0.1279,0.0250,-1.9694} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {-1.5381,-1.8859,-1.6653,-1.4158,-1.5924,-2.0998,-1.6921,-1.1283,-1.4518,-3.1657,-2.7359,0.8408,-1.6701,-3.1744,0.7649,-2.4330,3.3416,-4.1505,-3.3417,-2.3620,-2.4680,-0.0231,-2.6882,-1.3309,0.1018,-3.4665,-0.9837,-2.1617,-1.9464,-1.9813,-1.1316,-1.4458} Activity(exp=0): {0.0007,0.3464,-0.2833,0.2960} Activity(exp=1): {0.0006,-3.7447,-3.0320,-1.0702} Activity(exp=2): {0.0006,0.0006,0.0006} Activity(exp=3): {0.0006,0.9739} Activity(exp=4): {0.0006,0.0006} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Suggested variations: key=8;5;0, description = Initial model. > Optimizing variation "Initial model." (component2-2-variation0). >> Starting new optimization: component2-2-variation0. (2021-05-22 07:25:34.803). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[47,48,49,50]},{"h":[51,52,53,54]},{"h":[55,56,57]},{"h":[58,59]},{"h":[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],"activity":[[32,33,34,35],[36,37,38,39],[40,41,42],[43,44],[45,46]]},{},{}]} Value and gradient before optimization: ======================================= value = 4.2708255283702 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 = 1.2002037239120296E-6 Already at minimum! After: gradient norm = 1.2002037239120296E-6 >>> Parameters after optimization Count Table 0: --------------- h: {1.4049,0.7816,-0.2718,-1.9148} Count Table 1: --------------- h: {0.7888,1.0610,-0.1540,-1.6958} Count Table 2: --------------- h: {-0.0000,-0.0000,0.0000} Count Table 3: --------------- h: {0.1085,-0.1085} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-2.0840,-1.0262,0.0959} Activity(exp=1): {-0.0000,-0.9063,-1.8588,0.2872} Activity(exp=2): {0.0000,0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,0.0000} Binding mode 1: --------------- Mononucleotide: {-0.6239,-0.8398,-0.6469,-0.6385,-0.2015,-1.2473,-0.5965,-0.7038,-0.4966,-1.3359,-1.5851,0.6684,-0.4872,-1.7029,0.4252,-0.9842,1.0855,-1.4092,-1.4374,-0.9881,-1.2578,-0.8771,-1.1473,0.5331,-0.4718,-2.0319,-1.1341,0.8887,-0.8891,-2.0699,-0.2738,0.4837,1.1661,-1.5522,-0.8802,-1.4828,-1.6088,-0.1242,-1.7441,0.7280,-0.7939,-1.4692,-0.0659,-0.4201,-0.1637,-1.5106,-0.2947,-0.7801,-1.0095,-0.4098,-0.6647,-0.6650} Activity(exp=0): {0.0000,1.1629,-0.5280,-1.5676} Activity(exp=1): {0.0000,0.1279,0.0250,-1.9694} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {-1.5381,-1.8859,-1.6653,-1.4158,-1.5924,-2.0998,-1.6921,-1.1283,-1.4518,-3.1657,-2.7359,0.8408,-1.6701,-3.1744,0.7649,-2.4330,3.3416,-4.1505,-3.3417,-2.3620,-2.4680,-0.0231,-2.6882,-1.3309,0.1018,-3.4665,-0.9837,-2.1617,-1.9464,-1.9813,-1.1316,-1.4458} Activity(exp=0): {0.0007,0.3464,-0.2833,0.2960} Activity(exp=1): {0.0006,-3.7447,-3.0320,-1.0702} Activity(exp=2): {0.0006,0.0006,0.0006} Activity(exp=3): {0.0006,0.9739} Activity(exp=4): {0.0006,0.0006} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} The Likelihood DID NOT improve. Discarding fit component2-2-variation0. > No varitions possible for Binding mode 2. > Optimizing the full model (component2-4-all). >> Starting new optimization: component2-4-all. (2021-05-22 07:25:36.613). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[129,130,131,132]},{"h":[133,134,135,136]},{"h":[137,138,139]},{"h":[140,141]},{"h":[142,143]}],"bindingModeInteractions":[{}],"bindingModes":[{"mononucleotide":[],"activity":[[0,1,2,3],[4,5,6,7],[8,9,10],[11,12],[13,14]]},{"mononucleotide":[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],"activity":[[67,68,69,70],[71,72,73,74],[75,76,77],[78,79],[80,81]]},{"mononucleotide":[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],"activity":[[114,115,116,117],[118,119,120,121],[122,123,124],[125,126],[127,128]]},{},{}]} Value and gradient before optimization: ======================================= value = 4.270825528370203 gradient = {-0.0000,0.0003,0.0052,0.0070,-0.0000,0.0000,0.0001,0.0002,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0036,-0.0026,-0.0054,-0.0013,-0.0086,-0.0002,-0.0033,-0.0007,-0.0003,-0.0001,-0.0001,-0.0123,-0.0040,0.0018,-0.0092,-0.0015,-0.0145,0.0000,0.0002,0.0015,-0.0005,0.0059,0.0005,-0.0187,0.0050,-0.0004,0.0009,-0.0184,-0.0017,0.0002,0.0099,-0.0213,-0.0161,0.0008,0.0019,0.0005,0.0001,0.0032,-0.0005,-0.0156,0.0036,0.0005,-0.0095,-0.0074,-0.0084,-0.0006,-0.0040,0.0002,-0.0017,-0.0040,-0.0032,-0.0039,0.0000,-0.0003,-0.0052,-0.0070,0.0000,-0.0000,-0.0001,-0.0002,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000} gradient norm = 0.053637861905429046 Starting Function Value: 4.270825528370203 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 4.270141717917859 0.024002646767312 0.447494473393282 0.028695308983454 2 4 4.269811924379635 0.013437147958572 1.000000000000000 0.029384180315410 3 5 4.264305804890814 0.365490808357601 1.000000000000000 0.045317953144058 4 6 4.261551087851389 0.269825153057040 1.000000000000000 0.051820203060318 5 7 4.260011897357575 0.256064804615316 1.000000000000000 0.022990014231626 6 8 4.259537853899090 0.055486999123214 1.000000000000000 0.014150876959521 7 9 4.259063420254973 0.085796484170698 1.000000000000000 0.021260159342489 8 10 4.258545575128619 0.115995484026063 1.000000000000000 0.025976966183493 9 11 4.257531489185545 0.242692720683123 1.000000000000000 0.024178504989114 10 12 4.256487483412910 0.381557672394429 1.000000000000000 0.018679199044041 11 13 4.255858421779538 0.151565113950820 1.000000000000000 0.008866300157223 12 14 4.255549340782278 0.080245886738460 1.000000000000000 0.007485625157427 13 15 4.255321859470072 0.077643593940970 1.000000000000000 0.008479469172721 14 16 4.254913150958788 0.172362563102639 1.000000000000000 0.007909276268734 15 18 4.254820786476346 0.070569699216869 0.245144801106462 0.010524642192899 16 19 4.254620408874908 0.135045942905507 1.000000000000000 0.005515989186998 17 20 4.254499314100809 0.089272147206623 1.000000000000000 0.004128389919842 18 21 4.254328440511326 0.164777212564546 1.000000000000000 0.006143293865755 19 22 4.254212908440866 0.188245277484773 1.000000000000000 0.010905283270406 20 23 4.254060338498994 0.115738170693516 1.000000000000000 0.006224009295188 21 24 4.253943819917844 0.084446397521103 1.000000000000000 0.004358822386160 22 25 4.253842605362811 0.081424702941097 1.000000000000000 0.004731273454899 23 26 4.253740986511532 0.088101591955188 1.000000000000000 0.005483728771779 24 27 4.253589222362865 0.156993632352564 1.000000000000000 0.005655820119458 25 28 4.253440579591538 0.236513480953460 1.000000000000000 0.008285675863460 26 29 4.253279662751144 0.217509965993721 1.000000000000000 0.005219278257656 27 30 4.253169975164941 0.054687697569447 1.000000000000000 0.004121741188530 28 31 4.253083997776520 0.142589613713264 1.000000000000000 0.003183328665822 29 32 4.253015834277589 0.062294577363116 1.000000000000000 0.004804656124492 30 33 4.252940321324422 0.108196923944996 1.000000000000000 0.003352844914032 31 34 4.252869643759905 0.083728372272609 1.000000000000000 0.002760384256519 32 35 4.252787914888350 0.127717478541883 1.000000000000000 0.004398955942771 33 36 4.252717633673025 0.094134627207087 1.000000000000000 0.004630389429777 34 37 4.252630412128241 0.187051375745810 1.000000000000000 0.005552099195102 35 38 4.252563729306981 0.187751971724413 1.000000000000000 0.003818289531662 36 39 4.252525443525409 0.038510187006502 1.000000000000000 0.002318798281001 37 40 4.252495780515014 0.111536687937493 1.000000000000000 0.002339592204763 38 41 4.252449869664952 0.075209329681540 1.000000000000000 0.003900154283738 39 42 4.252372953365986 0.227159621714901 1.000000000000000 0.003235353892824 40 43 4.252295989788728 0.189432931845678 1.000000000000000 0.003467251018636 41 44 4.252217801207405 0.353383110374075 1.000000000000000 0.004778611687646 42 45 4.252151634195524 0.069034490709467 1.000000000000000 0.002368302388939 43 46 4.252101899645215 0.084964976911377 1.000000000000000 0.002719857463810 44 47 4.252066212447711 0.049999164475890 1.000000000000000 0.001924582142028 45 48 4.252020282350948 0.159756825297205 1.000000000000000 0.002030764579141 46 49 4.251979534227186 0.096491528894938 1.000000000000000 0.001727683297157 47 50 4.251942136863611 0.130996606893827 1.000000000000000 0.001588835051720 48 51 4.251902300763794 0.094513920318390 1.000000000000000 0.001851390706232 49 52 4.251877227296149 0.073399771698317 1.000000000000000 0.000989289960996 50 53 4.251863067238861 0.043325911499629 1.000000000000000 0.000907718061104 51 54 4.251843955092923 0.060798138607474 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367 4.251492521006483 0.035925377001568 1.000000000000000 0.000092158062837 353 368 4.251492485506878 0.027695413635548 1.000000000000000 0.000076308329926 354 369 4.251492451818911 0.028901219175692 1.000000000000000 0.000056836061824 355 370 4.251492416853540 0.029021266263919 1.000000000000000 0.000056124335560 356 371 4.251492384135160 0.024839371647694 1.000000000000000 0.000064287727062 357 372 4.251492367713270 0.030702717388203 1.000000000000000 0.000105701112103 358 373 4.251492338644650 0.003916356909217 1.000000000000000 0.000029985264333 359 374 4.251492331032601 0.005500945473750 1.000000000000000 0.000023427081946 360 375 4.251492323863335 0.002264397230717 1.000000000000000 0.000024943305656 361 376 4.251492319706034 0.007455344028620 1.000000000000000 0.000026026992294 362 377 4.251492316879914 0.005462600884938 1.000000000000000 0.000024859498780 363 378 4.251492315251908 0.002033802510233 1.000000000000000 0.000012321871002 364 379 4.251492313750050 0.002607220449547 1.000000000000000 0.000013426330994 365 380 4.251492312724112 0.000756108297573 1.000000000000000 0.000015154021639 366 381 4.251492311309680 0.001441195699413 1.000000000000000 0.000007177944796 367 382 4.251492311055144 0.001027011850148 1.000000000000000 0.000008462682216 368 383 4.251492310811029 0.001036286240848 1.000000000000000 0.000006224328517 369 384 4.251492310703972 0.000605857038406 1.000000000000000 0.000004864078051 370 385 4.251492310519958 0.001248662949667 1.000000000000000 0.000002705272230 371 386 4.251492310471590 0.001099896479691 1.000000000000000 0.000004426970953 372 387 4.251492310420609 0.000256395783521 1.000000000000000 0.000002387674748 373 388 4.251492310374220 0.000242986970646 1.000000000000000 0.000001818463494 374 389 4.251492310342012 0.000184558757672 1.000000000000000 0.000001788888620 375 390 4.251492310299771 0.000184558757672 1.000000000000000 0.000001359322936 Convergence criteria met. After: gradient norm = 1.3593229358580678E-6 >>> Parameters after optimization Count Table 0: --------------- h: {2.0541,1.4161,-0.0849,-3.3853} Count Table 1: --------------- h: {1.8507,1.3018,-0.6367,-2.5158} Count Table 2: --------------- h: {-0.0000,0.0000,-0.0000} Count Table 3: --------------- h: {0.1360,-0.1360} Count Table 4: --------------- h: {0.0000,-0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-2.4723,-2.4381,-3.9686} Activity(exp=1): {0.0000,-0.0343,-0.8631,0.5841} Activity(exp=2): {-0.0000,0.0000,-0.0000} Activity(exp=3): {0.0000,-0.2190} Activity(exp=4): {-0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {-0.6862,-0.9352,-0.7157,-0.7506,-0.2051,-1.3844,-0.6652,-0.8330,-0.5945,-1.4797,-1.6964,0.6830,-0.3021,-2.5912,0.6159,-0.8102,1.1579,-1.4357,-1.4641,-1.3458,-1.1133,-1.7427,-1.0470,0.8153,-0.9319,-1.8818,-1.3235,1.0495,-0.7733,-2.2420,-0.8053,0.7330,1.5996,-1.9043,-1.0586,-1.7244,-1.8129,-0.3092,-1.7495,0.7839,-1.0714,-1.5257,-0.0712,-0.4194,-0.1913,-1.6296,-0.3340,-0.9328,-1.1196,-0.4910,-0.7429,-0.7342} Activity(exp=0): {-0.0000,0.9018,-0.7040,-0.8044} Activity(exp=1): {0.0000,0.5721,-0.1438,-2.9094} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8848,-1.2762,-1.0516,-0.8530,-0.9646,-1.4805,-1.0790,-0.5415,-0.9615,-2.0861,-1.7795,0.7615,-1.0589,-2.5502,0.8685,-1.3250,2.0641,-4.2584,-1.2243,-0.6470,-1.6348,0.0927,-1.8149,-0.7086,0.1027,-2.1917,-0.7107,-1.2659,-1.2654,-1.3482,-0.5928,-0.8592} Activity(exp=0): {-0.0000,-0.4837,-0.3282,1.3876} Activity(exp=1): {-0.0000,-2.3885,-2.1455,-0.1904} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,0.0830} Activity(exp=4): {-0.0000,-0.0000} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} ================================== == Starts fiting Binding mode 3 == ================================== > Optimizing h (component3-0-h). >> Starting new optimization: component3-0-h. (2021-05-22 07:40:52.761). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[0,1,2,3]},{"h":[4,5,6,7]},{"h":[8,9,10]},{"h":[11,12]},{"h":[13,14]}],"bindingModeInteractions":[{}],"bindingModes":[{},{},{},{},{}]} Value and gradient before optimization: ======================================= value = 4.603176206432809 gradient = {-0.0338,0.0133,0.0151,0.0054,-0.1018,0.0309,-0.0197,0.0907,-0.2350,-0.0827,0.3177,-0.0000,0.0000,0.0000,-0.0000} gradient norm = 0.4295777111399 Starting Function Value: 4.603176206432809 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 2 4.319008494697840 1.000000000000000 2.327867517489359 0.171994233102598 2 3 4.259527551451352 0.777858104739964 1.000000000000000 0.072683612106215 3 4 4.249155452704818 0.202212343533682 1.000000000000000 0.035117820102449 4 5 4.243206513362885 0.296462563823622 1.000000000000000 0.011234692326318 5 6 4.242796444939256 0.099887163348002 1.000000000000000 0.005133057575135 6 7 4.242746203116359 0.026671378348020 1.000000000000000 0.001286510767462 7 8 4.242742131812151 0.006976101121952 1.000000000000000 0.000140194068011 8 9 4.242742057268740 0.000721111469034 1.000000000000000 0.000069738483880 9 10 4.242742032421516 0.000747392264923 1.000000000000000 0.000015761479149 10 12 4.242742031964280 0.000061292331625 0.499774175799001 0.000004562713051 11 13 4.242742031938891 0.000021602358352 1.000000000000000 0.000002813170105 12 14 4.242742031930480 0.000021602358352 1.000000000000000 0.000000245621591 Convergence criteria met. After: gradient norm = 2.4562159069823594E-7 >>> Parameters after optimization Count Table 0: --------------- h: {2.3201,1.3946,-0.2074,-3.5073} Count Table 1: --------------- h: {2.7163,1.3894,-0.8735,-3.2321} Count Table 2: --------------- h: {0.9524,0.0066,-0.9590} Count Table 3: --------------- h: {0.1360,-0.1360} Count Table 4: --------------- h: {-0.0000,0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-2.4723,-2.4381,-3.9686} Activity(exp=1): {0.0000,-0.0343,-0.8631,0.5841} Activity(exp=2): {-0.0000,0.0000,-0.0000} Activity(exp=3): {0.0000,-0.2190} Activity(exp=4): {-0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {-0.6862,-0.9352,-0.7157,-0.7506,-0.2051,-1.3844,-0.6652,-0.8330,-0.5945,-1.4797,-1.6964,0.6830,-0.3021,-2.5912,0.6159,-0.8102,1.1579,-1.4357,-1.4641,-1.3458,-1.1133,-1.7427,-1.0470,0.8153,-0.9319,-1.8818,-1.3235,1.0495,-0.7733,-2.2420,-0.8053,0.7330,1.5996,-1.9043,-1.0586,-1.7244,-1.8129,-0.3092,-1.7495,0.7839,-1.0714,-1.5257,-0.0712,-0.4194,-0.1913,-1.6296,-0.3340,-0.9328,-1.1196,-0.4910,-0.7429,-0.7342} Activity(exp=0): {-0.0000,0.9018,-0.7040,-0.8044} Activity(exp=1): {0.0000,0.5721,-0.1438,-2.9094} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8848,-1.2762,-1.0516,-0.8530,-0.9646,-1.4805,-1.0790,-0.5415,-0.9615,-2.0861,-1.7795,0.7615,-1.0589,-2.5502,0.8685,-1.3250,2.0641,-4.2584,-1.2243,-0.6470,-1.6348,0.0927,-1.8149,-0.7086,0.1027,-2.1917,-0.7107,-1.2659,-1.2654,-1.3482,-0.5928,-0.8592} Activity(exp=0): {-0.0000,-0.4837,-0.3282,1.3876} Activity(exp=1): {-0.0000,-2.3885,-2.1455,-0.1904} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,0.0830} Activity(exp=4): {-0.0000,-0.0000} Binding mode 3: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.8249,-1.2984,-1.4588,-1.6215} Activity(exp=1): {0.7773,0.7377,-0.0856,1.3411} Activity(exp=2): {0.7488,0.7488,0.7488} Activity(exp=3): {0.7657,0.5525} Activity(exp=4): {0.7488,0.7488} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} > Initial optimization (component3-1-f0). >> Starting new optimization: component3-1-f0. (2021-05-22 07:41:18.546). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[47,48,49,50]},{"h":[51,52,53,54]},{"h":[55,56,57]},{"h":[58,59]},{"h":[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],"activity":[[32,33,34,35],[36,37,38,39],[40,41,42],[43,44],[45,46]]},{}]} Value and gradient before optimization: ======================================= value = 4.24274203193048 gradient = {-0.0087,0.0120,0.0113,-0.0023,0.0019,0.0085,0.0104,-0.0086,-0.0108,0.0082,0.0097,0.0051,-0.0125,0.0095,0.0106,0.0047,-0.0035,0.0064,0.0085,0.0008,0.0003,0.0040,0.0178,-0.0099,-0.0066,0.0060,0.0139,-0.0011,0.0006,0.0032,0.0073,0.0011,0.0000,0.0033,0.0017,0.0002,0.0000,0.0032,0.0058,0.0036,0.0000,-0.0030,-0.0025,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-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 = 0.04771355162156633 Starting Function Value: 4.24274203193048 Iterations Fnc. 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158 4.163796930130152 0.003292680840125 1.000000000000000 0.000005921816222 153 159 4.163796929778973 0.001372673144049 1.000000000000000 0.000003698626639 154 160 4.163796929469593 0.001288260810731 1.000000000000000 0.000004330875330 155 161 4.163796929322076 0.000702574254766 1.000000000000000 0.000002946755769 156 162 4.163796929127415 0.001390005799148 1.000000000000000 0.000002397677885 157 163 4.163796928954488 0.000988688625698 1.000000000000000 0.000004953653650 158 164 4.163796928541125 0.001650827217692 1.000000000000000 0.000009815726701 159 165 4.163796927699099 0.001860851055442 1.000000000000000 0.000016176365245 160 166 4.163796925621355 0.003394299967830 1.000000000000000 0.000024798047533 161 167 4.163796921178278 0.006749652154322 1.000000000000000 0.000036008508403 162 168 4.163796912639333 0.015103840825905 1.000000000000000 0.000045827205328 163 169 4.163796899268317 0.028872147800690 1.000000000000000 0.000057472907975 164 170 4.163796880519630 0.023862736152218 1.000000000000000 0.000039985968998 165 171 4.163796850281112 0.044874430652312 1.000000000000000 0.000025351240323 166 172 4.163796839553998 0.014303964402797 1.000000000000000 0.000029302283102 167 173 4.163796827180105 0.021900324051085 1.000000000000000 0.000022615379124 168 174 4.163796822589282 0.012739138407185 1.000000000000000 0.000022472383989 169 175 4.163796820019026 0.001903491591514 1.000000000000000 0.000006259765697 170 176 4.163796819182662 0.000733303285288 1.000000000000000 0.000006306953499 171 177 4.163796818859729 0.001492823213653 1.000000000000000 0.000004121716636 172 178 4.163796818690638 0.001735848953613 1.000000000000000 0.000001415028369 173 179 4.163796818660558 0.001735848953613 1.000000000000000 0.000000920718163 Convergence criteria met. After: gradient norm = 9.207181625363944E-7 >>> Parameters after optimization Count Table 0: --------------- h: {2.1096,1.4195,-0.1148,-3.4143} Count Table 1: --------------- h: {1.9652,1.2810,-0.6833,-2.5630} Count Table 2: --------------- h: {0.6603,-0.0605,-0.5999} Count Table 3: --------------- h: {0.1360,-0.1360} Count Table 4: --------------- h: {0.0000,-0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-2.4723,-2.4381,-3.9686} Activity(exp=1): {0.0000,-0.0343,-0.8631,0.5841} Activity(exp=2): {-0.0000,0.0000,-0.0000} Activity(exp=3): {0.0000,-0.2190} Activity(exp=4): {-0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {-0.6862,-0.9352,-0.7157,-0.7506,-0.2051,-1.3844,-0.6652,-0.8330,-0.5945,-1.4797,-1.6964,0.6830,-0.3021,-2.5912,0.6159,-0.8102,1.1579,-1.4357,-1.4641,-1.3458,-1.1133,-1.7427,-1.0470,0.8153,-0.9319,-1.8818,-1.3235,1.0495,-0.7733,-2.2420,-0.8053,0.7330,1.5996,-1.9043,-1.0586,-1.7244,-1.8129,-0.3092,-1.7495,0.7839,-1.0714,-1.5257,-0.0712,-0.4194,-0.1913,-1.6296,-0.3340,-0.9328,-1.1196,-0.4910,-0.7429,-0.7342} Activity(exp=0): {-0.0000,0.9018,-0.7040,-0.8044} Activity(exp=1): {0.0000,0.5721,-0.1438,-2.9094} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8848,-1.2762,-1.0516,-0.8530,-0.9646,-1.4805,-1.0790,-0.5415,-0.9615,-2.0861,-1.7795,0.7615,-1.0589,-2.5502,0.8685,-1.3250,2.0641,-4.2584,-1.2243,-0.6470,-1.6348,0.0927,-1.8149,-0.7086,0.1027,-2.1917,-0.7107,-1.2659,-1.2654,-1.3482,-0.5928,-0.8592} Activity(exp=0): {-0.0000,-0.4837,-0.3282,1.3876} Activity(exp=1): {-0.0000,-2.3885,-2.1455,-0.1904} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,0.0830} Activity(exp=4): {-0.0000,-0.0000} Binding mode 3: --------------- Mononucleotide: {-1.3265,-1.5405,-1.3925,-0.7574,-1.3427,-2.1829,-1.6042,0.1129,0.5048,-3.3294,-1.7224,-0.4700,2.1046,-2.4345,-2.3899,-2.2971,-2.3067,-1.1998,-1.7589,0.2485,-1.5885,-2.1268,-0.4893,-0.8124,-0.6524,-2.4749,-0.4253,-1.4643,-1.7501,-0.7176,-1.2816,-1.2675} Activity(exp=0): {0.0000,-0.8779,-1.1304,-2.1243} Activity(exp=1): {0.0000,0.7298,-1.2295,-3.8178} Activity(exp=2): {0.0000,2.3175,1.1158} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Suggested variations: key=8;5;0, description = Initial model. > Optimizing variation "Initial model." (component3-2-variation0). >> Starting new optimization: component3-2-variation0. (2021-05-22 07:48:26.651). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[47,48,49,50]},{"h":[51,52,53,54]},{"h":[55,56,57]},{"h":[58,59]},{"h":[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],"activity":[[32,33,34,35],[36,37,38,39],[40,41,42],[43,44],[45,46]]},{}]} Value and gradient before optimization: ======================================= value = 4.1637968186605585 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 = 9.207181625356437E-7 Already at minimum! After: gradient norm = 9.207181625356437E-7 >>> Parameters after optimization Count Table 0: --------------- h: {2.1096,1.4195,-0.1148,-3.4143} Count Table 1: --------------- h: {1.9652,1.2810,-0.6833,-2.5630} Count Table 2: --------------- h: {0.6603,-0.0605,-0.5999} Count Table 3: --------------- h: {0.1360,-0.1360} Count Table 4: --------------- h: {0.0000,-0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-2.4723,-2.4381,-3.9686} Activity(exp=1): {0.0000,-0.0343,-0.8631,0.5841} Activity(exp=2): {-0.0000,0.0000,-0.0000} Activity(exp=3): {0.0000,-0.2190} Activity(exp=4): {-0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {-0.6862,-0.9352,-0.7157,-0.7506,-0.2051,-1.3844,-0.6652,-0.8330,-0.5945,-1.4797,-1.6964,0.6830,-0.3021,-2.5912,0.6159,-0.8102,1.1579,-1.4357,-1.4641,-1.3458,-1.1133,-1.7427,-1.0470,0.8153,-0.9319,-1.8818,-1.3235,1.0495,-0.7733,-2.2420,-0.8053,0.7330,1.5996,-1.9043,-1.0586,-1.7244,-1.8129,-0.3092,-1.7495,0.7839,-1.0714,-1.5257,-0.0712,-0.4194,-0.1913,-1.6296,-0.3340,-0.9328,-1.1196,-0.4910,-0.7429,-0.7342} Activity(exp=0): {-0.0000,0.9018,-0.7040,-0.8044} Activity(exp=1): {0.0000,0.5721,-0.1438,-2.9094} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8848,-1.2762,-1.0516,-0.8530,-0.9646,-1.4805,-1.0790,-0.5415,-0.9615,-2.0861,-1.7795,0.7615,-1.0589,-2.5502,0.8685,-1.3250,2.0641,-4.2584,-1.2243,-0.6470,-1.6348,0.0927,-1.8149,-0.7086,0.1027,-2.1917,-0.7107,-1.2659,-1.2654,-1.3482,-0.5928,-0.8592} Activity(exp=0): {-0.0000,-0.4837,-0.3282,1.3876} Activity(exp=1): {-0.0000,-2.3885,-2.1455,-0.1904} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,0.0830} Activity(exp=4): {-0.0000,-0.0000} Binding mode 3: --------------- Mononucleotide: {-1.3265,-1.5405,-1.3925,-0.7574,-1.3427,-2.1829,-1.6042,0.1129,0.5048,-3.3294,-1.7224,-0.4700,2.1046,-2.4345,-2.3899,-2.2971,-2.3067,-1.1998,-1.7589,0.2485,-1.5885,-2.1268,-0.4893,-0.8124,-0.6524,-2.4749,-0.4253,-1.4643,-1.7501,-0.7176,-1.2816,-1.2675} Activity(exp=0): {0.0000,-0.8779,-1.1304,-2.1243} Activity(exp=1): {0.0000,0.7298,-1.2295,-3.8178} Activity(exp=2): {0.0000,2.3175,1.1158} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} The Likelihood DID NOT improve. Discarding fit component3-2-variation0. > No varitions possible for Binding mode 3. > Optimizing the full model (component3-4-all). >> Starting new optimization: component3-4-all. (2021-05-22 07:48:29.026). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[176,177,178,179]},{"h":[180,181,182,183]},{"h":[184,185,186]},{"h":[187,188]},{"h":[189,190]}],"bindingModeInteractions":[{}],"bindingModes":[{"mononucleotide":[],"activity":[[0,1,2,3],[4,5,6,7],[8,9,10],[11,12],[13,14]]},{"mononucleotide":[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],"activity":[[67,68,69,70],[71,72,73,74],[75,76,77],[78,79],[80,81]]},{"mononucleotide":[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],"activity":[[114,115,116,117],[118,119,120,121],[122,123,124],[125,126],[127,128]]},{"mononucleotide":[129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],"activity":[[161,162,163,164],[165,166,167,168],[169,170,171],[172,173],[174,175]]},{}]} Value and gradient before optimization: ======================================= value = 4.16379681866056 gradient = {0.0000,0.0001,0.0001,0.0000,0.0000,-0.0005,0.0004,0.0001,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0003,0.0001,-0.0004,0.0002,-0.0000,0.0000,0.0002,0.0003,0.0004,-0.0011,0.0007,0.0002,-0.0018,0.0007,-0.0011,0.0003,0.0004,0.0003,0.0006,0.0001,0.0001,-0.0010,-0.0001,-0.0000,0.0000,-0.0001,0.0013,-0.0000,-0.0002,-0.0012,-0.0005,0.0001,0.0001,0.0001,0.0003,-0.0002,0.0001,-0.0004,-0.0000,-0.0002,-0.0003,0.0003,-0.0000,-0.0001,0.0001,-0.0002,-0.0001,0.0001,-0.0001,-0.0001,-0.0000,0.0000,-0.0002,0.0000,-0.0000,0.0005,-0.0005,-0.0001,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0002,-0.0000,-0.0001,-0.0001,0.0004,-0.0001,-0.0002,-0.0002,0.0001,0.0001,0.0001,-0.0002,0.0005,0.0000,-0.0008,0.0003,-0.0001,0.0000,0.0001,0.0000,0.0002,-0.0005,0.0001,0.0003,-0.0004,0.0002,0.0002,0.0001,0.0002,0.0000,-0.0002,0.0000,-0.0000,-0.0001,0.0001,-0.0000,-0.0000,0.0000,0.0001,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-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 = 0.00405712022191451 Starting Function Value: 4.16379681866056 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 4.163785345080312 0.005487283461264 1.352506990456904 0.005751815094886 2 4 4.163770098980148 0.004816968983395 1.000000000000000 0.005622319751298 3 5 4.163731160690750 0.129069514759825 1.000000000000000 0.016313458462905 4 6 4.163592616894454 0.030395622865964 1.000000000000000 0.004849016297676 5 7 4.163569323128742 0.022006407265530 1.000000000000000 0.001895535524597 6 8 4.163559693682026 0.006436735610759 1.000000000000000 0.001575271547415 7 9 4.163534994165064 0.033281276037451 1.000000000000000 0.002155674688151 8 10 4.163524121944624 0.028933568151775 1.000000000000000 0.003031538500462 9 11 4.163512259284203 0.027838176746667 1.000000000000000 0.001364245735068 10 12 4.163505294435028 0.011247151665275 1.000000000000000 0.001281570474026 11 13 4.163494604236684 0.022914356055629 1.000000000000000 0.001837025078038 12 14 4.163485083861327 0.023428824540351 1.000000000000000 0.001598851208286 13 15 4.163469015195914 0.051425346948617 1.000000000000000 0.001823334533900 14 16 4.163455008371335 0.057323891821417 1.000000000000000 0.001719098131379 15 17 4.163446061515309 0.033033119356469 1.000000000000000 0.002083422077552 16 18 4.163437598866437 0.018540634653959 1.000000000000000 0.001385135037036 17 19 4.163429378874577 0.023543939810437 1.000000000000000 0.000964561415138 18 20 4.163419724681476 0.039038435544572 1.000000000000000 0.001237137457693 19 21 4.163408914864598 0.053888666464855 1.000000000000000 0.001266595195586 20 22 4.163397148969999 0.069917399541343 1.000000000000000 0.001913268588206 21 23 4.163388232263967 0.046717334137093 1.000000000000000 0.001279458880967 22 24 4.163382574282166 0.012511522272164 1.000000000000000 0.000836172164338 23 25 4.163378109451797 0.013795330400904 1.000000000000000 0.000988849531921 24 26 4.163367968404470 0.039683424569686 1.000000000000000 0.001248090283346 25 27 4.163356938521822 0.089848905127272 1.000000000000000 0.002025756061896 26 28 4.163346565623035 0.066987067444554 1.000000000000000 0.000923685846478 27 29 4.163341491370147 0.014568039998135 1.000000000000000 0.000712561101738 28 30 4.163334575163228 0.039571110925907 1.000000000000000 0.000822947892970 29 31 4.163329256194207 0.036112453209339 1.000000000000000 0.001023322371861 30 32 4.163323114516996 0.056457943753552 1.000000000000000 0.000682181569149 31 33 4.163318974652388 0.019484405202637 1.000000000000000 0.000532002395023 32 34 4.163314071278003 0.029526496875437 1.000000000000000 0.000738438957821 33 35 4.163311172919189 0.038148327282719 1.000000000000000 0.001192989834572 34 36 4.163307360485458 0.021230050368625 1.000000000000000 0.000653968037150 35 37 4.163304187526277 0.027449230350474 1.000000000000000 0.000399778071352 36 38 4.163303104019413 0.016276910260114 1.000000000000000 0.000379063127814 37 39 4.163300840776734 0.023463357800385 1.000000000000000 0.000381929605410 38 40 4.163299829762206 0.025824151141722 1.000000000000000 0.000430884976678 39 41 4.163299195834632 0.010063135527533 1.000000000000000 0.000219395620871 40 42 4.163298676556842 0.005494804009029 1.000000000000000 0.000192118603928 41 43 4.163297879243877 0.010288124843583 1.000000000000000 0.000237886033970 42 44 4.163296445780075 0.023395165148890 1.000000000000000 0.000299340411748 43 45 4.163294278238158 0.040511636264911 1.000000000000000 0.000329990125286 44 47 4.163293504719658 0.022933069172902 0.264227159848288 0.000376305102343 45 48 4.163292148066644 0.028622073310850 1.000000000000000 0.000177659707190 46 49 4.163291336495628 0.015795674438008 1.000000000000000 0.000156447723719 47 50 4.163290455509451 0.018307635202816 1.000000000000000 0.000220095045801 48 51 4.163289694545375 0.029613623319206 1.000000000000000 0.000364928916595 49 52 4.163288815676942 0.015582282829368 1.000000000000000 0.000179078095001 50 53 4.163288265612919 0.010805244590575 1.000000000000000 0.000138017871537 51 54 4.163287787042031 0.013025060370445 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1.000000000000000 0.000003588326626 440 465 4.163254715705349 0.001263460447780 1.000000000000000 0.000004872902235 441 467 4.163254715546031 0.001221230530888 0.480191832001898 0.000004758312366 442 468 4.163254715358878 0.000663901612797 1.000000000000000 0.000003135188158 443 469 4.163254715168725 0.000609089567380 1.000000000000000 0.000003714793786 444 470 4.163254714984468 0.000667380035195 1.000000000000000 0.000003845790397 445 472 4.163254714881857 0.001062802453019 0.440688061869706 0.000005005372436 446 473 4.163254714725999 0.000609998074894 1.000000000000000 0.000002568749713 447 474 4.163254714622799 0.000707562474245 1.000000000000000 0.000002874588203 448 475 4.163254714511788 0.000932577104698 1.000000000000000 0.000004223014071 449 476 4.163254714431358 0.001239691397020 1.000000000000000 0.000006130134292 450 477 4.163254714329638 0.000366167346152 1.000000000000000 0.000003064629902 451 478 4.163254714219989 0.000451903683190 1.000000000000000 0.000002763703734 452 479 4.163254714153887 0.000279177466746 1.000000000000000 0.000003540435596 453 480 4.163254713975863 0.000798637295266 1.000000000000000 0.000004622576770 454 482 4.163254713904723 0.000844530229925 0.292915110079018 0.000004798401667 455 483 4.163254713795247 0.000501583068911 1.000000000000000 0.000002538444612 456 484 4.163254713704212 0.000326757424210 1.000000000000000 0.000002689996222 457 485 4.163254713602720 0.000313026684908 1.000000000000000 0.000003690619011 458 486 4.163254713449378 0.000523354214707 1.000000000000000 0.000003629211536 459 487 4.163254713375249 0.001205251506220 1.000000000000000 0.000008695381954 460 488 4.163254713167148 0.000335629718252 1.000000000000000 0.000002690166412 461 489 4.163254713091387 0.000199606542018 1.000000000000000 0.000002049127683 462 490 4.163254713014275 0.000388817365852 1.000000000000000 0.000002666754663 463 491 4.163254712910429 0.000480965889074 1.000000000000000 0.000002697399006 464 493 4.163254712852896 0.000325223048838 0.295440656251351 0.000004912684888 465 494 4.163254712719971 0.000900286122853 1.000000000000000 0.000002799901161 466 495 4.163254712614198 0.000810476703494 1.000000000000000 0.000001880597899 467 496 4.163254712481895 0.001126543347832 1.000000000000000 0.000001971435855 468 497 4.163254712368444 0.000937991588137 1.000000000000000 0.000002683846770 469 499 4.163254712306731 0.000748987500654 0.372838494451839 0.000003914826590 470 500 4.163254712221115 0.000748987500654 1.000000000000000 0.000001754226662 Convergence criteria met. After: gradient norm = 1.7542266621975882E-6 >>> Parameters after optimization Count Table 0: --------------- h: {2.5121,1.5833,-0.2646,-3.8308} Count Table 1: --------------- h: {2.3649,1.6351,-0.5740,-3.4260} Count Table 2: --------------- h: {-0.0268,0.1187,-0.0919} Count Table 3: --------------- h: {0.1772,-0.1772} Count Table 4: --------------- h: {0.0000,-0.0000} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {0.0000,-2.2045,-2.3740,-3.6857} Activity(exp=1): {-0.0000,0.0517,-0.6671,1.6161} Activity(exp=2): {0.0000,-0.8693,-0.3326} Activity(exp=3): {-0.0000,-0.1054} Activity(exp=4): {0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {-0.7046,-0.9542,-0.7297,-0.7674,-0.2025,-1.4238,-0.6801,-0.8494,-0.5836,-1.5494,-1.7668,0.7440,-0.2020,-2.9656,0.7612,-0.7494,1.2680,-1.5228,-1.5139,-1.3872,-1.1874,-1.7768,-1.0534,0.8619,-0.9438,-1.9087,-1.3441,1.0408,-0.8872,-2.2442,-0.7907,0.7663,1.6808,-2.0389,-1.0397,-1.7580,-1.9235,-0.2786,-1.7773,0.8237,-1.0900,-1.5447,-0.0828,-0.4384,-0.1986,-1.6548,-0.3537,-0.9487,-1.1349,-0.5093,-0.7602,-0.7514} Activity(exp=0): {0.0000,0.8993,-0.7424,-0.9635} Activity(exp=1): {0.0000,0.2844,-0.2494,-2.3843} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8936,-1.2590,-1.0381,-0.8407,-0.9825,-1.4597,-1.0625,-0.5266,-0.9351,-2.0810,-1.8064,0.7911,-1.2091,-2.4307,0.9476,-1.3392,2.1264,-4.3554,-1.3773,-0.4250,-1.6342,0.1217,-1.8154,-0.7034,0.1322,-2.2032,-0.7014,-1.2589,-1.2701,-1.3379,-0.5748,-0.8485} Activity(exp=0): {0.0000,-0.4537,-0.2651,1.4238} Activity(exp=1): {0.0000,-3.0311,-2.1765,0.5431} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,-0.0718} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {-1.2504,-1.4666,-1.3203,-0.6755,-1.2540,-2.1112,-1.5273,0.1798,0.5595,-3.2316,-1.6539,-0.3867,2.1507,-2.4205,-2.2995,-2.1435,-2.2152,-1.1282,-1.6821,0.3128,-1.5162,-2.0553,-0.4126,-0.7286,-0.5712,-2.3942,-0.3579,-1.3894,-1.6822,-0.6445,-1.2027,-1.1835} Activity(exp=0): {-0.0000,-0.7530,-0.7137,-0.6049} Activity(exp=1): {-0.0000,0.3299,-0.9067,-3.2000} Activity(exp=2): {-0.0000,0.8954,0.2403} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} ================================== == Starts fiting Binding mode 4 == ================================== > Optimizing h (component4-0-h). >> Starting new optimization: component4-0-h. (2021-05-22 08:17:19.579). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[0,1,2,3]},{"h":[4,5,6,7]},{"h":[8,9,10]},{"h":[11,12]},{"h":[13,14]}],"bindingModeInteractions":[{}],"bindingModes":[{},{},{},{},{}]} Value and gradient before optimization: ======================================= value = 4.278028850410224 gradient = {-0.0351,0.0160,0.0137,0.0054,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.2496,0.2496} gradient norm = 0.35532992778882333 Starting Function Value: 4.278028850410224 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 2 4.141716947239032 1.000000000000000 2.814285884172164 0.108248712851989 2 3 4.129645767966540 0.226912849333865 1.000000000000000 0.020016642399422 3 4 4.128926788516774 0.041781228530274 1.000000000000000 0.014700054047748 4 5 4.127886217713558 0.144302852854411 1.000000000000000 0.000932350121832 5 6 4.127885553685706 0.003643902920348 1.000000000000000 0.000414456851640 6 7 4.127885202541217 0.001619181042286 1.000000000000000 0.000050004893270 7 8 4.127885198793459 0.000151903737159 1.000000000000000 0.000005134992242 8 9 4.127885198735506 0.000019208697619 1.000000000000000 0.000001528453431 9 10 4.127885198730790 0.000019208697619 1.000000000000000 0.000000082562142 Convergence criteria met. After: gradient norm = 8.25621421480895E-8 >>> Parameters after optimization Count Table 0: --------------- h: {2.7836,1.5512,-0.3827,-3.9522} Count Table 1: --------------- h: {2.3649,1.6351,-0.5740,-3.4260} Count Table 2: --------------- h: {-0.0268,0.1187,-0.0919} Count Table 3: --------------- h: {0.1772,-0.1772} Count Table 4: --------------- h: {0.5509,-0.5509} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {0.0000,-2.2045,-2.3740,-3.6857} Activity(exp=1): {-0.0000,0.0517,-0.6671,1.6161} Activity(exp=2): {0.0000,-0.8693,-0.3326} Activity(exp=3): {-0.0000,-0.1054} Activity(exp=4): {0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {-0.7046,-0.9542,-0.7297,-0.7674,-0.2025,-1.4238,-0.6801,-0.8494,-0.5836,-1.5494,-1.7668,0.7440,-0.2020,-2.9656,0.7612,-0.7494,1.2680,-1.5228,-1.5139,-1.3872,-1.1874,-1.7768,-1.0534,0.8619,-0.9438,-1.9087,-1.3441,1.0408,-0.8872,-2.2442,-0.7907,0.7663,1.6808,-2.0389,-1.0397,-1.7580,-1.9235,-0.2786,-1.7773,0.8237,-1.0900,-1.5447,-0.0828,-0.4384,-0.1986,-1.6548,-0.3537,-0.9487,-1.1349,-0.5093,-0.7602,-0.7514} Activity(exp=0): {0.0000,0.8993,-0.7424,-0.9635} Activity(exp=1): {0.0000,0.2844,-0.2494,-2.3843} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8936,-1.2590,-1.0381,-0.8407,-0.9825,-1.4597,-1.0625,-0.5266,-0.9351,-2.0810,-1.8064,0.7911,-1.2091,-2.4307,0.9476,-1.3392,2.1264,-4.3554,-1.3773,-0.4250,-1.6342,0.1217,-1.8154,-0.7034,0.1322,-2.2032,-0.7014,-1.2589,-1.2701,-1.3379,-0.5748,-0.8485} Activity(exp=0): {0.0000,-0.4537,-0.2651,1.4238} Activity(exp=1): {0.0000,-3.0311,-2.1765,0.5431} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,-0.0718} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {-1.2504,-1.4666,-1.3203,-0.6755,-1.2540,-2.1112,-1.5273,0.1798,0.5595,-3.2316,-1.6539,-0.3867,2.1507,-2.4205,-2.2995,-2.1435,-2.2152,-1.1282,-1.6821,0.3128,-1.5162,-2.0553,-0.4126,-0.7286,-0.5712,-2.3942,-0.3579,-1.3894,-1.6822,-0.6445,-1.2027,-1.1835} Activity(exp=0): {-0.0000,-0.7530,-0.7137,-0.6049} Activity(exp=1): {-0.0000,0.3299,-0.9067,-3.2000} Activity(exp=2): {-0.0000,0.8954,0.2403} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 4: --------------- Mononucleotide: {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,-1.0000,-1.0000,-1.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,-1.0000,0.0000,-1.0000,0.0000,0.0000,0.0000,0.0000} Activity(exp=0): {-0.3307,-2.1850,-2.5047,-2.5211} Activity(exp=1): {-0.3778,-0.3395,-1.0540,1.2042} Activity(exp=2): {-0.4134,-1.2544,-0.7414} Activity(exp=3): {-0.3987,-0.5034} Activity(exp=4): {-0.4193,-0.4193} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} > Initial optimization (component4-1-f0). >> Starting new optimization: component4-1-f0. (2021-05-22 08:17:41.499). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[47,48,49,50]},{"h":[51,52,53,54]},{"h":[55,56,57]},{"h":[58,59]},{"h":[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],"activity":[[32,33,34,35],[36,37,38,39],[40,41,42],[43,44],[45,46]]}]} Value and gradient before optimization: ======================================= value = 4.127885198730791 gradient = {-0.0059,0.0044,-0.0032,-0.0021,-0.0072,0.0105,0.0035,-0.0135,0.0020,0.0067,0.0088,-0.0242,0.0047,-0.0001,-0.0179,0.0067,-0.0296,0.0123,0.0127,-0.0021,0.0039,-0.0033,0.0049,-0.0121,-0.0022,0.0042,-0.0066,-0.0021,-0.0086,0.0074,0.0070,-0.0125,-0.0000,0.0035,0.0014,0.0002,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0117,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000} gradient norm = 0.05890172427625707 Starting Function Value: 4.127885198730791 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 4.111428640846952 0.446946385559529 7.588001727475573 0.147351974244255 2 4 4.089423844061860 0.529619377849345 1.000000000000000 0.222641456609920 3 5 4.062639987961227 1.645207095146378 1.000000000000000 0.441139847932600 4 6 3.994340228612470 0.358543410242847 1.000000000000000 0.091241572189752 5 7 3.973582445776880 0.600597100600211 1.000000000000000 0.048886765545322 6 8 3.959653932340713 0.686195130369557 1.000000000000000 0.050824973099828 7 9 3.942639407627180 1.298610456633757 1.000000000000000 0.074077013390132 8 10 3.933067113443609 0.250770518496354 1.000000000000000 0.038240173004543 9 11 3.923425805941691 0.564136082541925 1.000000000000000 0.025130609024757 10 12 3.915248280416713 0.806979052260944 1.000000000000000 0.029062765384286 11 13 3.907586742669130 1.029855557372926 1.000000000000000 0.028419554551558 12 14 3.903629024677268 0.704226983496825 1.000000000000000 0.025436396452981 13 15 3.900423182838211 0.540994396765090 1.000000000000000 0.024509345647349 14 16 3.898300491901905 0.478091242310558 1.000000000000000 0.025483679913239 15 17 3.896779223988822 0.522040281231623 1.000000000000000 0.013005435314890 16 18 3.896191213888471 0.402403072229495 1.000000000000000 0.008079894168639 17 19 3.895478966385283 0.507305972320825 1.000000000000000 0.005953294536091 18 20 3.894951916497851 0.437768662562269 1.000000000000000 0.005908005947812 19 21 3.894418951018446 0.341685640673136 1.000000000000000 0.007941589934810 20 22 3.894192090353757 0.428424109841377 1.000000000000000 0.007837204340748 21 23 3.894067970289580 0.149275845280565 1.000000000000000 0.003691753185777 22 24 3.893986846026602 0.050972191693924 1.000000000000000 0.002634876193271 23 25 3.893852523027866 0.193865538513406 1.000000000000000 0.002325344869255 24 26 3.893686558507688 0.444369448854119 1.000000000000000 0.004372656590475 25 28 3.893594755607872 0.370114943474625 0.476407861695489 0.003060408760282 26 29 3.893535969690556 0.208869933339254 1.000000000000000 0.001560414054996 27 30 3.893496422489952 0.153617690436200 1.000000000000000 0.001464834523597 28 31 3.893435818628872 0.165117286243130 1.000000000000000 0.001591161280228 29 32 3.893310146106481 0.324555910220892 1.000000000000000 0.001640004688339 30 33 3.893180327606580 0.426230074167250 1.000000000000000 0.001681817536088 31 35 3.893170344188501 0.051872664943886 0.067188591875303 0.001832358929998 32 36 3.893130317385778 0.246984518460492 1.000000000000000 0.000865902068130 33 37 3.893120738862648 0.032958715152193 1.000000000000000 0.000401408542947 34 38 3.893115153994331 0.036510043179304 1.000000000000000 0.000405380744809 35 39 3.893111523120151 0.026134830664841 1.000000000000000 0.000332140922452 36 40 3.893108443850440 0.073137178757715 1.000000000000000 0.001480348450489 37 41 3.893102559584373 0.031333698493440 1.000000000000000 0.000498488065644 38 42 3.893100010585824 0.011790381432337 1.000000000000000 0.000451693707011 39 43 3.893092575520057 0.072557389998538 1.000000000000000 0.000459670716966 40 44 3.893085418123429 0.099295405652399 1.000000000000000 0.000464452515309 41 46 3.893083037592075 0.066785252967031 0.285137694703107 0.000805843852115 42 47 3.893078091072153 0.145938848440779 1.000000000000000 0.000365053898329 43 48 3.893075998166694 0.074789619823405 1.000000000000000 0.000379024766978 44 49 3.893072158647972 0.121497569447199 1.000000000000000 0.000424152782765 45 50 3.893068277749884 0.083858410630289 1.000000000000000 0.000417481393620 46 51 3.893064398807945 0.072079076361053 1.000000000000000 0.000254450252213 47 52 3.893061831090209 0.077476841134797 1.000000000000000 0.000194721442774 48 53 3.893059803112037 0.090166973583136 1.000000000000000 0.000226061913374 49 54 3.893058583385223 0.068892105807878 1.000000000000000 0.000143160937459 50 55 3.893057972943109 0.026290523216969 1.000000000000000 0.000164430123404 51 56 3.893057432889553 0.018888152548320 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0.060810160105765 1.000000000000000 0.000138566129910 65 70 3.893048406325440 0.083070214450273 1.000000000000000 0.000099043118379 66 71 3.893048195637712 0.023338938503424 1.000000000000000 0.000060293990936 67 72 3.893048153632348 0.009227264419460 1.000000000000000 0.000017772082944 68 73 3.893048140773413 0.004993318417670 1.000000000000000 0.000018571498532 69 74 3.893048121999118 0.002831801350388 1.000000000000000 0.000022386025039 70 75 3.893048027333142 0.016021826445178 1.000000000000000 0.000045991514455 71 76 3.893047874784087 0.027577197472004 1.000000000000000 0.000074780114045 72 77 3.893047496125469 0.068918871289245 1.000000000000000 0.000122445059958 73 78 3.893046803497229 0.127858521084915 1.000000000000000 0.000164338981326 74 79 3.893045764074704 0.207248245226298 1.000000000000000 0.000173575512977 75 81 3.893045377743196 0.109316723137781 0.480638512721283 0.000133953377950 76 82 3.893044863599101 0.091824238020791 1.000000000000000 0.000060136503574 77 83 3.893044696737837 0.031076408475541 1.000000000000000 0.000037979114680 78 84 3.893044657215235 0.021633337618098 1.000000000000000 0.000033288561937 79 85 3.893044594992562 0.015046345021223 1.000000000000000 0.000048235624193 80 86 3.893044351050294 0.032474200672095 1.000000000000000 0.000074947125211 81 87 3.893043858465095 0.057428601208811 1.000000000000000 0.000118067250682 82 88 3.893042778493414 0.192120119092927 1.000000000000000 0.000142372712522 83 89 3.893041823948700 0.362922361536342 1.000000000000000 0.000274565538096 84 90 3.893040746774211 0.211081779431948 1.000000000000000 0.000109074016368 85 91 3.893040157260066 0.251140581209374 1.000000000000000 0.000036844917369 86 92 3.893040077553094 0.083534965475180 1.000000000000000 0.000021874075888 87 93 3.893040034637648 0.034321259797408 1.000000000000000 0.000023895649660 88 94 3.893039925140599 0.068112819974164 1.000000000000000 0.000046503519155 89 95 3.893039727715410 0.089381335511965 1.000000000000000 0.000078658688771 90 96 3.893039223852359 0.181741102827892 1.000000000000000 0.000127170885470 91 97 3.893038284465208 0.290894874265269 1.000000000000000 0.000169800027068 92 98 3.893037068970850 0.351108168688804 1.000000000000000 0.000161239047512 93 100 3.893036821068586 0.078211674641405 0.371136432115986 0.000137599129949 94 101 3.893036346864382 0.080651409297251 1.000000000000000 0.000060494664473 95 102 3.893036217692694 0.092829149398873 1.000000000000000 0.000011658643358 96 103 3.893036208368329 0.018578913813389 1.000000000000000 0.000011727307080 97 104 3.893036195026572 0.015543169358679 1.000000000000000 0.000016126099077 98 105 3.893036159061775 0.021958750379224 1.000000000000000 0.000024302343772 99 106 3.893036063970441 0.031377196797605 1.000000000000000 0.000041506775085 100 107 3.893035824539148 0.058196228282975 1.000000000000000 0.000065687308152 101 108 3.893035289738895 0.142973751712196 1.000000000000000 0.000102173279926 102 109 3.893034351153881 0.321792670875729 1.000000000000000 0.000125609325060 103 110 3.893033458368865 0.457088990711687 1.000000000000000 0.000182630645758 104 111 3.893033070776026 0.192328317229590 1.000000000000000 0.000050545777074 105 112 3.893032986071124 0.068278038700518 1.000000000000000 0.000067397526226 106 114 3.893032976331930 0.003942907245807 0.207732941592765 0.000014992122717 107 115 3.893032973962494 0.015014137331104 1.000000000000000 0.000013081735561 108 116 3.893032961878345 0.004915403942716 1.000000000000000 0.000010913299020 109 117 3.893032886186541 0.022207599294163 1.000000000000000 0.000033133893844 110 118 3.893032768422796 0.033198074566456 1.000000000000000 0.000061208139872 111 119 3.893032393494498 0.127486138175138 1.000000000000000 0.000107892319747 112 120 3.893031768500589 0.236662000972759 1.000000000000000 0.000156986898356 113 121 3.893031059101853 0.375838793255423 1.000000000000000 0.000219237743946 114 122 3.893030855893282 0.411964554898997 1.000000000000000 0.000376860714708 115 123 3.893030411142103 0.146349597280110 1.000000000000000 0.000065015228728 116 124 3.893030372233382 0.044669856762598 1.000000000000000 0.000050632110040 117 125 3.893030371634273 0.012443525599404 1.000000000000000 0.000072988057078 118 126 3.893030364304236 0.008128104418222 1.000000000000000 0.000004285290361 119 127 3.893030364051759 0.001563827086348 1.000000000000000 0.000002615411235 120 128 3.893030363819753 0.001563827086348 1.000000000000000 0.000001283996567 Convergence criteria met. After: gradient norm = 1.2839965670603223E-6 >>> Parameters after optimization Count Table 0: --------------- h: {2.5139,1.5836,-0.2654,-3.8321} Count Table 1: --------------- h: {2.3649,1.6351,-0.5740,-3.4260} Count Table 2: --------------- h: {-0.0268,0.1187,-0.0919} Count Table 3: --------------- h: {0.1772,-0.1772} Count Table 4: --------------- h: {1.3500,-1.3500} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {0.0000,-2.2045,-2.3740,-3.6857} Activity(exp=1): {-0.0000,0.0517,-0.6671,1.6161} Activity(exp=2): {0.0000,-0.8693,-0.3326} Activity(exp=3): {-0.0000,-0.1054} Activity(exp=4): {0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {-0.7046,-0.9542,-0.7297,-0.7674,-0.2025,-1.4238,-0.6801,-0.8494,-0.5836,-1.5494,-1.7668,0.7440,-0.2020,-2.9656,0.7612,-0.7494,1.2680,-1.5228,-1.5139,-1.3872,-1.1874,-1.7768,-1.0534,0.8619,-0.9438,-1.9087,-1.3441,1.0408,-0.8872,-2.2442,-0.7907,0.7663,1.6808,-2.0389,-1.0397,-1.7580,-1.9235,-0.2786,-1.7773,0.8237,-1.0900,-1.5447,-0.0828,-0.4384,-0.1986,-1.6548,-0.3537,-0.9487,-1.1349,-0.5093,-0.7602,-0.7514} Activity(exp=0): {0.0000,0.8993,-0.7424,-0.9635} Activity(exp=1): {0.0000,0.2844,-0.2494,-2.3843} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8936,-1.2590,-1.0381,-0.8407,-0.9825,-1.4597,-1.0625,-0.5266,-0.9351,-2.0810,-1.8064,0.7911,-1.2091,-2.4307,0.9476,-1.3392,2.1264,-4.3554,-1.3773,-0.4250,-1.6342,0.1217,-1.8154,-0.7034,0.1322,-2.2032,-0.7014,-1.2589,-1.2701,-1.3379,-0.5748,-0.8485} Activity(exp=0): {0.0000,-0.4537,-0.2651,1.4238} Activity(exp=1): {0.0000,-3.0311,-2.1765,0.5431} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,-0.0718} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {-1.2504,-1.4666,-1.3203,-0.6755,-1.2540,-2.1112,-1.5273,0.1798,0.5595,-3.2316,-1.6539,-0.3867,2.1507,-2.4205,-2.2995,-2.1435,-2.2152,-1.1282,-1.6821,0.3128,-1.5162,-2.0553,-0.4126,-0.7286,-0.5712,-2.3942,-0.3579,-1.3894,-1.6822,-0.6445,-1.2027,-1.1835} Activity(exp=0): {-0.0000,-0.7530,-0.7137,-0.6049} Activity(exp=1): {-0.0000,0.3299,-0.9067,-3.2000} Activity(exp=2): {-0.0000,0.8954,0.2403} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 4: --------------- Mononucleotide: {-1.4813,-2.3672,-1.6136,-1.6078,-1.6542,-3.0179,-1.7486,-0.6492,-2.0896,-3.6943,-2.8200,1.5340,-1.7697,-4.1168,1.6583,-2.8416,2.6540,-3.1747,-3.9213,-2.6278,-3.6428,-0.9075,-1.9532,-0.5663,-1.2553,-2.7194,-0.9349,-2.1603,-1.9413,-1.8337,-1.9765,-1.3184} Activity(exp=0): {0.0000,-4.0345,-4.5669,-3.4052} Activity(exp=1): {0.0000,0.0000,0.0000,-0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,4.9370} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Suggested variations: key=8;5;0, description = Initial model. > Optimizing variation "Initial model." (component4-2-variation0). >> Starting new optimization: component4-2-variation0. (2021-05-22 08:23:00.525). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[47,48,49,50]},{"h":[51,52,53,54]},{"h":[55,56,57]},{"h":[58,59]},{"h":[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],"activity":[[32,33,34,35],[36,37,38,39],[40,41,42],[43,44],[45,46]]}]} Value and gradient before optimization: ======================================= value = 3.893030363819753 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 = 1.2839965670607406E-6 Already at minimum! After: gradient norm = 1.2839965670607406E-6 >>> Parameters after optimization Count Table 0: --------------- h: {2.5139,1.5836,-0.2654,-3.8321} Count Table 1: --------------- h: {2.3649,1.6351,-0.5740,-3.4260} Count Table 2: --------------- h: {-0.0268,0.1187,-0.0919} Count Table 3: --------------- h: {0.1772,-0.1772} Count Table 4: --------------- h: {1.3500,-1.3500} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {0.0000,-2.2045,-2.3740,-3.6857} Activity(exp=1): {-0.0000,0.0517,-0.6671,1.6161} Activity(exp=2): {0.0000,-0.8693,-0.3326} Activity(exp=3): {-0.0000,-0.1054} Activity(exp=4): {0.0000,-0.0000} Binding mode 1: --------------- Mononucleotide: {-0.7046,-0.9542,-0.7297,-0.7674,-0.2025,-1.4238,-0.6801,-0.8494,-0.5836,-1.5494,-1.7668,0.7440,-0.2020,-2.9656,0.7612,-0.7494,1.2680,-1.5228,-1.5139,-1.3872,-1.1874,-1.7768,-1.0534,0.8619,-0.9438,-1.9087,-1.3441,1.0408,-0.8872,-2.2442,-0.7907,0.7663,1.6808,-2.0389,-1.0397,-1.7580,-1.9235,-0.2786,-1.7773,0.8237,-1.0900,-1.5447,-0.0828,-0.4384,-0.1986,-1.6548,-0.3537,-0.9487,-1.1349,-0.5093,-0.7602,-0.7514} Activity(exp=0): {0.0000,0.8993,-0.7424,-0.9635} Activity(exp=1): {0.0000,0.2844,-0.2494,-2.3843} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8936,-1.2590,-1.0381,-0.8407,-0.9825,-1.4597,-1.0625,-0.5266,-0.9351,-2.0810,-1.8064,0.7911,-1.2091,-2.4307,0.9476,-1.3392,2.1264,-4.3554,-1.3773,-0.4250,-1.6342,0.1217,-1.8154,-0.7034,0.1322,-2.2032,-0.7014,-1.2589,-1.2701,-1.3379,-0.5748,-0.8485} Activity(exp=0): {0.0000,-0.4537,-0.2651,1.4238} Activity(exp=1): {0.0000,-3.0311,-2.1765,0.5431} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,-0.0718} Activity(exp=4): {0.0000,0.0000} Binding mode 3: --------------- Mononucleotide: {-1.2504,-1.4666,-1.3203,-0.6755,-1.2540,-2.1112,-1.5273,0.1798,0.5595,-3.2316,-1.6539,-0.3867,2.1507,-2.4205,-2.2995,-2.1435,-2.2152,-1.1282,-1.6821,0.3128,-1.5162,-2.0553,-0.4126,-0.7286,-0.5712,-2.3942,-0.3579,-1.3894,-1.6822,-0.6445,-1.2027,-1.1835} Activity(exp=0): {-0.0000,-0.7530,-0.7137,-0.6049} Activity(exp=1): {-0.0000,0.3299,-0.9067,-3.2000} Activity(exp=2): {-0.0000,0.8954,0.2403} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 4: --------------- Mononucleotide: {-1.4813,-2.3672,-1.6136,-1.6078,-1.6542,-3.0179,-1.7486,-0.6492,-2.0896,-3.6943,-2.8200,1.5340,-1.7697,-4.1168,1.6583,-2.8416,2.6540,-3.1747,-3.9213,-2.6278,-3.6428,-0.9075,-1.9532,-0.5663,-1.2553,-2.7194,-0.9349,-2.1603,-1.9413,-1.8337,-1.9765,-1.3184} Activity(exp=0): {0.0000,-4.0345,-4.5669,-3.4052} Activity(exp=1): {0.0000,0.0000,0.0000,-0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,4.9370} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} The Likelihood DID NOT improve. Discarding fit component4-2-variation0. > No varitions possible for Binding mode 4. > Optimizing the full model (component4-4-all). >> Starting new optimization: component4-4-all. (2021-05-22 08:23:03.016). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[223,224,225,226]},{"h":[227,228,229,230]},{"h":[231,232,233]},{"h":[234,235]},{"h":[236,237]}],"bindingModeInteractions":[{}],"bindingModes":[{"mononucleotide":[],"activity":[[0,1,2,3],[4,5,6,7],[8,9,10],[11,12],[13,14]]},{"mononucleotide":[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],"activity":[[67,68,69,70],[71,72,73,74],[75,76,77],[78,79],[80,81]]},{"mononucleotide":[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],"activity":[[114,115,116,117],[118,119,120,121],[122,123,124],[125,126],[127,128]]},{"mononucleotide":[129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160],"activity":[[161,162,163,164],[165,166,167,168],[169,170,171],[172,173],[174,175]]},{"mononucleotide":[176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207],"activity":[[208,209,210,211],[212,213,214,215],[216,217,218],[219,220],[221,222]]}]} Value and gradient before optimization: ======================================= value = 3.8930303638197565 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,-0.0001,-0.0000,-0.0000,-0.0000,-0.0000,-0.0001,-0.0000,-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,-0.0001,-0.0001,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0001,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0001,-0.0000,0.0000,0.0001,-0.0000,0.0001,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,-0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000,-0.0000,0.0000,-0.0000,0.0000,-0.0000,-0.0000,-0.0000,0.0000,0.0000,-0.0000} gradient norm = 2.468931489958512E-4 Starting Function Value: 3.8930303638197565 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 3.893030339223501 0.000183094710448 0.741594941749743 0.000155074174918 2 4 3.893030326648654 0.000123990109259 1.000000000000000 0.000107526634429 3 5 3.893030308492173 0.000287528456896 1.000000000000000 0.000087444575778 4 6 3.893030290413082 0.000383199039745 1.000000000000000 0.000095411545346 5 7 3.893030258701813 0.000882251628158 1.000000000000000 0.000106116694764 6 8 3.893030248676446 0.001337868734889 1.000000000000000 0.000184575610471 7 9 3.893030224940679 0.000220679178692 1.000000000000000 0.000058604867593 8 10 3.893030218164022 0.000200676434891 1.000000000000000 0.000037510177533 9 11 3.893030211446752 0.000381154132363 1.000000000000000 0.000037690539857 10 12 3.893030204798929 0.000512409668803 1.000000000000000 0.000038892917215 11 14 3.893030201757067 0.000377476590944 0.492291834613100 0.000040415749791 12 15 3.893030198608016 0.000243191818023 1.000000000000000 0.000028922003510 13 16 3.893030193627481 0.000456523945299 1.000000000000000 0.000038202592364 14 17 3.893030187429516 0.000669379680171 1.000000000000000 0.000045746786441 15 18 3.893030176346926 0.001247793560338 1.000000000000000 0.000044171902045 16 20 3.893030169673180 0.001246633455620 0.474306067243864 0.000091458271457 17 21 3.893030156254080 0.001663542562431 1.000000000000000 0.000047230713782 18 22 3.893030145315602 0.001297743733835 1.000000000000000 0.000039967068796 19 23 3.893030127212030 0.002445141617711 1.000000000000000 0.000055111511587 20 24 3.893030103166634 0.003398527739824 1.000000000000000 0.000063285419413 21 25 3.893030063111260 0.007559692871986 1.000000000000000 0.000113134296269 22 26 3.893030026302526 0.005372174989287 1.000000000000000 0.000055971175977 23 27 3.893029997623460 0.003784949348418 1.000000000000000 0.000053393855081 24 28 3.893029962646144 0.004264211546455 1.000000000000000 0.000067760566381 25 29 3.893029912193784 0.011680989917360 1.000000000000000 0.000166534737762 26 30 3.893029836845174 0.009238552898608 1.000000000000000 0.000094393898737 27 31 3.893029764482255 0.008649725244173 1.000000000000000 0.000084974107817 28 32 3.893029667209580 0.015645270503275 1.000000000000000 0.000097149963854 29 33 3.893029573665181 0.017036667012622 1.000000000000000 0.000118294745096 30 34 3.893029465760353 0.030652610339470 1.000000000000000 0.000123083405414 31 35 3.893029367363795 0.006559421831098 1.000000000000000 0.000089872586368 32 36 3.893029242923132 0.010521459993503 1.000000000000000 0.000122344512823 33 37 3.893029112962621 0.018662573474702 1.000000000000000 0.000147884353201 34 38 3.893028922918661 0.046527867517043 1.000000000000000 0.000167957531140 35 39 3.893028757483114 0.023260088886706 1.000000000000000 0.000108724997851 36 40 3.893028616857215 0.023301554501105 1.000000000000000 0.000119483140279 37 41 3.893028514307729 0.018600062540440 1.000000000000000 0.000131118098870 38 42 3.893028379946234 0.021487959058340 1.000000000000000 0.000092511455149 39 43 3.893028232938470 0.021312079421584 1.000000000000000 0.000102894731071 40 44 3.893028047605374 0.030459637710684 1.000000000000000 0.000116470609181 41 45 3.893027798781906 0.042837296228216 1.000000000000000 0.000109608692898 42 46 3.893027500864010 0.060212714232548 1.000000000000000 0.000185228732145 43 47 3.893027310600361 0.035988547803033 1.000000000000000 0.000108615601189 44 48 3.893027154933221 0.024806612635069 1.000000000000000 0.000120586458333 45 49 3.893026867057593 0.044514252317297 1.000000000000000 0.000156058826598 46 50 3.893026603921801 0.051430290898445 1.000000000000000 0.000091992498018 47 51 3.893026423908579 0.030767171156893 1.000000000000000 0.000111758096814 48 52 3.893026150934225 0.052356290048039 1.000000000000000 0.000127685670931 49 53 3.893025958183734 0.036802094004207 1.000000000000000 0.000109877354657 50 54 3.893025712018051 0.054051808596102 1.000000000000000 0.000129279386989 51 55 3.893025494170549 0.068796386035371 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0.039703797189959 1.000000000000000 0.000072143141992 65 70 3.893022445574010 0.039322440175381 1.000000000000000 0.000084087621911 66 71 3.893022264481742 0.062232907522616 1.000000000000000 0.000246814664124 67 72 3.893022104652815 0.012310912158576 1.000000000000000 0.000108978367783 68 73 3.893021985925572 0.015116449385403 1.000000000000000 0.000067575785451 69 74 3.893021926902092 0.011166281048759 1.000000000000000 0.000079551691545 70 75 3.893021724812474 0.041380555589791 1.000000000000000 0.000090724482795 71 76 3.893021458693203 0.062301193608837 1.000000000000000 0.000083165392114 72 77 3.893021309937502 0.050345566692558 1.000000000000000 0.000140041765280 73 78 3.893021212397227 0.009231909630521 1.000000000000000 0.000056175710389 74 79 3.893021124757274 0.007233246471740 1.000000000000000 0.000078018691638 75 80 3.893021023918541 0.014507862948429 1.000000000000000 0.000097099234833 76 81 3.893020796971797 0.043804088950176 1.000000000000000 0.000116522622411 77 82 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1.000000000000000 0.000005861957373 340 362 3.893004145231358 0.000674399582221 1.000000000000000 0.000005453084731 341 363 3.893004144467683 0.001808260604680 1.000000000000000 0.000006021474190 342 365 3.893004144308592 0.000625872721231 0.265516579758819 0.000007602234635 343 366 3.893004144038234 0.000771157332114 1.000000000000000 0.000004732413118 344 367 3.893004143763474 0.000855295633070 1.000000000000000 0.000003627718827 345 368 3.893004143432425 0.001289879020627 1.000000000000000 0.000004704753557 346 369 3.893004143007936 0.001981796549644 1.000000000000000 0.000005282248900 347 371 3.893004142842254 0.001236621002801 0.337711426931019 0.000007404800777 348 372 3.893004142458152 0.002325890521394 1.000000000000000 0.000003932902458 349 373 3.893004142208029 0.001408364744157 1.000000000000000 0.000002572269843 350 374 3.893004141965788 0.001598167598346 1.000000000000000 0.000004673157675 351 375 3.893004141953179 0.001835709160813 1.000000000000000 0.000008679825624 352 376 3.893004141772299 0.000726024573163 1.000000000000000 0.000002664005779 353 377 3.893004141706868 0.000726024573163 1.000000000000000 0.000002005574624 Convergence criteria met. After: gradient norm = 2.0055746240755246E-6 >>> Parameters after optimization Count Table 0: --------------- h: {3.7609,1.9984,-0.7176,-5.0417} Count Table 1: --------------- h: {2.7225,1.7452,-0.6865,-3.7812} Count Table 2: --------------- h: {0.1092,0.1186,-0.2279} Count Table 3: --------------- h: {0.2669,-0.2669} Count Table 4: --------------- h: {0.0606,-0.0606} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-1.3744,-1.5272,-3.1057} Activity(exp=1): {-0.0000,0.2990,-0.4446,1.8583} Activity(exp=2): {-0.0000,-0.7332,-0.1967} Activity(exp=3): {-0.0000,0.0732} Activity(exp=4): {-0.0000,-2.5813} Binding mode 1: --------------- Mononucleotide: {-0.6659,-0.9155,-0.6910,-0.7287,-0.1638,-1.3851,-0.6414,-0.8108,-0.5450,-1.5108,-1.7280,0.7826,-0.1630,-2.9280,0.8001,-0.7104,1.3066,-1.4840,-1.4752,-1.3486,-1.1487,-1.7381,-1.0148,0.9004,-0.9051,-1.8699,-1.3057,1.0796,-0.8484,-2.2057,-0.7523,0.8052,1.7194,-2.0001,-1.0012,-1.7192,-1.8851,-0.2399,-1.7386,0.8624,-1.0513,-1.5060,-0.0441,-0.3997,-0.1600,-1.6162,-0.3149,-0.9101,-1.0962,-0.4707,-0.7215,-0.7128} Activity(exp=0): {-0.0000,1.2300,-0.3774,-0.7086} Activity(exp=1): {0.0000,0.0291,-0.5297,-2.6445} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8374,-1.2024,-0.9819,-0.7847,-0.9263,-1.4025,-1.0063,-0.4712,-0.8793,-2.0213,-1.7501,0.8443,-1.1528,-2.3694,1.0004,-1.2846,2.1863,-4.3138,-1.3093,-0.3695,-1.5761,0.1778,-1.7597,-0.6484,0.1893,-2.1472,-0.6466,-1.2019,-1.2134,-1.2819,-0.5183,-0.7928} Activity(exp=0): {-0.0000,-0.0703,0.1548,1.7340} Activity(exp=1): {-0.0000,-3.2202,-2.4036,0.3390} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.3401} Activity(exp=4): {-0.0000,-0.0000} Binding mode 3: --------------- Mononucleotide: {-1.1996,-1.4157,-1.2695,-0.6247,-1.2031,-2.0606,-1.4763,0.2305,0.6106,-3.1819,-1.6028,-0.3355,2.2024,-2.3680,-2.2451,-2.0988,-2.1644,-1.0775,-1.6312,0.3635,-1.4653,-2.0044,-0.3619,-0.6779,-0.5205,-2.3434,-0.3071,-1.3385,-1.6312,-0.5937,-1.1518,-1.1327} Activity(exp=0): {0.0000,-0.3280,-0.2518,-0.2682} Activity(exp=1): {0.0000,0.1696,-1.0898,-3.3340} Activity(exp=2): {0.0000,0.6240,-0.0312} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {-1.5004,-2.3861,-1.6328,-1.6270,-1.6734,-3.0368,-1.7677,-0.6684,-2.1093,-3.7112,-2.8394,1.5136,-1.7883,-4.1375,1.6392,-2.8597,2.6293,-3.1962,-3.9294,-2.6500,-3.6615,-0.9269,-1.9723,-0.5857,-1.2744,-2.7384,-0.9542,-2.1794,-1.9604,-1.8527,-1.9957,-1.3376} Activity(exp=0): {-0.0000,-3.2167,-3.7560,-2.6920} Activity(exp=1): {-0.0000,-0.0000,-0.0000,0.0000} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,2.5184} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,0.0000,0.0000,0.0000} Activity(exp=1): {0.0000,0.0000,0.0000,0.0000} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} ============================================== == Starts fiting Binding mode interaction 0 == ============================================== > Optimizing h (component5-0-h). >> Starting new optimization: component5-0-h. (2021-05-22 08:49:12.828). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[0,1,2,3]},{"h":[4,5,6,7]},{"h":[8,9,10]},{"h":[11,12]},{"h":[13,14]}],"bindingModeInteractions":[{}],"bindingModes":[{},{},{},{},{}]} Value and gradient before optimization: ======================================= value = 3.9221696964693953 gradient = {-0.0107,-0.0285,-0.0213,0.0604,0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000,0.0000,0.0000,-0.0000,0.0000,-0.0000} gradient norm = 0.07090975900336972 Starting Function Value: 3.9221696964693953 Iterations Fnc. Calls Likelihood Distance Moved Step Alpha Gradient Norm 1 3 3.906212671891864 0.453089564735177 6.389664428469518 0.028938254296949 2 4 3.903077066131297 0.171606365092915 1.000000000000000 0.011915169521460 3 5 3.902486853912969 0.141596801936810 1.000000000000000 0.006022164452440 4 6 3.902406261546452 0.033100549276648 1.000000000000000 0.001377578820820 5 7 3.902401685363782 0.007228737796511 1.000000000000000 0.000015841691406 6 8 3.902401684678901 0.000093261712168 1.000000000000000 0.000003356945339 7 10 3.902401684666813 0.000093261712168 0.408920366315684 0.000000185924384 Convergence criteria met. After: gradient norm = 1.8592438425966645E-7 >>> Parameters after optimization Count Table 0: --------------- h: {4.0352,2.2444,-0.7339,-5.5456} Count Table 1: --------------- h: {2.7225,1.7452,-0.6865,-3.7812} Count Table 2: --------------- h: {0.1092,0.1186,-0.2279} Count Table 3: --------------- h: {0.2669,-0.2669} Count Table 4: --------------- h: {0.0606,-0.0606} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-1.3744,-1.5272,-3.1057} Activity(exp=1): {-0.0000,0.2990,-0.4446,1.8583} Activity(exp=2): {-0.0000,-0.7332,-0.1967} Activity(exp=3): {-0.0000,0.0732} Activity(exp=4): {-0.0000,-2.5813} Binding mode 1: --------------- Mononucleotide: {-0.6659,-0.9155,-0.6910,-0.7287,-0.1638,-1.3851,-0.6414,-0.8108,-0.5450,-1.5108,-1.7280,0.7826,-0.1630,-2.9280,0.8001,-0.7104,1.3066,-1.4840,-1.4752,-1.3486,-1.1487,-1.7381,-1.0148,0.9004,-0.9051,-1.8699,-1.3057,1.0796,-0.8484,-2.2057,-0.7523,0.8052,1.7194,-2.0001,-1.0012,-1.7192,-1.8851,-0.2399,-1.7386,0.8624,-1.0513,-1.5060,-0.0441,-0.3997,-0.1600,-1.6162,-0.3149,-0.9101,-1.0962,-0.4707,-0.7215,-0.7128} Activity(exp=0): {-0.0000,1.2300,-0.3774,-0.7086} Activity(exp=1): {0.0000,0.0291,-0.5297,-2.6445} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8374,-1.2024,-0.9819,-0.7847,-0.9263,-1.4025,-1.0063,-0.4712,-0.8793,-2.0213,-1.7501,0.8443,-1.1528,-2.3694,1.0004,-1.2846,2.1863,-4.3138,-1.3093,-0.3695,-1.5761,0.1778,-1.7597,-0.6484,0.1893,-2.1472,-0.6466,-1.2019,-1.2134,-1.2819,-0.5183,-0.7928} Activity(exp=0): {-0.0000,-0.0703,0.1548,1.7340} Activity(exp=1): {-0.0000,-3.2202,-2.4036,0.3390} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.3401} Activity(exp=4): {-0.0000,-0.0000} Binding mode 3: --------------- Mononucleotide: {-1.1996,-1.4157,-1.2695,-0.6247,-1.2031,-2.0606,-1.4763,0.2305,0.6106,-3.1819,-1.6028,-0.3355,2.2024,-2.3680,-2.2451,-2.0988,-2.1644,-1.0775,-1.6312,0.3635,-1.4653,-2.0044,-0.3619,-0.6779,-0.5205,-2.3434,-0.3071,-1.3385,-1.6312,-0.5937,-1.1518,-1.1327} Activity(exp=0): {0.0000,-0.3280,-0.2518,-0.2682} Activity(exp=1): {0.0000,0.1696,-1.0898,-3.3340} Activity(exp=2): {0.0000,0.6240,-0.0312} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {-1.5004,-2.3861,-1.6328,-1.6270,-1.6734,-3.0368,-1.7677,-0.6684,-2.1093,-3.7112,-2.8394,1.5136,-1.7883,-4.1375,1.6392,-2.8597,2.6293,-3.1962,-3.9294,-2.6500,-3.6615,-0.9269,-1.9723,-0.5857,-1.2744,-2.7384,-0.9542,-2.1794,-1.9604,-1.8527,-1.9957,-1.3376} Activity(exp=0): {-0.0000,-3.2167,-3.7560,-2.6920} Activity(exp=1): {-0.0000,-0.0000,-0.0000,0.0000} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,2.5184} Binding mode interaction 0: --------------------------- Activity(exp=0): {2.8206,1.7726,1.4731,1.3280} Activity(exp=1): {3.5079,3.7698,3.0305,5.3085} Activity(exp=2): {3.4516,2.7436,3.2565} Activity(exp=3): {3.4748,3.5372} Activity(exp=4): {3.4453,1.2165} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} > Initial optimization (component5-1-f0). >> Starting new optimization: component5-1-f0. (2021-05-22 08:49:36.373). >>> Packing before optimization Packing: 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Value and gradient before optimization: ======================================= value = 3.9024016846668186 gradient = 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gradient norm = 0.011543350321866113 Starting Function Value: 3.9024016846668186 Iterations Fnc. 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1.000000000000000 0.000011114854288 165 175 3.887506212070843 0.003695338147696 1.000000000000000 0.000013154404470 166 176 3.887506208541656 0.006231989635389 1.000000000000000 0.000016639863591 167 177 3.887506204096468 0.007212157740894 1.000000000000000 0.000010855922980 168 178 3.887506201114945 0.004891708733480 1.000000000000000 0.000006161635187 169 179 3.887506199359624 0.004206031087771 1.000000000000000 0.000006932470207 170 180 3.887506197548460 0.005226575092491 1.000000000000000 0.000009948075112 171 181 3.887506194807572 0.008509597524041 1.000000000000000 0.000011077602350 172 182 3.887506193666515 0.006980012409574 1.000000000000000 0.000024707558866 173 183 3.887506191505039 0.002685582787068 1.000000000000000 0.000006127806065 174 184 3.887506190380106 0.003233655876611 1.000000000000000 0.000004867906715 175 185 3.887506189415112 0.003232116090141 1.000000000000000 0.000006762898442 176 186 3.887506188317104 0.004427592531811 1.000000000000000 0.000005134918632 177 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1.000000000000000 0.000004193717321 190 200 3.887506178052424 0.002023819248496 1.000000000000000 0.000004520822074 191 201 3.887506177621056 0.003678187250659 1.000000000000000 0.000002883646651 192 202 3.887506177360254 0.002021061584231 1.000000000000000 0.000001526807657 193 203 3.887506177212381 0.001008807788963 1.000000000000000 0.000001890901531 194 204 3.887506177068348 0.000687010372144 1.000000000000000 0.000003184405052 195 205 3.887506176782309 0.001091840957988 1.000000000000000 0.000004976075466 196 206 3.887506176187125 0.001939587201974 1.000000000000000 0.000007075302993 197 207 3.887506175098996 0.003471310360436 1.000000000000000 0.000008331658392 198 208 3.887506173751120 0.004718342275736 1.000000000000000 0.000007083726992 199 209 3.887506173446116 0.004255809659484 1.000000000000000 0.000009692935152 200 210 3.887506172821179 0.001633743938823 1.000000000000000 0.000001639352537 201 211 3.887506172734605 0.000642684298476 1.000000000000000 0.000001123024308 202 212 3.887506172691377 0.000642684298476 1.000000000000000 0.000000888655906 Convergence criteria met. After: gradient norm = 8.886559063458183E-7 >>> Parameters after optimization Count Table 0: --------------- h: {3.9215,2.0879,-0.7596,-5.2498} Count Table 1: --------------- h: {2.7225,1.7452,-0.6865,-3.7812} Count Table 2: --------------- h: {0.1092,0.1186,-0.2279} Count Table 3: --------------- h: {0.2669,-0.2669} Count Table 4: --------------- h: {0.0606,-0.0606} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {-0.0000,-1.3744,-1.5272,-3.1057} Activity(exp=1): {-0.0000,0.2990,-0.4446,1.8583} Activity(exp=2): {-0.0000,-0.7332,-0.1967} Activity(exp=3): {-0.0000,0.0732} Activity(exp=4): {-0.0000,-2.5813} Binding mode 1: --------------- Mononucleotide: {-0.6659,-0.9155,-0.6910,-0.7287,-0.1638,-1.3851,-0.6414,-0.8108,-0.5450,-1.5108,-1.7280,0.7826,-0.1630,-2.9280,0.8001,-0.7104,1.3066,-1.4840,-1.4752,-1.3486,-1.1487,-1.7381,-1.0148,0.9004,-0.9051,-1.8699,-1.3057,1.0796,-0.8484,-2.2057,-0.7523,0.8052,1.7194,-2.0001,-1.0012,-1.7192,-1.8851,-0.2399,-1.7386,0.8624,-1.0513,-1.5060,-0.0441,-0.3997,-0.1600,-1.6162,-0.3149,-0.9101,-1.0962,-0.4707,-0.7215,-0.7128} Activity(exp=0): {-0.0000,1.2300,-0.3774,-0.7086} Activity(exp=1): {0.0000,0.0291,-0.5297,-2.6445} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 2: --------------- Mononucleotide: {-0.8374,-1.2024,-0.9819,-0.7847,-0.9263,-1.4025,-1.0063,-0.4712,-0.8793,-2.0213,-1.7501,0.8443,-1.1528,-2.3694,1.0004,-1.2846,2.1863,-4.3138,-1.3093,-0.3695,-1.5761,0.1778,-1.7597,-0.6484,0.1893,-2.1472,-0.6466,-1.2019,-1.2134,-1.2819,-0.5183,-0.7928} Activity(exp=0): {-0.0000,-0.0703,0.1548,1.7340} Activity(exp=1): {-0.0000,-3.2202,-2.4036,0.3390} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.3401} Activity(exp=4): {-0.0000,-0.0000} Binding mode 3: --------------- Mononucleotide: {-1.1996,-1.4157,-1.2695,-0.6247,-1.2031,-2.0606,-1.4763,0.2305,0.6106,-3.1819,-1.6028,-0.3355,2.2024,-2.3680,-2.2451,-2.0988,-2.1644,-1.0775,-1.6312,0.3635,-1.4653,-2.0044,-0.3619,-0.6779,-0.5205,-2.3434,-0.3071,-1.3385,-1.6312,-0.5937,-1.1518,-1.1327} Activity(exp=0): {0.0000,-0.3280,-0.2518,-0.2682} Activity(exp=1): {0.0000,0.1696,-1.0898,-3.3340} Activity(exp=2): {0.0000,0.6240,-0.0312} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {-1.5004,-2.3861,-1.6328,-1.6270,-1.6734,-3.0368,-1.7677,-0.6684,-2.1093,-3.7112,-2.8394,1.5136,-1.7883,-4.1375,1.6392,-2.8597,2.6293,-3.1962,-3.9294,-2.6500,-3.6615,-0.9269,-1.9723,-0.5857,-1.2744,-2.7384,-0.9542,-2.1794,-1.9604,-1.8527,-1.9957,-1.3376} Activity(exp=0): {-0.0000,-3.2167,-3.7560,-2.6920} Activity(exp=1): {-0.0000,-0.0000,-0.0000,0.0000} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,2.5184} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0009,1.8321,-0.0693,-0.6347} Activity(exp=1): {0.0011,0.0012,0.0009,0.0017} Activity(exp=2): {0.0011,0.0009,0.0010} Activity(exp=3): {0.0011,0.0011} Activity(exp=4): {0.0011,0.0004} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011,-0.2839,-0.3137,-0.3020,-0.2741,0.0244,-0.1910,-0.2359,-0.0885,0.0286,0.0005}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011,-0.2839,-0.3137,-0.3020,-0.2741,0.0244,-0.1910,-0.2359,-0.0885,0.0286}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011,-0.2839,-0.3137,-0.3020,-0.2741,0.0244,-0.1910,-0.2359,-0.0885}, {0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011,-0.2839,-0.3137,-0.3020,-0.2741,0.0244,-0.1910,-0.2359}, {-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011,-0.2839,-0.3137,-0.3020,-0.2741,0.0244,-0.1910}, {-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011,-0.2839,-0.3137,-0.3020,-0.2741,0.0244}, {1.6774,-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011,-0.2839,-0.3137,-0.3020,-0.2741}, {0.1901,1.6774,-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011,-0.2839,-0.3137,-0.3020}, {0.1533,0.1901,1.6774,-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011,-0.2839,-0.3137}, {-0.1002,0.1533,0.1901,1.6774,-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011,-0.2839}, {0.8983,-0.1002,0.1533,0.1901,1.6774,-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354,-0.4011}, {1.4342,0.8983,-0.1002,0.1533,0.1901,1.6774,-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144,-0.4354}, {1.4153,1.4342,0.8983,-0.1002,0.1533,0.1901,1.6774,-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731,-0.3144}, {1.5407,1.4153,1.4342,0.8983,-0.1002,0.1533,0.1901,1.6774,-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699,-0.2731}, {0.4232,1.5407,1.4153,1.4342,0.8983,-0.1002,0.1533,0.1901,1.6774,-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394,-0.2699}, {0.0127,0.4232,1.5407,1.4153,1.4342,0.8983,-0.1002,0.1533,0.1901,1.6774,-1.0215,-0.2239,0.0186,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0123,-1.3302,-0.6055,-0.2080,-0.4335,-0.4003,-0.3428,-0.2349,-0.3264,-0.1222,-0.0239,-0.3564,-0.3134,-0.3394}, 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{{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=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}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} Position Matrix(exp=4, strand 1=1, strand 2=1): {{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} > Optimizing the full model (component5-4-all). >> Starting new optimization: component5-4-all. (2021-05-22 09:54:06.098). >>> Packing before optimization Packing: {"enrichmentModel":[{},{},{},{},{}],"countTable":[{"h":[594,595,596,597]},{"h":[598,599,600,601]},{"h":[602,603,604]},{"h":[605,606]},{"h":[607,608]}],"bindingModeInteractions":[{"activity":[[579,580,581,582],[583,584,585,586],[587,588,589],[590,591],[592,593]],"positionMatrix":[[[[[-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251],[-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250],[-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249],[252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248],[253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247],[254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246],[255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245],[256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244],[257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243],[258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242],[259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241],[260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240],[261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239],[262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238],[263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237],[264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235,236],[265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234,235],[266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233,234],[267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232,233],[268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231,232],[269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230,231],[270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229,230],[271,270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228,229],[272,271,270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227,228],[273,272,271,270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226,227],[274,273,272,271,270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225,226],[275,274,273,272,271,270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224,225],[276,275,274,273,272,271,270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223,224],[277,276,275,274,273,272,271,270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1,223],[278,277,276,275,274,273,272,271,270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1,-1],[279,278,277,276,275,274,273,272,271,270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1,-1],[280,279,278,277,276,275,274,273,272,271,270,269,268,267,266,265,264,263,262,261,260,259,258,257,256,255,254,253,252,-1,-1,-1,-1]],[[281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,-1,-1,-1,-1],[282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,-1,-1,-1,-1,-1],[283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,-1,-1,-1,-1,-1,-1],[284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,-1,-1,-1,-1,-1,-1,310],[285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,3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Value and gradient before optimization: ======================================= value = 3.8875061726913827 gradient = 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gradient norm = 0.012924921124622112 Starting Function Value: 3.8875061726913827 Iterations Fnc. 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507 3.884804333909521 0.002073102753180 1.000000000000000 0.000012131106427 478 508 3.884804333277717 0.001443055157644 1.000000000000000 0.000005630652799 479 509 3.884804332773162 0.002755040685087 1.000000000000000 0.000005175953488 480 510 3.884804332302033 0.001916578315017 1.000000000000000 0.000006452411659 481 511 3.884804331297111 0.005207562241486 1.000000000000000 0.000008367831164 482 512 3.884804330719065 0.003373062845574 1.000000000000000 0.000010371770677 483 513 3.884804330156790 0.001168790735689 1.000000000000000 0.000004656906734 484 514 3.884804329827561 0.000766872649332 1.000000000000000 0.000004497866918 485 515 3.884804329507013 0.000710546863700 1.000000000000000 0.000005090177916 486 516 3.884804328841221 0.002906696704612 1.000000000000000 0.000005162910724 487 518 3.884804328667960 0.001480621893188 0.264007087816842 0.000006258997112 488 519 3.884804328330914 0.002590472832199 1.000000000000000 0.000003509007201 489 520 3.884804328085624 0.001544905140099 1.000000000000000 0.000003504902853 490 521 3.884804327630536 0.002426493694749 1.000000000000000 0.000004884496301 491 522 3.884804327021097 0.001977833213401 1.000000000000000 0.000006996398848 492 523 3.884804326799289 0.006248043428315 1.000000000000000 0.000012107211596 493 524 3.884804325936583 0.003011674119069 1.000000000000000 0.000004099761412 494 525 3.884804325636577 0.001148584191282 1.000000000000000 0.000003808881013 495 526 3.884804325247557 0.000712275844751 1.000000000000000 0.000003806406279 496 528 3.884804325042818 0.000928832986600 0.428895833217435 0.000007949655074 497 529 3.884804324698949 0.001536266072367 1.000000000000000 0.000004287806312 498 530 3.884804324457191 0.001732016564385 1.000000000000000 0.000002791328247 499 531 3.884804324214155 0.001575934937307 1.000000000000000 0.000003470469749 500 532 3.884804323904874 0.001263450122345 1.000000000000000 0.000004080643433 >>> Maximum iteration count reached. After: gradient norm = 4.080643433406408E-6 >>> Parameters after optimization Count Table 0: --------------- h: {3.8086,2.2140,-0.7343,-5.2882} Count Table 1: --------------- h: {2.7195,1.7484,-0.6822,-3.7856} Count Table 2: --------------- h: {0.1228,0.1187,-0.2414} Count Table 3: --------------- h: {0.2885,-0.2885} Count Table 4: --------------- h: {0.1459,-0.1459} Binding mode 0: --------------- Mononucleotide: {} Activity(exp=0): {0.0000,-1.5995,-1.8196,-2.6418} Activity(exp=1): {0.0000,0.2867,-0.4671,1.7731} Activity(exp=2): {-0.0000,-0.7192,-0.1829} Activity(exp=3): {0.0000,-0.0427} Activity(exp=4): {-0.0000,-2.6114} Binding mode 1: --------------- Mononucleotide: {-0.6883,-0.9148,-0.6852,-0.7390,-0.1633,-1.3923,-0.6395,-0.8322,-0.5668,-1.5086,-1.7445,0.7926,-0.1418,-3.0125,0.8385,-0.7114,1.3336,-1.4974,-1.4825,-1.3811,-1.1774,-1.6821,-1.0601,0.8924,-0.9097,-1.8723,-1.3167,1.0714,-0.8592,-2.2347,-0.7594,0.8259,1.7535,-2.0195,-1.0009,-1.7603,-1.9253,-0.2146,-1.7582,0.8708,-1.0496,-1.5388,-0.0361,-0.4027,-0.1645,-1.6235,-0.3109,-0.9284,-1.1248,-0.4619,-0.7107,-0.7299} Activity(exp=0): {-0.0000,0.6687,-0.5958,-0.8408} Activity(exp=1): {0.0000,-0.0383,-0.6224,-2.7647} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,-0.0000} Binding mode 2: --------------- Mononucleotide: {-0.7388,-1.0754,-0.8827,-0.7119,-0.8560,-1.2481,-0.8999,-0.4048,-0.7900,-1.7933,-1.5509,0.7254,-1.0486,-2.1338,0.8989,-1.1253,1.9813,-4.3045,-0.9202,-0.1654,-1.3555,0.1111,-1.5822,-0.5822,0.2081,-2.0190,-0.6073,-0.9907,-1.0828,-1.1800,-0.4196,-0.7265} Activity(exp=0): {-0.0000,-0.4001,0.3515,1.7746} Activity(exp=1): {0.0000,-3.1039,-2.2905,0.5054} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {0.0000,-0.2458} Activity(exp=4): {-0.0000,-0.0000} Binding mode 3: --------------- Mononucleotide: {-1.1934,-1.4095,-1.2626,-0.6193,-1.1964,-2.0603,-1.4674,0.2392,0.6195,-3.1647,-1.6136,-0.3260,2.1979,-2.3574,-2.2478,-2.0775,-2.1581,-1.0708,-1.6251,0.3691,-1.4592,-1.9953,-0.3587,-0.6716,-0.5166,-2.3351,-0.3005,-1.3325,-1.6225,-0.5873,-1.1475,-1.1275} Activity(exp=0): {0.0000,-0.4914,-0.1564,-0.1237} Activity(exp=1): {0.0000,0.1361,-1.0878,-3.2995} Activity(exp=2): {0.0000,0.5964,-0.0585} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Binding mode 4: --------------- Mononucleotide: {-1.4554,-2.2041,-1.5854,-1.5150,-1.5669,-2.7420,-1.7127,-0.7381,-2.0196,-3.2617,-2.8714,1.3929,-1.5388,-4.4128,1.7484,-2.5565,2.4834,-3.2679,-3.5871,-2.3882,-3.4566,-0.6798,-1.9845,-0.6390,-1.0220,-2.6934,-0.9965,-2.0479,-1.9320,-1.8149,-1.6564,-1.3564} Activity(exp=0): {-0.0000,-3.7557,-3.8202,-2.8153} Activity(exp=1): {-0.0000,-0.0000,-0.0000,0.0000} Activity(exp=2): {-0.0000,-0.0000,-0.0000} Activity(exp=3): {-0.0000,-0.0000} Activity(exp=4): {-0.0000,2.4654} Binding mode interaction 0: --------------------------- Activity(exp=0): {0.0000,1.8328,0.0237,-0.6546} Activity(exp=1): {0.0000,0.0000,0.0000,0.0001} Activity(exp=2): {0.0000,0.0000,0.0000} Activity(exp=3): {0.0000,0.0000} Activity(exp=4): {0.0000,0.0000} Position Matrix(exp=0, strand 1=0, strand 2=0): {{0.0000,0.0000,0.0000,0.0000,0.0154,-1.4672,-0.5599,-0.2043,-0.4846,-0.3551,-0.3519,-0.2304,-0.3662,-0.1165,0.0345,-0.4129,-0.3511,-0.3817,-0.3316,-0.2887,-0.3577,-0.5195,-0.4727,-0.3363,-0.4087,-0.3364,-0.2863,0.1108,-0.2734,-0.3619,-0.1506,0.0252,0.0003}, 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{0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}, {0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000}} > Optimization done.
Probound Model
±
Optimized model:
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