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Add updated version of Pipdream JSON file (Not verified)

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data/pipedream_summary_updated.json 0 → 100644
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{
"GPhL_pipedream" : {
"command" : "pipedream -nthreads 6 -rhofit /crimsXdata/CRIMS-ARCHITECTURE/REFERENCE-MODELS/merck/2020/20201001_proxima1/cifs/1_c617989dstructure.cif -xyzin /crimsXdata/CRIMS-ARCHITECTURE/REFERENCE-MODELS/merck/2020/20201001_proxima1/pded-20201001-px1-894d59aa/pipedream-phenix-raph-0e66e23c/apo_model.pdb -hklref /crimsXdata/CRIMS-ARCHITECTURE/REFERENCE-MODELS/merck/2020/20201001_proxima1/pded-20201001-px1-894d59aa/pipedream-phenix-raph-0e66e23c/apo_model.mtz -rhothorough -postthorough -h5master P-41312/X-33483/D-3120/PDEd-CD028448_C7-4_MSC2355255A-1_1_master.h5 -d /crimsXdata/CRIMS-ARCHITECTURE/DATA-PROCESSING/merck/2020/20201001_proxima1/P-41312/X-33483/D-3120_pipedream4",
"jsonversion" : "0.0.1",
"runby" : "crimsrobot : inext1 : 16:50:18 on Wed Mar 17 2021",
"runfrom" : "/crimsXdata/CRIMS-ARCHITECTURE/IMAGES/merck/2020/20201001_proxima1",
"jobid" : "5fcfe238-cc8d-4466-8679-9a5136486bbb",
"output" : "/crimsXdata/CRIMS-ARCHITECTURE/IMAGES/merck/2020/20201001_proxima1//crimsXdata/CRIMS-ARCHITECTURE/DATA-PROCESSING/merck/2020/20201001_proxima1/P-41312/X-33483/D-3120_pipedream4",
"version" : "1.3.0 <2021-02-24>"
},
"ligandfitting" : {
"type" : "Rhofit",
"ligands" : [
{
"validationstatistics" : {
"ligandstatistics" : [
{
"ligandomin" : "1.00",
"mogulzbond" : "0.374",
"ligandbmin" : " 21.85",
"mogulring" : "0/4",
"moguldihe" : "0/6",
"ligandbavg" : "29.06",
"mogulangl" : "0/45",
"mogulbond" : "0/38",
"ligandbmax" : " 36.51",
"ligandid" : "LIG A4000",
"ligandomax" : "1.00",
"ligandcc" : "0.927",
"mogulzangl" : "0.550"
},
{
"here" : "second ligand statistics"
}
],
"molprobity" : {
"molprobitypercentile" : "(percentile: 49.7 N=48274, 1.80A+/-0.25A) ",
"ramaoutlierpercent" : "0.00",
"cbetadeviations" : "1",
"ramafavoredpercent" : 97.89,
"poorrotamers" : 6,
"rmsbonds" : 0.0123,
"rmsangles" : 1.54,
"clashpercentile" : "(percentile: 80.7 N=48931, 1.80A+/-0.25A) ",
"poorrotamerspercent" : 4.51,
"clashscore" : 2.34,
"ramafavored" : "139",
"molprobityscore" : 1.54,
"ramaoutliers" : "0"
}
},
"solutions" : [
{
"closecontacts" : "",
"chain" : "A",
"contactscore" : "0.1",
"ligandstrain" : "10.6",
"poorfit" : "0/34",
"output" : "Hit_00_00_000.pdb",
"correlationcoefficient" : "0.7959",
"rhofitscore" : "-1782.7"
},
{
"here" : "second solution"
}
],
"postrefinement" : {
"cycles" : [
{
"cycle_number?" : "0",
"WilsonB" : "18.84",
"Rfree" : 0.255206,
"MeanB" : "25.54",
"type" : "BUSTER",
"step" : "initial",
"RMSbonds" : 0.00802735,
"RMSangles" : 0.969623,
"R" : 0.209836
},
{
"cycle_number?" : "1",
"R" : 0.201638,
"RMSangles" : 0.978341,
"step" : "final",
"RMSbonds" : 0.00811111,
"MeanB" : "26.41",
"type" : "BUSTER",
"WilsonB" : "18.84",
"Rfree" : 0.247927,
"WatersPresent" : "155"
},
{
"cycle_number?" : "2",
"Rfree" : 0.253958,
"WilsonB" : "18.84",
"step" : "refinement",
"RMSbonds" : 0.00802904,
"MeanB" : "25.89",
"type" : "BUSTER",
"RMSangles" : 0.969742,
"R" : 0.207245
}
]
},
"id" : "1_c617989dstructure"
},
{
"here" : "second ligand"
}
]
},
"dataprocessing" : {
"datatype" : "images",
"referencedata" : {
"cell" : {
"gamma" : "120.000",
"a" : "55.601",
"alpha" : "90.000",
"b" : "55.601",
"beta" : "90.000",
"c" : "115.008"
},
"symmetry" : "154"
},
"processingtype" : "autoPROC",
"processingdata" : {
"AutoProcscaling" : {
"recordTimeStamp" : "2021-03-17 18:27:53",
"resolutionEllipsoidAxis13" : ".00000",
"resolutionEllipsoidAxis33" : "1.00000",
"resolutionEllipsoidAxis23" : ".00000",
"resolutionEllipsoidValue2" : "2.42300",
"resolutionEllipsoidAxis21" : ".00000",
"resolutionEllipsoidAxis31" : ".00000",
"resolutionEllipsoidAxis22" : "1.00000",
"resolutionEllipsoidAxis32" : ".00000",
"resolutionEllipsoidValue3" : "1.75600",
"resolutionEllipsoidAxis12" : ".00000",
"resolutionEllipsoidValue1" : "2.42300",
"resolutionEllipsoidAxis11" : "1.00000"
},
"AutoProcScalingStatistics" : {
"innerShell" : {
"multiplicity" : "8.2",
"resolutionLimitLow" : "48.263",
"rMeasWithinIPlusIMinus" : ".114",
"DanoOverSigDano" : ".640",
"completenessSpherical" : "100.0",
"nTotalUniqueObservations" : "547",
"rMerge" : ".101",
"rPimWithinIPlusIMinus" : ".051",
"anomalousCompletenessEllipsoidal" : "100.0",
"nTotalObservations" : "4474",
"completenessEllipsoidal" : "100.0",
"anomalousCompleteness" : "100.0",
"anomalousMultiplicity" : "4.9",
"resolutionLimitHigh" : "6.241",
"completeness" : "100.0",
"ccHalf" : "0.990",
"rPimAllIPlusIMinus" : ".038",
"meanIOverSigI" : "15.4",
"anomalousCompletenessSpherical" : "100.0",
"ccAnomalous" : "-0.081",
"rMeasAllIPlusIMinus" : ".108"
},
"overall" : {
"nTotalObservations" : "104256",
"completenessEllipsoidal" : "91.2",
"anomalousMultiplicity" : "5.3",
"anomalousCompleteness" : "90.9",
"resolutionLimitHigh" : "1.796",
"completeness" : "91.2",
"ccHalf" : "0.991",
"rPimAllIPlusIMinus" : ".103",
"meanIOverSigI" : "6.7",
"ccAnomalous" : "-0.035",
"anomalousCompletenessSpherical" : "50.0",
"rMeasAllIPlusIMinus" : ".328",
"resolutionLimitLow" : "48.263",
"multiplicity" : "9.9",
"rMeasWithinIPlusIMinus" : ".355",
"DanoOverSigDano" : ".760",
"completenessSpherical" : "52.7",
"nTotalUniqueObservations" : "10546",
"rMerge" : ".311",
"rPimWithinIPlusIMinus" : ".151",
"anomalousCompletenessEllipsoidal" : "90.9"
},
"outerShell" : {
"DanoOverSigDano" : ".758",
"completenessSpherical" : "8.8",
"rMerge" : "1.874",
"nTotalUniqueObservations" : "525",
"rPimWithinIPlusIMinus" : ".693",
"anomalousCompletenessEllipsoidal" : "75.5",
"multiplicity" : "13.9",
"resolutionLimitLow" : "2.027",
"rMeasWithinIPlusIMinus" : "1.965",
"ccHalf" : "0.635",
"rPimAllIPlusIMinus" : ".513",
"meanIOverSigI" : "1.7",
"anomalousCompletenessSpherical" : "7.3",
"ccAnomalous" : "-0.023",
"rMeasAllIPlusIMinus" : "1.945",
"nTotalObservations" : "7322",
"completenessEllipsoidal" : "76.8",
"anomalousCompleteness" : "75.5",
"anomalousMultiplicity" : "8.0",
"resolutionLimitHigh" : "1.796",
"completeness" : "76.8"
}
},
"AutoProc" : {
"refinedCell_beta" : "90.000",
"refinedCell_b" : "55.729",
"wavelength" : ".97856",
"refinedCell_a" : "55.729",
"refinedCell_alpha" : "90.000",
"spaceGroup" : "P 32 2 1",
"refinedCell_c" : "115.250",
"refinedCell_gamma" : "120.000"
}
}
},
"refinement" : {
"Cycles" : [
{
"cycle_number?" : "2",
"R" : 0.219373,
"RMSangles" : 0.986999,
"RMSbonds" : 0.00849398,
"step" : "final",
"type" : "BUSTER",
"MeanB" : "25.54",
"Rfree" : 0.262637,
"WilsonB" : "18.84",
"WatersPresent" : "121"
},
{
"cycle_number?" : "0",
"WilsonB" : "",
"Rfree" : 0.312092,
"MeanB" : "",
"type" : "BUSTER",
"RMSbonds" : 0.0103442,
"step" : "initial",
"R" : 0.318089,
"RMSangles" : 1.03551
},
{
"cycle_number?" : "1",
"R" : 0.263322,
"RMSangles" : "0.956230",
"type" : "BUSTER",
"MeanB" : "21.61",
"RMSbonds" : 0.00799684,
"step" : "refinement",
"WilsonB" : "18.84",
"Rfree" : 0.297255
},
{
"cycle_number?" : "3",
"R" : "0.228701",
"RMSangles" : "0.971963",
"MeanB" : "25.54",
"type" : "BUSTER",
"RMSbonds" : "0.00794350",
"step" : "ligand-detection",
"WatersPresent" : "121",
"Rfree" : "0.272720",
"WilsonB" : "18.84"
}
],
"models" : [
{
"number" : 1,
"LMRscore" : "33.1",
"modelname" : "apo"
},
{
"here" : "second model"
}
],
"selectedmodel" : "/crimsXdata/CRIMS-ARCHITECTURE/REFERENCE-MODELS/merck/2020/20201001_proxima1/pded-20201001-px1-894d59aa/pipedream-phenix-raph-0e66e23c/apo_model.pdb",
"refinementprotocol" : "Default"
}
}
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