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Add sample data files

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data/jsonexamples_andrew/pipedream/6-pipedream_summary.json 0 → 100644
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{
"GPhL_pipedream" : {
"runfrom" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial4",
"jobid" : "ab5fe2be-9d14-4c38-a46f-2bb482192fe2",
"command" : "pipedream -autoprocdir results/20210705/process -nofreeref -xyzin 6cby-input.pdb -rhofit grade-LIG.cif -xclusters 2 -d fff1",
"terminationstatus" : "COMPLETED",
"runby" : "asharff : escher : 16:05:04 on Fri Jul 9 2021",
"version" : "__VERSION__ <__DATE__>",
"jsonversion" : "0.0.4",
"output" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial4/fff1"
},
"ligandfitting" : {
"type" : "Rhofit",
"ligands" : [
{
"ligandname" : "grade-LIG",
"solutions" : [
{
"output" : "Hit_00_00_000.pdb",
"contactscore" : 0,
"correlationcoefficient" : 0.8702,
"chain" : "B",
"solution_number" : 1,
"closecontacts" : "",
"ligandstrain" : -4.4,
"rhofitscore" : -1528.2,
"poorfit" : "0/36"
},
{
"contactscore" : 0,
"output" : "Hit_01_00_000.pdb",
"correlationcoefficient" : 0.8783,
"closecontacts" : "",
"solution_number" : 2,
"chain" : "A",
"rhofitscore" : -1474.9,
"ligandstrain" : -6.3,
"poorfit" : "0/36"
}
],
"postrefinement" : [
{
"WilsonB" : 28.35,
"Rfree" : 0.23754,
"RMSangles" : 0.884527,
"cycle_number" : 0,
"R" : 0.212545,
"RMSbonds" : 0.00812243,
"WatersPresent" : null,
"MeanB" : 31.26,
"step" : "initial",
"type" : "BUSTER"
},
{
"type" : "BUSTER",
"step" : "final",
"WatersPresent" : 756,
"RMSbonds" : 0.00816878,
"MeanB" : 31.32,
"R" : 0.204523,
"cycle_number" : 1,
"RMSangles" : 0.894371,
"WilsonB" : 28.35,
"Rfree" : 0.234138
}
],
"validationstatistics" : {
"molprobity" : {
"clashscore" : 1.07,
"cbetadeviations" : 0,
"molprobityscore" : 1.08,
"ramafavoredpercent" : 98.22,
"poorrotamers" : 14,
"poorrotamerspercent" : 2.28,
"rmsbonds" : 0.0114,
"rmsangles" : 1.48,
"ramaoutlierpercent" : 0,
"clashpercentile" : "(percentile: 94.2 N=41210, 1.68A+/-0.25A) ",
"ramafavored" : 829,
"ramaoutliers" : 0,
"molprobitypercentile" : "(percentile: 84.1 N=40590, 1.68A+/-0.25A) "
},
"ligandstatistics" : [
{
"ligandomin" : 1,
"mogulangl" : "1/32",
"mogulring" : "0/2",
"ligandbmax" : 24.64,
"ligandresno" : "4000",
"ligandid" : "LIG A4000",
"ligandchain" : "A",
"ligandomax" : 1,
"mogulzangl" : 1.4,
"mogulzbond" : 1.118,
"moguldihe" : "0/1",
"mogulbond" : "0/38",
"ligandbmin" : 18.81,
"ligandbavg" : 20.91,
"ligandcc" : 0.96
},
{
"ligandbmin" : 19.51,
"mogulbond" : "0/38",
"ligandbavg" : 21,
"ligandcc" : 0.958,
"moguldihe" : "0/1",
"ligandchain" : "B",
"ligandid" : "LIG B4000",
"mogulzbond" : 1.104,
"ligandomax" : 1,
"mogulzangl" : 1.486,
"mogulangl" : "1/32",
"ligandomin" : 1,
"ligandresno" : "4000",
"mogulring" : "0/2",
"ligandbmax" : 23.13
}
]
}
}
]
},
"refinement" : {
"selectedmodel" : "6cby-input.pdb",
"Cycles" : [
{
"R" : 0.455174,
"step" : "initial",
"type" : "BUSTER",
"MeanB" : null,
"RMSbonds" : 0.0103079,
"WatersPresent" : null,
"Rfree" : 0.445699,
"WilsonB" : null,
"cycle_number" : 0,
"RMSangles" : 1.09477
},
{
"WilsonB" : 28.35,
"Rfree" : 0.29327,
"cycle_number" : 1,
"RMSangles" : 0.870744,
"R" : 0.270907,
"step" : "refinement",
"type" : "BUSTER",
"RMSbonds" : 0.0079089,
"WatersPresent" : null,
"MeanB" : 29.16
},
{
"cycle_number" : 2,
"RMSangles" : 0.893797,
"WilsonB" : 28.35,
"Rfree" : 0.244699,
"step" : "final",
"type" : "BUSTER",
"WatersPresent" : 662,
"RMSbonds" : 0.00825558,
"MeanB" : 31.26,
"R" : 0.215411
},
{
"WilsonB" : 28.35,
"Rfree" : 0.250721,
"cycle_number" : 3,
"RMSangles" : 0.892493,
"R" : 0.221951,
"type" : "BUSTER",
"step" : "ligand-detection",
"WatersPresent" : 671,
"RMSbonds" : 0.00817662,
"MeanB" : 31.26
}
],
"refinementprotocol" : "Default",
"models" : [
{
"number" : 1,
"LMRscore" : 24.4,
"modelname" : "6cby-input"
}
]
},
"dataprocessing" : {
"processingdata" : {
"AutoProc" : {
"refinedCell_c" : "64.389",
"refinedCell_gamma" : "90.000",
"refinedCell_b" : "116.975",
"spaceGroup" : "P 1 21 1",
"refinedCell_alpha" : "90.000",
"refinedCell_beta" : "92.547",
"refinedCell_a" : "57.988",
"wavelength" : ".97926"
},
"AutoProcscaling" : {
"resolutionEllipsoidAxis21" : ".00000",
"resolutionEllipsoidAxis22" : "1.00000",
"resolutionEllipsoidValue2" : "1.81000",
"resolutionEllipsoidValue1" : "1.68100",
"resolutionEllipsoidAxis32" : ".00000",
"resolutionEllipsoidAxis31" : "-.22319",
"resolutionEllipsoidAxis12" : ".00000",
"resolutionEllipsoidAxis11" : ".97475",
"recordTimeStamp" : "2021-07-05 08:46:02",
"resolutionEllipsoidValue3" : "1.87200",
"resolutionEllipsoidAxis23" : ".00000",
"resolutionEllipsoidAxis13" : ".22319",
"resolutionEllipsoidAxis33" : ".97475"
},
"AutoProcScalingStatistics" : [
{
"resolutionLimitLow" : "64.325",
"scalingStatisticsType" : "overall",
"rMerge" : ".087",
"anomalousCompletenessEllipsoidal" : "91.7",
"resolutionLimitHigh" : "1.681",
"rMeasWithinIPlusIMinus" : ".097",
"anomalousCompletenessSpherical" : "76.7",
"anomalousMultiplicity" : "2.7",
"completenessSpherical" : "78.1",
"rPimWithinIPlusIMinus" : ".057",
"meanIOverSigI" : "12.6",
"anomalousCompleteness" : "91.7",
"DanoOverSigDano" : ".848",
"nTotalObservations" : "393991",
"ccHalf" : "0.999",
"completeness" : "93.2",
"rMeasAllIPlusIMinus" : ".097",
"multiplicity" : "5.2",
"ccAnomalous" : "0.033",
"completenessEllipsoidal" : "93.2",
"rPimAllIPlusIMinus" : ".042",
"nTotalUniqueObservations" : "75926"
},
{
"rMerge" : ".032",
"anomalousCompletenessEllipsoidal" : "96.4",
"resolutionLimitLow" : "64.325",
"scalingStatisticsType" : "innerShell",
"rMeasWithinIPlusIMinus" : ".033",
"anomalousCompletenessSpherical" : "96.4",
"resolutionLimitHigh" : "4.853",
"completenessSpherical" : "98.3",
"meanIOverSigI" : "38.7",
"rPimWithinIPlusIMinus" : ".019",
"anomalousMultiplicity" : "2.7",
"DanoOverSigDano" : "1.021",
"anomalousCompleteness" : "96.4",
"ccHalf" : "0.999",
"nTotalObservations" : "20598",
"completeness" : "98.3",
"rMeasAllIPlusIMinus" : ".035",
"multiplicity" : "5.1",
"completenessEllipsoidal" : "98.3",
"ccAnomalous" : "0.206",
"rPimAllIPlusIMinus" : ".015",
"nTotalUniqueObservations" : "4050"
},
{
"anomalousCompleteness" : "52.7",
"DanoOverSigDano" : ".793",
"anomalousMultiplicity" : "2.8",
"meanIOverSigI" : "1.6",
"rPimWithinIPlusIMinus" : ".758",
"completenessSpherical" : "16.7",
"resolutionLimitHigh" : "1.681",
"anomalousCompletenessSpherical" : "16.3",
"rMeasWithinIPlusIMinus" : "1.320",
"scalingStatisticsType" : "outerShell",
"resolutionLimitLow" : "1.830",
"anomalousCompletenessEllipsoidal" : "52.7",
"rMerge" : "1.175",
"nTotalUniqueObservations" : "3642",
"rPimAllIPlusIMinus" : ".540",
"ccAnomalous" : "-0.000",
"completenessEllipsoidal" : "53.6",
"multiplicity" : "5.6",
"completeness" : "53.6",
"rMeasAllIPlusIMinus" : "1.296",
"nTotalObservations" : "20258",
"ccHalf" : "0.480"
}
]
},
"referencedata" : {
"symmetry" : "4",
"cell" : {
"alpha" : "90.000",
"a" : "58.020",
"b" : "117.031",
"gamma" : "90.000",
"beta" : "92.540",
"c" : "64.444"
}
},
"processingtype" : "autoPROC",
"datatype" : "images"
}
}
data/jsonexamples_andrew/pipedream/README.txt
+ 3
− 2
View file @ d45e951b
1. A single input model with a monomer in the asu. 1 ligand
1. A single input model with a monomer in the asu. 1 ligand.
2. A single input model with a homotrimer in the asu. 1 ligand but 3 binding sites (1 per chain).
3. A single input model with a monomer in the asu. 2 input ligands
4. 3 input models( all with a monomer in the asu. 1 ligand.
5. A single input model with a monomer in the asu. 1 ligand (Added chain/residue name to solutions container)
5. A single input model with a monomer in the asu. 1 ligand (Added chain/residue name to solutions container).
5. Latest version of Pipedream output before official release from Global Phasing.
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