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Add new JSON sample data

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data/jsonexamples_andrew/1-pipedream_summary.json 0 → 100644
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View file @ 75093ab1
{
"refinement" : {
"Cycles" : [
{
"Rfree" : 0.445719,
"step" : "initial",
"cycle_number" : 0,
"RMSbonds" : 0.0103018,
"type" : "BUSTER",
"RMSangles" : 1.09501,
"R" : 0.454558,
"WatersPresent" : null,
"MeanB" : null,
"WilsonB" : null
},
{
"WilsonB" : 28.35,
"R" : 0.270707,
"MeanB" : 29.22,
"WatersPresent" : null,
"RMSbonds" : 0.00790915,
"cycle_number" : 1,
"RMSangles" : 0.872085,
"type" : "BUSTER",
"Rfree" : 0.292751,
"step" : "refinement"
},
{
"transcis" : 0,
"hbondflip" : 19,
"pepflip" : "N/A",
"cistrans" : 0,
"cycle_number" : 2,
"type" : "pdb-redo",
"changedrot" : 46,
"watersremoved" : 0,
"step" : "remediation"
},
{
"RMSbonds" : 0.00830937,
"cycle_number" : 3,
"type" : "BUSTER",
"RMSangles" : 0.905608,
"Rfree" : 0.235121,
"step" : "final",
"WilsonB" : 28.35,
"R" : 0.204029,
"MeanB" : 32.38,
"WatersPresent" : 691
},
{
"RMSangles" : 0.900876,
"type" : "BUSTER",
"cycle_number" : 4,
"RMSbonds" : 0.00822846,
"step" : "ligand-detection",
"Rfree" : 0.242613,
"WilsonB" : 28.35,
"WatersPresent" : 710,
"MeanB" : 32.38,
"R" : 0.211697
}
],
"models" : [
{
"modelname" : "6cby-input",
"number" : 1,
"LMRscore" : 44.8
}
],
"refinementprotocol" : "Default",
"selectedmodel" : "6cby-input.pdb"
},
"GPhL_pipedream" : {
"runfrom" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial4",
"output" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial4/results/20210705",
"command" : "pipedream -imagedir SMYD2_6cbx/data -nofreeref -useaniso -apcommands \"ReversePhi=yes IgnoreImageZero=yes\" -xyzin 6cby-input.pdb -chains \"A B\" -remediate -sidechainrebuild -rhofit grade-LIG.cif -xclusters 2 -d results/20210705",
"runby" : "asharff : escher : 08:27:12 on Mon Jul 5 2021",
"version" : "__VERSION__ <__DATE__>",
"jsonversion" : "0.0.3",
"terminationstatus" : "COMPLETED",
"jobid" : "d9429ffe-50a1-4330-879a-65d39338f358"
},
"dataprocessing" : {
"processingdata" : {
"AutoProcscaling" : {
"resolutionEllipsoidAxis11" : ".97475",
"resolutionEllipsoidValue1" : "1.68100",
"resolutionEllipsoidAxis13" : ".22319",
"resolutionEllipsoidAxis23" : ".00000",
"resolutionEllipsoidAxis22" : "1.00000",
"resolutionEllipsoidAxis33" : ".97475",
"resolutionEllipsoidAxis12" : ".00000",
"resolutionEllipsoidAxis32" : ".00000",
"resolutionEllipsoidAxis31" : "-.22319",
"resolutionEllipsoidValue3" : "1.87200",
"resolutionEllipsoidAxis21" : ".00000",
"resolutionEllipsoidValue2" : "1.81000",
"recordTimeStamp" : "2021-07-05 08:46:02"
},
"AutoProcScalingStatistics" : {
"outerShell" : {
"DanoOverSigDano" : ".793",
"anomalousCompletenessSpherical" : "16.3",
"meanIOverSigI" : "1.6",
"rPimWithinIPlusIMinus" : ".758",
"multiplicity" : "5.6",
"rMerge" : "1.175",
"resolutionLimitLow" : "1.830",
"completenessEllipsoidal" : "53.6",
"nTotalUniqueObservations" : "3642",
"anomalousMultiplicity" : "2.8",
"ccAnomalous" : "-0.000",
"anomalousCompletenessEllipsoidal" : "52.7",
"rMeasWithinIPlusIMinus" : "1.320",
"nTotalObservations" : "20258",
"anomalousCompleteness" : "52.7",
"rPimAllIPlusIMinus" : ".540",
"rMeasAllIPlusIMinus" : "1.296",
"completeness" : "53.6",
"ccHalf" : "0.480",
"completenessSpherical" : "16.7",
"resolutionLimitHigh" : "1.681"
},
"overall" : {
"DanoOverSigDano" : ".848",
"anomalousCompletenessSpherical" : "76.7",
"meanIOverSigI" : "12.6",
"rPimWithinIPlusIMinus" : ".057",
"multiplicity" : "5.2",
"rMerge" : ".087",
"completenessEllipsoidal" : "93.2",
"resolutionLimitLow" : "64.325",
"nTotalUniqueObservations" : "75926",
"anomalousMultiplicity" : "2.7",
"rMeasWithinIPlusIMinus" : ".097",
"ccAnomalous" : "0.033",
"anomalousCompletenessEllipsoidal" : "91.7",
"nTotalObservations" : "393991",
"anomalousCompleteness" : "91.7",
"rPimAllIPlusIMinus" : ".042",
"rMeasAllIPlusIMinus" : ".097",
"completeness" : "93.2",
"ccHalf" : "0.999",
"completenessSpherical" : "78.1",
"resolutionLimitHigh" : "1.681"
},
"innerShell" : {
"completeness" : "98.3",
"rMeasAllIPlusIMinus" : ".035",
"rPimAllIPlusIMinus" : ".015",
"completenessSpherical" : "98.3",
"resolutionLimitHigh" : "4.853",
"ccHalf" : "0.999",
"nTotalUniqueObservations" : "4050",
"anomalousMultiplicity" : "2.7",
"completenessEllipsoidal" : "98.3",
"resolutionLimitLow" : "64.325",
"nTotalObservations" : "20598",
"anomalousCompleteness" : "96.4",
"rMeasWithinIPlusIMinus" : ".033",
"ccAnomalous" : "0.206",
"anomalousCompletenessEllipsoidal" : "96.4",
"rMerge" : ".032",
"rPimWithinIPlusIMinus" : ".019",
"meanIOverSigI" : "38.7",
"DanoOverSigDano" : "1.021",
"anomalousCompletenessSpherical" : "96.4",
"multiplicity" : "5.1"
}
},
"AutoProc" : {
"wavelength" : ".97926",
"spaceGroup" : "P 1 21 1",
"refinedCell_beta" : "92.547",
"refinedCell_b" : "116.975",
"refinedCell_c" : "64.389",
"refinedCell_gamma" : "90.000",
"refinedCell_alpha" : "90.000",
"refinedCell_a" : "57.988"
}
},
"processingtype" : "autoPROC",
"datatype" : "images",
"referencedata" : {
"cell" : {
"alpha" : "90.000",
"b" : "117.031",
"beta" : "92.540",
"c" : "64.444",
"gamma" : "90.000",
"a" : "58.020"
},
"symmetry" : "4"
}
},
"ligandfitting" : {
"type" : "Rhofit",
"ligands" : [
{
"solutions" : [
{
"correlationcoefficient" : 0.8977,
"output" : "Hit_00_00_000.pdb",
"rhofitscore" : -1771.6,
"ligandstrain" : -2.4,
"chain" : "B",
"closecontacts" : "",
"solution_number" : 1,
"poorfit" : "0/36",
"contactscore" : 0
},
{
"ligandstrain" : -5.2,
"rhofitscore" : -1555.8,
"chain" : "A",
"closecontacts" : "",
"correlationcoefficient" : 0.8759,
"output" : "Hit_01_00_000.pdb",
"solution_number" : 2,
"poorfit" : "0/36",
"contactscore" : 0
}
],
"ligandname" : "grade-LIG",
"validationstatistics" : {
"ligandstatistics" : [
{
"ligandomax" : 1,
"mogulzangl" : 1.401,
"ligandomin" : 1,
"mogulbond" : "0/38",
"ligandcc" : 0.961,
"moguldihe" : "0/1",
"ligandbmin" : 18.34,
"mogulzbond" : 1.135,
"mogulring" : "0/2",
"ligandbmax" : 25.17,
"ligandid" : "LIG A4000",
"mogulangl" : "1/32",
"ligandbavg" : 20.73
},
{
"ligandbavg" : 21.34,
"mogulangl" : "1/32",
"ligandid" : "LIG B4000",
"mogulzbond" : 1.082,
"mogulring" : "0/2",
"ligandbmax" : 23.8,
"ligandbmin" : 19.91,
"mogulbond" : "0/38",
"ligandcc" : 0.963,
"moguldihe" : "0/1",
"ligandomin" : 1,
"mogulzangl" : 1.49,
"ligandomax" : 1
}
],
"molprobity" : {
"poorrotamers" : 15,
"ramafavoredpercent" : 98.22,
"cbetadeviations" : 0,
"rmsbonds" : 0.0117,
"clashpercentile" : "(percentile: 88.9 N=41210, 1.68A+/-0.25A) ",
"poorrotamerspercent" : 2,
"molprobitypercentile" : "(percentile: 80.1 N=40590, 1.68A+/-0.25A) ",
"ramaoutlierpercent" : 0,
"molprobityscore" : 1.13,
"rmsangles" : 1.48,
"ramaoutliers" : 0,
"clashscore" : 1.57,
"ramafavored" : 829
}
},
"postrefinement" : [
{
"WatersPresent" : null,
"MeanB" : 32.38,
"R" : 0.201342,
"WilsonB" : 28.35,
"step" : "initial",
"Rfree" : 0.228701,
"type" : "BUSTER",
"RMSangles" : 0.896618,
"RMSbonds" : 0.00818761,
"cycle_number" : 0
},
{
"Rfree" : 0.223919,
"step" : "final",
"RMSbonds" : 0.00815796,
"cycle_number" : 1,
"RMSangles" : 0.898311,
"type" : "BUSTER",
"R" : 0.194171,
"WatersPresent" : 796,
"MeanB" : 32.43,
"WilsonB" : 28.35
}
]
}
]
}
}
data/jsonexamples_andrew/1-summary.out 0 → 100644
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View file @ 75093ab1
##############################################################################
## [pipedream] Automatic data processing and structure refinement ##
##############################################################################
Copyright (C) 2011-__YEAR__ by Global Phasing Limited
All rights reserved.
This software is proprietary to and embodies the confidential
technology of Global Phasing Limited (GPhL). Possession, use,
duplication or dissemination of the software is authorised
only pursuant to a valid written licence from GPhL.
Version: __VERSION__ <__DATE__>
------------------------------------------------------------------------------
Authors: Sharff A, Keller P, Vonrhein C, Smart O, Womack T,
Flensburg C, Paciorek W, Bricogne G (__YEAR__).
Pipedream version __VERSION__. Global Phasing Ltd.,
Cambridge, United Kingdom.
Partial support by EU project: SILVER (FP7-HEALTH-F3-2010-260644)
Contact: buster-develop@globalphasing.com
==============================================================================
Program citations:
autoPROC : Vonrhein, C., Flensburg, C., Keller, P., Sharff, A., Smart, O., Paciorek, W.,
Womack, T. and Bricogne, G. (2011). Data processing and analysis with
the autoPROC toolbox. Acta Cryst. D67, 293-302.
Phaser : McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C.
and Read, R.J. (2007). Phaser Crystallographic Software. J. Appl. Cryst., 40, 658-674.
BUSTER : Bricogne G., Blanc E., Brandl M., Flensburg C., Keller P., Paciorek W.,
Roversi, P., Sharff A., Smart O.S., Vonrhein C. and Womack T.O. (__YEAR__).
BUSTER version 2.13.0. Cambridge, United Kingdom: Global Phasing Ltd.
PDB_REDO : Joosten, R.P., Joosten, K., Cohen, S.X., Vriend, G. and Perrakis, A. (2011),
Automatic rebuilding and optimization of crystallographic structures in the
Protein Data Bank. Bioinformatics, 27, 3392-3398.
=======================================
Processing and Refinement Summary
=======================================
Pipedream version: __VERSION__ <__DATE__>
Run by asharff on escher at 08:27:12 on Mon Jul 5 2021
Run from /.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial4
Job ID: d9429ffe-50a1-4330-879a-65d39338f358
Command run: pipedream -imagedir SMYD2_6cbx/data -nofreeref -useaniso \
-apcommands "ReversePhi=yes IgnoreImageZero=yes" -xyzin \
6cby-input.pdb -chains "A B" -remediate -sidechainrebuild -rhofit \
grade-LIG.cif -xclusters 2 -d results/20210705
All output in /.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial4/results/20210705
WARNING : Reference structure factors
(results/20210705/6cby-input_nowater.mtz) have been back-calculated
from reference model with sfall!
NOTE : You are running Pipedream without a common Free R set. This is not
adviseable as it may compromise cross-validation!
==================================================
*********** autoPROC (Data Processing) ***********
==================================================
Data successfully processed by autoPROC.
Summary of anisotropic data analysis:
Reference model cell 58.0200 117.0310 64.4440 90.0 92.5 90.0
Spacegroup name P21
Unit cell parameters 57.988 116.975 64.389 90.000 92.547 90.000
Wavelength 0.97926 A
Diffraction limits & principal axes of ellipsoid fitted to diffraction cut-off surface:
1.681 0.9748 0.0000 0.2232 0.980 _a_* + 0.200 _c_*
1.810 0.0000 1.0000 0.0000 _b_*
1.872 -0.2232 0.0000 0.9748 -0.200 _a_* + 0.980 _c_*
Number of RUNs (sweeps) contributing to this dataset = 2
Criteria used in determination of diffraction limits:
-----------------------------------------------------
local(I/sigI) >= 1.20
Per-reflection cut-off Operational Resolution
-----------------------------------------------------------------
I/sigma(I) >= 2.0 : 2.0392 A for 54550 reflections
I/sigma(I) >= 1.0 : 1.9447 A for 62967 reflections
I/sigma(I) >= 0.0 : 1.8694 A for 70711 reflections
all : 1.8261 A for 75926 reflections
Overall InnerShell OuterShell
---------------------------------------------------------------------------
Low resolution limit 64.325 64.325 1.830
High resolution limit 1.681 4.853 1.681
Rmeas 0.097 0.035 1.296
Rpim 0.042 0.015 0.540
Total number of observations 393991 20598 20258
Total number unique 75926 4050 3642
Mean(I)/sd(I) 12.6 38.7 1.6
Completeness (spherical) 78.1 98.3 16.7
Completeness (ellipsoidal) 93.2 98.3 53.6
Multiplicity 5.2 5.1 5.6
CC(1/2) 0.999 0.999 0.480
Anomalous completeness (spherical) 76.7 96.4 16.3
Anomalous completeness (ellipsoidal) 91.7 96.4 52.7
Anomalous multiplicity 2.7 2.7 2.8
CC(ano) 0.033 0.206 -0.000
|DANO|/sd(DANO) 0.848 1.021 0.793
For full details please see results/20210705/process.out
and results/20210705/process/summary.html.
Output file (used in all subsequent steps): results/20210705/process/staraniso_alldata-unique.mtz
Full reflection data and data quality metrics:
results/20210705/process/Data_1_autoPROC_STARANISO_all.cif (deposition-ready)
==================================================
******************* limited MR *******************
==================================================
Limited MR procedure run with 2 independently defined units.
MR solution found with score (TFZ) 44.8
For further details please see MR/*{rotation or translation}.out
Output pdb file: MR/phaser.3.pdb
=================================================================================================
****** BUSTER refinement and unmodelled density elicitation (default protocol - version 2) ******
=================================================================================================
BUSTER refinement
=================
Run_1: Standard refinement, including Rigid Body at big cycle 1
Run_2: adding TLS, 1st and 2nd shell water placement
See Pipedream manual for full details
------------------------------------------------------------------------------------------------------
| Step | R | Rfree | RMS (bonds) | RMS (angles) | Mean B | Wilson B |
------------------------------------------------------------------------------------------------------
| Initial | 0.4546 | 0.4457 | 0.01030 | 1.09501 | | |
| After 1st refinement (Run_1) | 0.2707 | 0.2928 | 0.00791 | 0.87208 | 29.22 | 28.35 |
| Final* (Run_2) | 0.2040 | 0.2351 | 0.00831 | 0.90561 | 32.38 | 28.35 |
------------------------------------------------------------------------------------------------------
Waters in final model = 691
* Input model remediated by SideAide, correcting sidechain rotamers.
-------------------------------------------
Summary of outcome of PDB_REDO remediation:
Number of residues with changed rotamers = 46
Number of residues with H-bond flips = 19
Number of residues with cis-trans isomerisation = 0
Number of residues with trans-cis isomerisation = 0
Number of peptide bonds flipped = N/A
Number of waters removed = 0
For full details of affected residues, please see coot scripts results/20210705/pdbredo_coot_tour.{scm/py}.
To view outcome in coot use command:
"coot -p results/20210705/sideaide.pdb -p results/20210705/refine1/refine.pdb \
--auto results/20210705/refine1/refine.mtz -script results/20210705/pdbredo_coot_tour.{scm/py}"
-------------------------------------------
For further details please see refine.out
Output files:
model:
refine/refine.pdb
refine/BUSTER_model.cif (deposition-ready)
reflection data and map coefficients:
refine/refine.mtz
refine/BUSTER_refln.cif (deposition-ready)
Unmodelled density elicitation:
===============================
Run_3: TLS, -L, calculation of map coefficients limited to 1.9A resolution
Potential ligand sites identified = 3
Site 1 with (estimated) volume of 153.51 A^3 and contacts <=2.5A: B137(HIS) B181(CYS) B182(ASN) B183(GLY) B206(ASN) B207(HIS) B258(TYR) B260(PHE) B263(GLU)
Site 3 with (estimated) volume of 144.61 A^3 and contacts <=2.5A: A16(GLY) A137(HIS) A183(GLY) A206(ASN) A207(HIS) A258(TYR) A260(PHE) A263(GLU)
Site 5 with (estimated) volume of 51.60 A^3 and contacts <=2.5A: A283(SER) B5(GLY) B10(GLU) B11(ARG)
For further details please see refine-L.out
Output files:
refine-L/refine.mtz
==================================================
*********** Ligand Fitting with Rhofit ***********
==================================================
++++++++++++++++++++++++++++++++++++++++++
| Running rhofit with ligand *grade-LIG* |
++++++++++++++++++++++++++++++++++++++++++
For output and further details please see rhofit-grade-LIG/
rhofit ligand LigProt Poorly
total Correl strain contact fitting LigProt contact to residues
File Chain score coeff score score atoms (% means zero weighted in score)
=================================================================================================
Hit_00_00_000.pdb B -1771.6 0.8977 -2.4 0.0 0/36 W|13:HOH% W|14:HOH% W|18:HOH% W|26:HOH% W|367:HOH% W|373:HOH% W|545:HOH% W|546:HOH% W|6:HOH% W|8:HOH%
Hit_01_00_000.pdb A -1555.8 0.8759 -5.2 0.0 0/36 W|12:HOH% W|2:HOH% W|363:HOH% W|365:HOH% W|370:HOH% W|41:HOH% W|459:HOH% W|4:HOH% W|78:HOH% W|80:HOH%
To view the output solutions from Rhofit in coot use the command:
visualise-rhofit-coot results/20210705/rhofit-grade-LIG
Post refinement of "best" solution will be carried out.
Hydrogen atoms will be added to the fit ligand(s) with full occupancy
Output file: rhofit-grade-LIG/merged-hydrogenated.pdb
BUSTER post-refinement
======================
------------------------------------------------------------------------------------------------------
| Step | R | Rfree | RMS (bonds) | RMS (angles) | Mean B | Wilson B |
------------------------------------------------------------------------------------------------------
| Initial | 0.2013 | 0.2287 | 0.00819 | 0.89662 | 32.38 | 28.35 |
| Final | 0.1942 | 0.2239 | 0.00816 | 0.89831 | 32.43 | 28.35 |
------------------------------------------------------------------------------------------------------
Waters in final model = 796
For further details please see postrefine-grade-LIG.out
Output files:
model:
postrefine-grade-LIG/refine.pdb
postrefine-grade-LIG/BUSTER_model.cif (deposition-ready)
reflection data and map coefficients:
postrefine-grade-LIG/refine.mtz
postrefine-grade-LIG/BUSTER_refln.cif (deposition-ready)
==================================================
************* Validation statistics **************
==================================================
-------------------------------------------------------------------------------------------
| Quality metric | Value | Percent | Remark |
-------------------------------------------------------------------------------------------
| Clashscore, all atoms | 1.5700 | | (percentile: 88.9 N=41210, 1.68A+/-0.25A) |
| Poor rotamers | 15 | 2.00 % | Goal: < 0.3% |
| Ramachandran outliers | 0 | 0.00 % | Goal: < 0.2% |
| Ramachandran favored | 829 | 98.22 % | Goal: > 98% |
| Cbeta deviations > 0.25A | 0 | | Goal: 0 |
| Molprobity score | 1.13 | | (percentile: 80.1 N=40590, 1.68A+/-0.25A) |
| RMS (bonds) | 0.0117 | | |
| RMS (angles) | 1.4800 | | |
-------------------------------------------------------------------------------------------
Ligand Refinement Statistics
----------------------------
-----------------------------------------------------------------------------------------------------------------------------
| Ligand | CC(2mFo-DFc) | min(B) | avg(B) | max(B) | min(occupancy) | max(occupancy) |
-----------------------------------------------------------------------------------------------------------------------------
| LIG A4000 | 0.961 | 18.34 | 20.73 | 25.17 | 1.00 | 1.00 |
| LIG B4000 | 0.963 | 19.91 | 21.34 | 23.80 | 1.00 | 1.00 |
-----------------------------------------------------------------------------------------------------------------------------
Ligand Mogul Statistics
-----------------------
-----------------------------------------------------------------------------------------------------------------------------
| Ligand | 'bad' bonds | 'bad' bond angles | 'unusual' dihedrals | 'bad' rings | bonds rms Z | angles rms Z |
-----------------------------------------------------------------------------------------------------------------------------
| LIG A4000 | 0/38 | 1/32 | 0/1 | 0/2 | 1.135 | 1.401 |
| LIG B4000 | 0/38 | 1/32 | 0/1 | 0/2 | 1.082 | 1.490 |
-----------------------------------------------------------------------------------------------------------------------------
For buster-report output see:
report-grade-LIG/index.html
=======================================
Successful termination!
Run took 02:01:44 h:m:s to complete
data/jsonexamples_andrew/2-pipedream_summary.json 0 → 100644
+ 235
− 0
View file @ 75093ab1
{
"ligandfitting" : {
"type" : "Rhofit",
"ligands" : [
{
"validationstatistics" : {
"molprobity" : {
"clashpercentile" : "(percentile: 92.1 N=47431, 2.10A+/-0.25A) ",
"cbetadeviations" : 5,
"molprobityscore" : 1.45,
"rmsangles" : 1.58,
"poorrotamers" : 34,
"ramafavored" : 1077,
"ramafavoredpercent" : 97.38,
"ramaoutlierpercent" : 0,
"poorrotamerspercent" : 3.55,
"rmsbonds" : 0.0117,
"clashscore" : 1.63,
"molprobitypercentile" : "(percentile: 70.5 N=46877, 2.10A+/-0.25A) ",
"ramaoutliers" : 0
},
"ligandstatistics" : [
{
"ligandomin" : 0.9,
"ligandbavg" : 38.16,
"ligandbmax" : 55.44,
"mogulring" : "0/4",
"mogulzbond" : 0.397,
"ligandomax" : 0.9,
"mogulzangl" : 0.816,
"mogulangl" : "0/90",
"mogulbond" : "0/66",
"ligandid" : "LIG A4000",
"ligandbmin" : 32.37,
"ligandcc" : 0.886,
"moguldihe" : "1/25"
},
{
"ligandbavg" : 37.58,
"ligandomin" : 0.88,
"ligandbmax" : 53.33,
"mogulring" : "0/4",
"ligandomax" : 0.88,
"mogulzbond" : 0.507,
"mogulzangl" : 0.698,
"mogulangl" : "0/90",
"ligandid" : "LIG B4000",
"ligandbmin" : 31.64,
"mogulbond" : "0/66",
"ligandcc" : 0.933,
"moguldihe" : "3/25"
},
{
"ligandomax" : 1,
"mogulzbond" : 0.464,
"mogulring" : "0/4",
"ligandbmax" : 48.16,
"ligandomin" : 1,
"ligandbavg" : 34.93,
"moguldihe" : "2/25",
"ligandcc" : 0.958,
"ligandid" : "LIG C4000",
"ligandbmin" : 30.08,
"mogulbond" : "0/66",
"mogulzangl" : 0.831,
"mogulangl" : "0/90"
}
]
},
"postrefinement" : [
{
"cycle_number" : 0,
"type" : "BUSTER",
"R" : 0.194535,
"RMSangles" : 0.965228,
"WatersPresent" : null,
"MeanB" : 45.03,
"step" : "initial",
"RMSbonds" : 0.00801741,
"WilsonB" : 41.16,
"Rfree" : 0.225594
},
{
"cycle_number" : 1,
"type" : "BUSTER",
"R" : 0.180338,
"RMSangles" : 0.976673,
"WatersPresent" : 833,
"MeanB" : 45.73,
"step" : "final",
"RMSbonds" : 0.00805862,
"WilsonB" : 41.16,
"Rfree" : 0.20928
}
],
"solutions" : [
{
"chain" : "C",
"correlationcoefficient" : 0.8343,
"output" : "Hit_00_00_000.pdb",
"contactscore" : 11.4,
"poorfit" : "0/63",
"rhofitscore" : -3098.9,
"ligandstrain" : 54.3,
"closecontacts" : "",
"solution_number" : 1
},
{
"correlationcoefficient" : 0.7688,
"contactscore" : 3.7,
"output" : "Hit_01_00_000.pdb",
"poorfit" : "0/63",
"chain" : "A",
"closecontacts" : "",
"solution_number" : 2,
"rhofitscore" : -2724.8,
"ligandstrain" : 26
},
{
"chain" : "B",
"poorfit" : "6/63",
"output" : "Hit_02_00_000.pdb",
"contactscore" : 26.5,
"correlationcoefficient" : 0.8235,
"ligandstrain" : 32.5,
"rhofitscore" : -2621.4,
"solution_number" : 3,
"closecontacts" : ""
}
],
"ligandname" : "grade-LIG"
}
]
},
"dataprocessing" : {
"inputdata" : {
"cell" : {
"b" : 102.483,
"c" : 100.186,
"alpha" : 90,
"a" : 81.417,
"gamma" : 90,
"beta" : 103.529
},
"symmetry" : 4,
"reshigh" : 2.1,
"reslo" : 79.1579
},
"datatype" : "mtz",
"processingtype" : "unknown",
"referencedata" : {
"symmetry" : 4,
"cell" : {
"beta" : 104.502,
"gamma" : 90,
"b" : 104.592,
"c" : 100.155,
"alpha" : 90,
"a" : 82.155
}
}
},
"GPhL_pipedream" : {
"runfrom" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial2",
"jobid" : "fba34f24-e0a1-4837-be09-88e2d3280cd1",
"jsonversion" : "0.0.3",
"runby" : "asharff : escher : 10:08:26 on Sun Jul 4 2021",
"output" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial2/results/20210704",
"command" : "pipedream -hklin 3i25.mtz -xyzin input.pdb -hklref 3nsh.mtz -chains \"A B C\" -rhofit grade-LIG.cif -xclusters 3 -rhothorough -d results/20210704",
"terminationstatus" : "COMPLETED",
"version" : "__VERSION__ <__DATE__>"
},
"refinement" : {
"refinementprotocol" : "Default",
"Cycles" : [
{
"RMSangles" : 1.63036,
"cycle_number" : 0,
"type" : "BUSTER",
"R" : 0.322444,
"MeanB" : null,
"step" : "initial",
"RMSbonds" : 0.0212043,
"Rfree" : 0.334853,
"WilsonB" : null,
"WatersPresent" : null
},
{
"cycle_number" : 1,
"type" : "BUSTER",
"R" : 0.259261,
"RMSangles" : 0.96992,
"WatersPresent" : null,
"MeanB" : 40.5,
"step" : "refinement",
"RMSbonds" : 0.00790166,
"WilsonB" : 41.16,
"Rfree" : 0.28433
},
{
"RMSbonds" : 0.00826953,
"Rfree" : 0.22939,
"WilsonB" : 41.16,
"MeanB" : 45.03,
"step" : "final",
"WatersPresent" : 738,
"RMSangles" : 0.981052,
"type" : "BUSTER",
"R" : 0.197924,
"cycle_number" : 2
},
{
"WilsonB" : 41.16,
"Rfree" : 0.24219,
"RMSbonds" : 0.00788766,
"step" : "ligand-detection",
"MeanB" : 45.03,
"WatersPresent" : 677,
"RMSangles" : 0.96824,
"R" : 0.214191,
"type" : "BUSTER",
"cycle_number" : 3
}
],
"selectedmodel" : "input.pdb",
"models" : [
{
"modelname" : "input",
"number" : 1,
"LMRscore" : 81.5
}
]
}
}
data/jsonexamples_andrew/2-summary.out 0 → 100644
+ 278
− 0
View file @ 75093ab1
##############################################################################
## [pipedream] Automatic data processing and structure refinement ##
##############################################################################
Copyright (C) 2011-__YEAR__ by Global Phasing Limited
All rights reserved.
This software is proprietary to and embodies the confidential
technology of Global Phasing Limited (GPhL). Possession, use,
duplication or dissemination of the software is authorised
only pursuant to a valid written licence from GPhL.
Version: __VERSION__ <__DATE__>
------------------------------------------------------------------------------
Authors: Sharff A, Keller P, Vonrhein C, Smart O, Womack T,
Flensburg C, Paciorek W, Bricogne G (__YEAR__).
Pipedream version __VERSION__. Global Phasing Ltd.,
Cambridge, United Kingdom.
Partial support by EU project: SILVER (FP7-HEALTH-F3-2010-260644)
Contact: buster-develop@globalphasing.com
==============================================================================
Program citations:
Phaser : McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C.
and Read, R.J. (2007). Phaser Crystallographic Software. J. Appl. Cryst., 40, 658-674.
BUSTER : Bricogne G., Blanc E., Brandl M., Flensburg C., Keller P., Paciorek W.,
Roversi, P., Sharff A., Smart O.S., Vonrhein C. and Womack T.O. (__YEAR__).
BUSTER version 2.13.0. Cambridge, United Kingdom: Global Phasing Ltd.
=======================================
Processing and Refinement Summary
=======================================
Pipedream version: __VERSION__ <__DATE__>
Run by asharff on escher at 10:08:26 on Sun Jul 4 2021
Run from /.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial2
Job ID: fba34f24-e0a1-4837-be09-88e2d3280cd1
Command run: pipedream -hklin 3i25.mtz -xyzin input.pdb -hklref 3nsh.mtz \
-chains "A B C" -rhofit grade-LIG.cif -xclusters 3 -rhothorough \
-d results/20210704
All output in /.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial2/results/20210704
==================================================
************* Input data is MTZ file *************
==================================================
Checking indexing consistency against reference mtz file 3nsh.mtz.
No need to reindex input data.
Copying Freer column from the reference file 3nsh.mtz to the input mtz file.
Any pre-existing Freer set in the input file will be discarded.
Consistently indexed mtz file with reference Freer is in consistent-input.mtz
Cell dimensions and space group information:
Reference data = 82.155 104.592 100.155 90.000 104.502 90.000 'P 1 21 1' ( 4)
Experimental data = 81.417 102.483 100.186 90.000 103.529 90.000 'P 1 21 1' ( 4)
NOTE : Due to a significant difference in cell dimensions between the input
data and the reference mtz file (at least one of the cell axes differ
in length by more than 0.5 x resolution limit), the independence of the
Free R set cannot be guaranteed.
Resolution limits of input data are 79.16A - 2.10A.
==================================================
******************* limited MR *******************
==================================================
Limited MR procedure run with 3 independently defined units.
MR solution found with score (TFZ) 81.5
For further details please see MR/*{rotation or translation}.out
Output pdb file: MR/phaser.3.pdb
=================================================================================================
****** BUSTER refinement and unmodelled density elicitation (default protocol - version 2) ******
=================================================================================================
BUSTER refinement
=================
Run_1: Standard refinement, including Rigid Body at big cycle 1
Run_2: adding TLS, 1st and 2nd shell water placement
See Pipedream manual for full details
------------------------------------------------------------------------------------------------------
| Step | R | Rfree | RMS (bonds) | RMS (angles) | Mean B | Wilson B |
------------------------------------------------------------------------------------------------------
| Initial | 0.3224 | 0.3349 | 0.02120 | 1.63036 | | |
| After 1st refinement (Run_1) | 0.2593 | 0.2843 | 0.00790 | 0.96992 | 40.5 | 41.16 |
| Final (Run_2) | 0.1979 | 0.2294 | 0.00827 | 0.98105 | 45.03 | 41.16 |
------------------------------------------------------------------------------------------------------
Waters in final model = 738
For further details please see refine.out
Output files:
model:
refine/refine.pdb
refine/BUSTER_model.cif (deposition-ready)
reflection data and map coefficients:
refine/refine.mtz
refine/BUSTER_refln.cif (deposition-ready)
Unmodelled density elicitation:
===============================
Run_3: TLS, -L, calculation of map coefficients limited to 1.9A resolution
Potential ligand sites identified = 6
Site 1 with (estimated) volume of 292.30 A^3 and contacts <=1.5A: C38(ASP) C234(ASP)
Site 3 with (estimated) volume of 276.76 A^3 and contacts <=1.5A: A17(GLY) A114(PHE)
Site 5 with (estimated) volume of 249.74 A^3 and contacts <=1.5A: B40(GLY) B204(TYR) B234(ASP) C168(ASN)
Site 7 with (estimated) volume of 64.20 A^3 and contacts <=1.5A: B196(TYR) B296(GLU)
Site 9 with (estimated) volume of 62.05 A^3 and contacts <=1.5A: A211(ARG) A378(GLY) A379(PRO) A381(VAL) C211(ARG) C381(VAL)
Site 11 with (estimated) volume of 59.30 A^3 and contacts <=1.5A: A196(TYR) A296(GLU) A352(ASP)
For further details please see refine-L.out
Output files:
refine-L/refine.mtz
==================================================
*********** Ligand Fitting with Rhofit ***********
==================================================
++++++++++++++++++++++++++++++++++++++++++
| Running rhofit with ligand *grade-LIG* |
++++++++++++++++++++++++++++++++++++++++++
For output and further details please see rhofit-grade-LIG/
rhofit ligand LigProt Poorly
total Correl strain contact fitting LigProt contact to residues
File Chain score coeff score score atoms (% means zero weighted in score)
=================================================================================================
Hit_00_00_000.pdb C -3098.9 0.8343 54.3 11.4 0/63 C|239:ASN C|241:ARG C|335:THR C|80:GLY W|14:HOH% W|2:HOH% W|402:HOH% W|403:HOH% W|43:HOH% W|4:HOH% W|575:HOH% W|660:HOH% W|7:HOH% W|85:HOH%
Hit_01_00_000.pdb A -2724.8 0.7688 26.0 3.7 0/63 A|241:ARG A|335:THR A|338:VAL A|41:SER B|167:LEU W|10:HOH% W|159:HOH% W|38:HOH% W|405:HOH% W|407:HOH% W|41:HOH% W|573:HOH% W|574:HOH% W|63:HOH% W|661:HOH% W|79:HOH% W|80:HOH%
Hit_02_00_000.pdb B -2621.4 0.8235 32.5 26.5 6/63 B|204:TYR B|234:ASP B|335:THR B|338:VAL B|40:GLY B|80:GLY C|168:ASN W|104:HOH% W|151:HOH% W|177:HOH% W|18:HOH% W|1:HOH% W|409:HOH% W|40:HOH% W|44:HOH% W|455:HOH% W|57:HOH% W|659:HOH W|659:HOH%
To view the output solutions from Rhofit in coot use the command:
visualise-rhofit-coot results/20210704/rhofit-grade-LIG
Post refinement of "best" solution will be carried out.
Hydrogen atoms will be added to the fit ligand(s) with full occupancy
Output file: rhofit-grade-LIG/merged-hydrogenated.pdb
BUSTER post-refinement
======================
------------------------------------------------------------------------------------------------------
| Step | R | Rfree | RMS (bonds) | RMS (angles) | Mean B | Wilson B |
------------------------------------------------------------------------------------------------------
| Initial | 0.1945 | 0.2256 | 0.00802 | 0.96523 | 45.03 | 41.16 |
| Final | 0.1803 | 0.2093 | 0.00806 | 0.97667 | 45.73 | 41.16 |
------------------------------------------------------------------------------------------------------
Waters in final model = 833
For further details please see postrefine-grade-LIG.out
Output files:
model:
postrefine-grade-LIG/refine.pdb
postrefine-grade-LIG/BUSTER_model.cif (deposition-ready)
reflection data and map coefficients:
postrefine-grade-LIG/refine.mtz
postrefine-grade-LIG/BUSTER_refln.cif (deposition-ready)
==================================================
************* Validation statistics **************
==================================================
-------------------------------------------------------------------------------------------
| Quality metric | Value | Percent | Remark |
-------------------------------------------------------------------------------------------
| Clashscore, all atoms | 1.6300 | | (percentile: 92.1 N=47431, 2.10A+/-0.25A) |
| Poor rotamers | 34 | 3.55 % | Goal: < 0.3% |
| Ramachandran outliers | 0 | 0.00 % | Goal: < 0.2% |
| Ramachandran favored | 1077 | 97.38 % | Goal: > 98% |
| Cbeta deviations > 0.25A | 5 | | Goal: 0 |
| Molprobity score | 1.45 | | (percentile: 70.5 N=46877, 2.10A+/-0.25A) |
| RMS (bonds) | 0.0117 | | |
| RMS (angles) | 1.5800 | | |
-------------------------------------------------------------------------------------------
Ligand Refinement Statistics
----------------------------
-----------------------------------------------------------------------------------------------------------------------------
| Ligand | CC(2mFo-DFc) | min(B) | avg(B) | max(B) | min(occupancy) | max(occupancy) |
-----------------------------------------------------------------------------------------------------------------------------
| LIG A4000 | 0.886 | 32.37 | 38.16 | 55.44 | 0.90 | 0.90 |
| LIG B4000 | 0.933 | 31.64 | 37.58 | 53.33 | 0.88 | 0.88 |
| LIG C4000 | 0.958 | 30.08 | 34.93 | 48.16 | 1.00 | 1.00 |
-----------------------------------------------------------------------------------------------------------------------------
Ligand Mogul Statistics
-----------------------
-----------------------------------------------------------------------------------------------------------------------------
| Ligand | 'bad' bonds | 'bad' bond angles | 'unusual' dihedrals | 'bad' rings | bonds rms Z | angles rms Z |
-----------------------------------------------------------------------------------------------------------------------------
| LIG A4000 | 0/66 | 0/90 | 1/25 | 0/4 | 0.397 | 0.816 |
| LIG B4000 | 0/66 | 0/90 | 3/25 | 0/4 | 0.507 | 0.698 |
| LIG C4000 | 0/66 | 0/90 | 2/25 | 0/4 | 0.464 | 0.831 |
-----------------------------------------------------------------------------------------------------------------------------
For buster-report output see:
report-grade-LIG/index.html
=======================================
Successful termination!
Run took 02:30:02 h:m:s to complete
data/jsonexamples_andrew/3-pipedream_summary.json 0 → 100644
+ 259
− 0
View file @ 75093ab1
{
"dataprocessing" : {
"referencedata" : {
"cell" : {
"a" : 54.268,
"b" : 58.462,
"alpha" : 90,
"c" : 66.267,
"beta" : 90,
"gamma" : 90
},
"symmetry" : 19
},
"datatype" : "mtz",
"processingtype" : "unknown",
"inputdata" : {
"reshigh" : 1.6982,
"reslo" : 19.8514,
"symmetry" : 19,
"cell" : {
"alpha" : 90,
"a" : 54.537,
"b" : 57.911,
"gamma" : 90,
"beta" : 90,
"c" : 66.625
}
}
},
"refinement" : {
"selectedmodel" : "input.pdb",
"refinementprotocol" : "Default",
"models" : [
{
"modelname" : "input",
"LMRscore" : 27.3,
"number" : 1
}
],
"Cycles" : [
{
"MeanB" : null,
"RMSbonds" : 0.00676234,
"step" : "initial",
"cycle_number" : 0,
"Rfree" : 0.253755,
"WilsonB" : null,
"type" : "BUSTER",
"RMSangles" : 1.01015,
"WatersPresent" : null,
"R" : 0.25073
},
{
"MeanB" : 17.75,
"RMSbonds" : 0.00815136,
"cycle_number" : 1,
"step" : "refinement",
"Rfree" : 0.220545,
"type" : "BUSTER",
"WilsonB" : 17.79,
"RMSangles" : 1.07807,
"WatersPresent" : null,
"R" : 0.185886
},
{
"RMSbonds" : 0.00823966,
"MeanB" : 17.72,
"step" : "final",
"cycle_number" : 2,
"Rfree" : 0.218339,
"WilsonB" : 17.79,
"type" : "BUSTER",
"WatersPresent" : 306,
"RMSangles" : 1.07498,
"R" : 0.184783
},
{
"WatersPresent" : 320,
"RMSangles" : 1.0768,
"R" : 0.179247,
"cycle_number" : 3,
"step" : "ligand-detection",
"type" : "BUSTER",
"WilsonB" : 17.79,
"Rfree" : 0.211188,
"MeanB" : 17.72,
"RMSbonds" : 0.0081964
}
]
},
"ligandfitting" : {
"type" : "Rhofit",
"ligands" : [
{
"postrefinement" : [
{
"R" : 0.188362,
"RMSangles" : 1.0734,
"WatersPresent" : null,
"MeanB" : 17.72,
"RMSbonds" : 0.00818193,
"Rfree" : 0.221954,
"WilsonB" : 17.79,
"type" : "BUSTER",
"cycle_number" : 0,
"step" : "initial"
},
{
"RMSbonds" : 0.00807943,
"MeanB" : 18.05,
"cycle_number" : 1,
"step" : "final",
"Rfree" : 0.211086,
"type" : "BUSTER",
"WilsonB" : 17.79,
"RMSangles" : 1.07013,
"WatersPresent" : 336,
"R" : 0.179147
}
],
"validationstatistics" : {
"molprobity" : {
"poorrotamers" : 2,
"ramafavoredpercent" : 98.19,
"ramafavored" : 217,
"rmsangles" : 1.59,
"cbetadeviations" : 0,
"clashscore" : 1.8,
"molprobitypercentile" : "(percentile: 91.4 N=40830, 1.70A+/-0.25A) ",
"molprobityscore" : 0.97,
"ramaoutlierpercent" : 0,
"rmsbonds" : 0.0138,
"clashpercentile" : "(percentile: 86.2 N=41457, 1.70A+/-0.25A) ",
"poorrotamerspercent" : 1.09,
"ramaoutliers" : 0
},
"ligandstatistics" : [
{
"mogulring" : "0/1",
"ligandomin" : 0.91,
"ligandbmax" : 53.18,
"ligandbmin" : 52.13,
"ligandid" : "L01 A4000",
"ligandomax" : 0.91,
"ligandbavg" : 52.45,
"mogulzangl" : 0.445,
"mogulangl" : "0/11",
"mogulzbond" : 0.753,
"moguldihe" : "0/1",
"ligandcc" : 0.65,
"mogulbond" : "0/9"
}
]
},
"solutions" : [
{
"ligandstrain" : 0,
"solution_number" : 1,
"poorfit" : "2/10",
"contactscore" : 0,
"closecontacts" : "",
"correlationcoefficient" : 0.6119,
"rhofitscore" : -141,
"chain" : "A",
"output" : "Hit_00_00_000.pdb"
}
],
"ligandname" : "grade-L01"
},
{
"postrefinement" : [
{
"MeanB" : 18.05,
"RMSbonds" : 0.00819827,
"WilsonB" : 17.79,
"type" : "BUSTER",
"Rfree" : 0.219751,
"cycle_number" : 0,
"step" : "initial",
"R" : 0.185995,
"RMSangles" : 1.06384,
"WatersPresent" : null
},
{
"cycle_number" : 1,
"step" : "final",
"Rfree" : 0.207479,
"type" : "BUSTER",
"WilsonB" : 17.79,
"RMSbonds" : 0.00817447,
"MeanB" : 17.74,
"RMSangles" : 1.05998,
"WatersPresent" : 336,
"R" : 0.177997
}
],
"validationstatistics" : {
"ligandstatistics" : [
{
"ligandbavg" : 18.88,
"ligandid" : "L02 A4000",
"ligandomax" : 0.77,
"ligandomin" : 0.77,
"ligandbmax" : 20.38,
"ligandbmin" : 16.57,
"mogulring" : "0/1",
"mogulangl" : "0/8",
"mogulzangl" : 0.526,
"moguldihe" : "0/0",
"mogulbond" : "0/7",
"ligandcc" : 0.664,
"mogulzbond" : 0.969
}
],
"molprobity" : {
"poorrotamers" : 2,
"ramafavored" : 217,
"ramafavoredpercent" : 98.19,
"rmsangles" : 1.58,
"cbetadeviations" : 0,
"clashscore" : 1.2,
"molprobityscore" : 0.86,
"molprobitypercentile" : "(percentile: 95.4 N=40830, 1.70A+/-0.25A) ",
"ramaoutlierpercent" : 0,
"clashpercentile" : "(percentile: 93.0 N=41457, 1.70A+/-0.25A) ",
"rmsbonds" : 0.0138,
"poorrotamerspercent" : 1.09,
"ramaoutliers" : 0
}
},
"solutions" : [
{
"correlationcoefficient" : 0.6295,
"rhofitscore" : -160.7,
"chain" : "A",
"output" : "Hit_00_00_000.pdb",
"solution_number" : 1,
"poorfit" : "3/7",
"ligandstrain" : 0,
"contactscore" : 0,
"closecontacts" : ""
}
],
"ligandname" : "grade-L02"
}
]
},
"GPhL_pipedream" : {
"terminationstatus" : "COMPLETED",
"jobid" : "5b92df59-28d2-4840-aefa-b9b2a28298ba",
"output" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial3/results/20210702",
"runfrom" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial3",
"command" : "pipedream -hklin 3rxt.mtz -xyzin input.pdb -hklref 3rxe.mtz -keepwater -nowateradd -rhofit grade-L01.cif,grade-L02.cif -d results/20210702",
"jsonversion" : "0.0.3",
"version" : "__VERSION__ <__DATE__>",
"runby" : "asharff : escher : 17:59:06 on Fri Jul 2 2021"
}
}
data/jsonexamples_andrew/3-summary.out 0 → 100644
+ 355
− 0
View file @ 75093ab1
##############################################################################
## [pipedream] Automatic data processing and structure refinement ##
##############################################################################
Copyright (C) 2011-__YEAR__ by Global Phasing Limited
All rights reserved.
This software is proprietary to and embodies the confidential
technology of Global Phasing Limited (GPhL). Possession, use,
duplication or dissemination of the software is authorised
only pursuant to a valid written licence from GPhL.
Version: __VERSION__ <__DATE__>
------------------------------------------------------------------------------
Authors: Sharff A, Keller P, Vonrhein C, Smart O, Womack T,
Flensburg C, Paciorek W, Bricogne G (__YEAR__).
Pipedream version __VERSION__. Global Phasing Ltd.,
Cambridge, United Kingdom.
Partial support by EU project: SILVER (FP7-HEALTH-F3-2010-260644)
Contact: buster-develop@globalphasing.com
==============================================================================
Program citations:
Phaser : McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C.
and Read, R.J. (2007). Phaser Crystallographic Software. J. Appl. Cryst., 40, 658-674.
BUSTER : Bricogne G., Blanc E., Brandl M., Flensburg C., Keller P., Paciorek W.,
Roversi, P., Sharff A., Smart O.S., Vonrhein C. and Womack T.O. (__YEAR__).
BUSTER version 2.13.0. Cambridge, United Kingdom: Global Phasing Ltd.
=======================================
Processing and Refinement Summary
=======================================
Pipedream version: __VERSION__ <__DATE__>
Run by asharff on escher at 17:59:06 on Fri Jul 2 2021
Run from /.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial3
Job ID: 5b92df59-28d2-4840-aefa-b9b2a28298ba
Command run: pipedream -hklin 3rxt.mtz -xyzin input.pdb -hklref 3rxe.mtz \
-keepwater -nowateradd -rhofit grade-L01.cif,grade-L02.cif -d \
results/20210702
All output in /.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial3/results/20210702
==================================================
************* Input data is MTZ file *************
==================================================
Checking indexing consistency against reference mtz file 3rxe.mtz.
No need to reindex input data.
Copying Freer column from the reference file 3rxe.mtz to the input mtz file.
Any pre-existing Freer set in the input file will be discarded.
Consistently indexed mtz file with reference Freer is in consistent-input.mtz
Cell dimensions and space group information:
Reference data = 54.268 58.462 66.267 90.000 90.000 90.000 'P 21 21 21' ( 19)
Experimental data = 54.537 57.911 66.625 90.000 90.000 90.000 'P 21 21 21' ( 19)
Resolution limits of input data are 19.85A - 1.70A.
==================================================
******************* limited MR *******************
==================================================
Limited MR procedure run with 1 independently defined units.
MR solution found with score (TFZ) 27.3
For further details please see MR/*{rotation or translation}.out
Output pdb file: MR/phaser.3.pdb
=================================================================================================
****** BUSTER refinement and unmodelled density elicitation (default protocol - version 2) ******
=================================================================================================
BUSTER refinement
=================
Run_1: Standard refinement, including Rigid Body at big cycle 1
Run_2: adding TLS, 1st and 2nd shell water placement
See Pipedream manual for full details
------------------------------------------------------------------------------------------------------
| Step | R | Rfree | RMS (bonds) | RMS (angles) | Mean B | Wilson B |
------------------------------------------------------------------------------------------------------
| Initial | 0.2507 | 0.2538 | 0.00676 | 1.01015 | | |
| After 1st refinement (Run_1) | 0.1859 | 0.2205 | 0.00815 | 1.07807 | 17.75 | 17.79 |
| Final (Run_2) | 0.1848 | 0.2183 | 0.00824 | 1.07498 | 17.72 | 17.79 |
------------------------------------------------------------------------------------------------------
Waters in final model = 306
For further details please see refine.out
Output files:
model:
refine/refine.pdb
refine/BUSTER_model.cif (deposition-ready)
reflection data and map coefficients:
refine/refine.mtz
refine/BUSTER_refln.cif (deposition-ready)
Unmodelled density elicitation:
===============================
Run_3: TLS, -L, calculation of map coefficients limited to 1.9A resolution
Potential ligand sites identified = 0
For further details please see refine-L.out
Output files:
refine-L/refine.mtz
==================================================
*********** Ligand Fitting with Rhofit ***********
==================================================
++++++++++++++++++++++++++++++++++++++++++
| Running rhofit with ligand *grade-L01* |
++++++++++++++++++++++++++++++++++++++++++
For output and further details please see rhofit-grade-L01/
rhofit ligand LigProt Poorly
total Correl strain contact fitting LigProt contact to residues
File Chain score coeff score score atoms (% means zero weighted in score)
=================================================================================================
Hit_00_00_000.pdb A -141.0 0.6119 0.0 0.0 2/10 A|301:HOH% A|339:HOH% A|372:HOH% A|95:ASN
To view the output solutions from Rhofit in coot use the command:
visualise-rhofit-coot results/20210702/rhofit-grade-L01
Post refinement of "best" solution will be carried out.
Hydrogen atoms will be added to the fit ligand(s) with full occupancy
Output file: rhofit-grade-L01/merged-hydrogenated.pdb
BUSTER post-refinement
======================
------------------------------------------------------------------------------------------------------
| Step | R | Rfree | RMS (bonds) | RMS (angles) | Mean B | Wilson B |
------------------------------------------------------------------------------------------------------
| Initial | 0.1884 | 0.2220 | 0.00818 | 1.07340 | 17.72 | 17.79 |
| Final | 0.1791 | 0.2111 | 0.00808 | 1.07013 | 18.05 | 17.79 |
------------------------------------------------------------------------------------------------------
Waters in final model = 336
For further details please see postrefine-grade-L01.out
Output files:
model:
postrefine-grade-L01/refine.pdb
postrefine-grade-L01/BUSTER_model.cif (deposition-ready)
reflection data and map coefficients:
postrefine-grade-L01/refine.mtz
postrefine-grade-L01/BUSTER_refln.cif (deposition-ready)
==================================================
************* Validation statistics **************
==================================================
-------------------------------------------------------------------------------------------
| Quality metric | Value | Percent | Remark |
-------------------------------------------------------------------------------------------
| Clashscore, all atoms | 1.8000 | | (percentile: 86.2 N=41457, 1.70A+/-0.25A) |
| Poor rotamers | 2 | 1.09 % | Goal: < 0.3% |
| Ramachandran outliers | 0 | 0.00 % | Goal: < 0.2% |
| Ramachandran favored | 217 | 98.19 % | Goal: > 98% |
| Cbeta deviations > 0.25A | 0 | | Goal: 0 |
| Molprobity score | 0.97 | | (percentile: 91.4 N=40830, 1.70A+/-0.25A) |
| RMS (bonds) | 0.0138 | | |
| RMS (angles) | 1.5900 | | |
-------------------------------------------------------------------------------------------
Ligand Refinement Statistics
----------------------------
-----------------------------------------------------------------------------------------------------------------------------
| Ligand | CC(2mFo-DFc) | min(B) | avg(B) | max(B) | min(occupancy) | max(occupancy) |
-----------------------------------------------------------------------------------------------------------------------------
| L01 A4000 | 0.650 | 52.13 | 52.45 | 53.18 | 0.91 | 0.91 |
-----------------------------------------------------------------------------------------------------------------------------
Ligand Mogul Statistics
-----------------------
-----------------------------------------------------------------------------------------------------------------------------
| Ligand | 'bad' bonds | 'bad' bond angles | 'unusual' dihedrals | 'bad' rings | bonds rms Z | angles rms Z |
-----------------------------------------------------------------------------------------------------------------------------
| L01 A4000 | 0/9 | 0/11 | 0/1 | 0/1 | 0.753 | 0.445 |
-----------------------------------------------------------------------------------------------------------------------------
For buster-report output see:
report-grade-L01/index.html
=======================================
++++++++++++++++++++++++++++++++++++++++++
| Running rhofit with ligand *grade-L02* |
++++++++++++++++++++++++++++++++++++++++++
For output and further details please see rhofit-grade-L02/
rhofit ligand LigProt Poorly
total Correl strain contact fitting LigProt contact to residues
File Chain score coeff score score atoms (% means zero weighted in score)
=================================================================================================
Hit_00_00_000.pdb A -160.7 0.6295 0.0 0.0 3/7 A|283:HOH% A|304:HOH% A|372:HOH% A|74:ASN A|76:VAL A|82:PHE
To view the output solutions from Rhofit in coot use the command:
visualise-rhofit-coot results/20210702/rhofit-grade-L02
Post refinement of "best" solution will be carried out.
Hydrogen atoms will be added to the fit ligand(s) with full occupancy
Output file: rhofit-grade-L02/merged-hydrogenated.pdb
BUSTER post-refinement
======================
------------------------------------------------------------------------------------------------------
| Step | R | Rfree | RMS (bonds) | RMS (angles) | Mean B | Wilson B |
------------------------------------------------------------------------------------------------------
| Initial | 0.1860 | 0.2198 | 0.00820 | 1.06384 | 18.05 | 17.79 |
| Final | 0.1780 | 0.2075 | 0.00817 | 1.05998 | 17.74 | 17.79 |
------------------------------------------------------------------------------------------------------
Waters in final model = 336
For further details please see postrefine-grade-L02.out
Output files:
model:
postrefine-grade-L02/refine.pdb
postrefine-grade-L02/BUSTER_model.cif (deposition-ready)
reflection data and map coefficients:
postrefine-grade-L02/refine.mtz
postrefine-grade-L02/BUSTER_refln.cif (deposition-ready)
==================================================
************* Validation statistics **************
==================================================
-------------------------------------------------------------------------------------------
| Quality metric | Value | Percent | Remark |
-------------------------------------------------------------------------------------------
| Clashscore, all atoms | 1.2000 | | (percentile: 93.0 N=41457, 1.70A+/-0.25A) |
| Poor rotamers | 2 | 1.09 % | Goal: < 0.3% |
| Ramachandran outliers | 0 | 0.00 % | Goal: < 0.2% |
| Ramachandran favored | 217 | 98.19 % | Goal: > 98% |
| Cbeta deviations > 0.25A | 0 | | Goal: 0 |
| Molprobity score | 0.86 | | (percentile: 95.4 N=40830, 1.70A+/-0.25A) |
| RMS (bonds) | 0.0138 | | |
| RMS (angles) | 1.5800 | | |
-------------------------------------------------------------------------------------------
Ligand Refinement Statistics
----------------------------
-----------------------------------------------------------------------------------------------------------------------------
| Ligand | CC(2mFo-DFc) | min(B) | avg(B) | max(B) | min(occupancy) | max(occupancy) |
-----------------------------------------------------------------------------------------------------------------------------
| L02 A4000 | 0.664 | 16.57 | 18.88 | 20.38 | 0.77 | 0.77 |
-----------------------------------------------------------------------------------------------------------------------------
Ligand Mogul Statistics
-----------------------
-----------------------------------------------------------------------------------------------------------------------------
| Ligand | 'bad' bonds | 'bad' bond angles | 'unusual' dihedrals | 'bad' rings | bonds rms Z | angles rms Z |
-----------------------------------------------------------------------------------------------------------------------------
| L02 A4000 | 0/7 | 0/8 | 0/0 | 0/1 | 0.969 | 0.526 |
-----------------------------------------------------------------------------------------------------------------------------
For buster-report output see:
report-grade-L02/index.html
=======================================
Successful termination!
Run took 00:25:40 h:m:s to complete
data/jsonexamples_andrew/4-pipedream_summary.json 0 → 100644
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− 0
View file @ 75093ab1
{
"ligandfitting" : {
"type" : "Rhofit",
"ligands" : [
{
"solutions" : [
{
"contactscore" : 0,
"closecontacts" : "",
"rhofitscore" : -1976.8,
"output" : "Hit_00_00_000.pdb",
"solution_number" : 1,
"ligandstrain" : 15.1,
"correlationcoefficient" : 0.8237,
"chain" : "A",
"poorfit" : "0/41"
}
],
"validationstatistics" : {
"molprobity" : {
"clashscore" : 0,
"molprobityscore" : 1.06,
"rmsangles" : 1.6,
"rmsbonds" : 0.0121,
"poorrotamers" : 17,
"cbetadeviations" : 1,
"ramafavoredpercent" : 98.05,
"ramafavored" : 352,
"poorrotamerspercent" : 5.41,
"clashpercentile" : "(percentile: 99.4 N=50613, 1.91A+/-0.25A) ",
"ramaoutlierpercent" : 0,
"molprobitypercentile" : "(percentile: 89.3 N=50034, 1.91A+/-0.25A) ",
"ramaoutliers" : 0
},
"ligandstatistics" : [
{
"moguldihe" : "1/11",
"ligandomin" : 0.82,
"ligandid" : "1R6 A4000",
"mogulring" : "0/3",
"ligandbmax" : 45.99,
"ligandomax" : 0.82,
"mogulangl" : "0/61",
"mogulzangl" : 0.964,
"mogulzbond" : 1.215,
"ligandbmin" : 31.92,
"ligandcc" : 0.93,
"ligandbavg" : 36.11,
"mogulbond" : "1/46"
}
]
},
"postrefinement" : [
{
"RMSangles" : 0.997267,
"type" : "BUSTER",
"WilsonB" : 31.31,
"cycle_number" : 0,
"RMSbonds" : 0.00833401,
"MeanB" : 46.98,
"R" : 0.214341,
"WatersPresent" : null,
"Rfree" : 0.252025,
"step" : "initial"
},
{
"R" : 0.207073,
"MeanB" : 49.15,
"RMSbonds" : 0.00809347,
"cycle_number" : 1,
"step" : "final",
"Rfree" : 0.250653,
"WatersPresent" : 377,
"type" : "BUSTER",
"RMSangles" : 0.988097,
"WilsonB" : 31.31
}
],
"ligandname" : "1R6.grade_PDB_ligand"
}
]
},
"dataprocessing" : {
"referencedata" : {
"symmetry" : 178,
"cell" : {
"gamma" : 120,
"alpha" : 90,
"a" : 103.243,
"b" : 103.243,
"c" : 169.108,
"beta" : 90
}
},
"datatype" : "mtz",
"inputdata" : {
"reslo" : 27.9307,
"cell" : {
"alpha" : 90,
"a" : 102.48,
"gamma" : 120,
"beta" : 90,
"b" : 102.48,
"c" : 169.495
},
"reshigh" : 1.9115,
"symmetry" : 178
},
"processingtype" : "unknown"
},
"refinement" : {
"models" : [
{
"LMRscore" : 52,
"number" : 1,
"modelname" : "1-1w50"
},
{
"modelname" : "2-4dh6",
"number" : 2,
"LMRscore" : 56.8
},
{
"LMRscore" : 53.1,
"number" : 3,
"modelname" : "3-4j0p"
}
],
"selectedmodel" : "4dh6.pdb",
"refinementprotocol" : "Default",
"Cycles" : [
{
"WatersPresent" : null,
"step" : "initial",
"Rfree" : 0.352125,
"RMSbonds" : 0.010085,
"cycle_number" : 0,
"R" : 0.354932,
"MeanB" : null,
"WilsonB" : null,
"type" : "BUSTER",
"RMSangles" : 0.98686
},
{
"step" : "refinement",
"Rfree" : 0.330985,
"WatersPresent" : null,
"MeanB" : 35.53,
"R" : 0.303921,
"cycle_number" : 1,
"RMSbonds" : 0.00816357,
"WilsonB" : 31.31,
"RMSangles" : 0.980675,
"type" : "BUSTER"
},
{
"step" : "final",
"Rfree" : 0.254656,
"WatersPresent" : 323,
"MeanB" : 46.98,
"R" : 0.214914,
"RMSbonds" : 0.00853429,
"cycle_number" : 2,
"WilsonB" : 31.31,
"RMSangles" : 1.01029,
"type" : "BUSTER"
},
{
"WilsonB" : 31.31,
"RMSangles" : 0.999903,
"type" : "BUSTER",
"step" : "ligand-detection",
"Rfree" : 0.274171,
"WatersPresent" : 313,
"MeanB" : 46.98,
"R" : 0.230398,
"cycle_number" : 3,
"RMSbonds" : 0.00831549
}
]
},
"GPhL_pipedream" : {
"jobid" : "dab062c4-2d0c-4aa6-bc59-d1bd89ce50c2",
"jsonversion" : "0.0.3",
"command" : "pipedream -hklin 4ke1.mtz -nofreeref -xyzin 1w50.pdb,4dh6.pdb,4j0p.pdb -rhofit 1R6.grade_PDB_ligand.cif -rhothorough -d results/20210704",
"runfrom" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial5",
"runby" : "asharff : escher : 18:53:52 on Sun Jul 4 2021",
"version" : "__VERSION__ <__DATE__>",
"output" : "/.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial5/results/20210704",
"terminationstatus" : "COMPLETED"
}
}
data/jsonexamples_andrew/4-summary.out 0 → 100644
+ 364
− 0
View file @ 75093ab1
##############################################################################
## [pipedream] Automatic data processing and structure refinement ##
##############################################################################
Copyright (C) 2011-__YEAR__ by Global Phasing Limited
All rights reserved.
This software is proprietary to and embodies the confidential
technology of Global Phasing Limited (GPhL). Possession, use,
duplication or dissemination of the software is authorised
only pursuant to a valid written licence from GPhL.
Version: __VERSION__ <__DATE__>
------------------------------------------------------------------------------
Authors: Sharff A, Keller P, Vonrhein C, Smart O, Womack T,
Flensburg C, Paciorek W, Bricogne G (__YEAR__).
Pipedream version __VERSION__. Global Phasing Ltd.,
Cambridge, United Kingdom.
Partial support by EU project: SILVER (FP7-HEALTH-F3-2010-260644)
Contact: buster-develop@globalphasing.com
==============================================================================
Program citations:
Phaser : McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C.
and Read, R.J. (2007). Phaser Crystallographic Software. J. Appl. Cryst., 40, 658-674.
BUSTER : Bricogne G., Blanc E., Brandl M., Flensburg C., Keller P., Paciorek W.,
Roversi, P., Sharff A., Smart O.S., Vonrhein C. and Womack T.O. (__YEAR__).
BUSTER version 2.13.0. Cambridge, United Kingdom: Global Phasing Ltd.
=======================================
Processing and Refinement Summary
=======================================
Pipedream version: __VERSION__ <__DATE__>
Run by asharff on escher at 18:53:52 on Sun Jul 4 2021
Run from /.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial5
Job ID: dab062c4-2d0c-4aa6-bc59-d1bd89ce50c2
Command run: pipedream -hklin 4ke1.mtz -nofreeref -xyzin \
1w50.pdb,4dh6.pdb,4j0p.pdb -rhofit 1R6.grade_PDB_ligand.cif \
-rhothorough -d results/20210704
All output in /.net/fs3/scratch_fs1/asharff/pipedream-tutorials/tutorial5/results/20210704
WARNING : Reference structure factors (results/20210704/1-1w50_nowater.mtz)
have been back-calculated from reference model with sfall!
NOTE : You are running Pipedream without a common Free R set. This is not
adviseable as it may compromise cross-validation!
==================================================
************* Input data is MTZ file *************
==================================================
Checking indexing consistency against reference mtz file results/20210704/1-1w50_nowater.mtz.
No need to reindex input data.
Using Freer column already present in the input mtz file.
Cell dimensions and space group information:
Reference data = 103.243 103.243 169.108 90.000 90.000 120.000 'P 61 2 2' (178)
Experimental data = 102.480 102.480 169.495 90.000 90.000 120.000 'P 61 2 2' (178)
Resolution limits of input data are 27.93A - 1.91A.
==================================================
****************** Input models ******************
==================================================
You are running pipedream with 3 input pdb files.
Limited MR and initial refinement will be run on each
of the input models, after which the model that best
fits the data will be chosen. Further steps will only
be run on the selected model.
The input models (in order) are:
1: 1w50.pdb (located in current directory)
2: 4dh6.pdb (located in current directory)
3: 4j0p.pdb (located in current directory)
==================================================
******************* limited MR *******************
==================================================
Limited MR procedure run with 1 independently defined units.
1-1w50: MR solution found with score (TFZ) 52.0
For further details please see 1-1w50/MR/*{rotation or translation}.out
Output pdb file: 1-1w50/MR/phaser.3.pdb
2-4dh6: MR solution found with score (TFZ) 56.8
For further details please see 2-4dh6/MR/*{rotation or translation}.out
Output pdb file: 2-4dh6/MR/phaser.3.pdb
3-4j0p: MR solution found with score (TFZ) 53.1
For further details please see 3-4j0p/MR/*{rotation or translation}.out
Output pdb file: 3-4j0p/MR/phaser.3.pdb
==================================================
***************** Model selection ****************
==================================================
For the results of initial refinement and the edstats output
for each of the input models, please see:
results/20210704/1-1w50/refine1/refine.log
results/20210704/1-1w50/refine1/edstats.out
results/20210704/2-4dh6/refine1/refine.log
results/20210704/2-4dh6/refine1/edstats.out
results/20210704/3-4j0p/refine1/refine.log
results/20210704/3-4j0p/refine1/edstats.out
The residues, automatically selected by pipedream
from comparison of pairwise mainchain RMS deviations
(deviations > 1.5), that will be used to assess which
one of the input models gives the best fit to the
input data are listed in the file:
results/20210704/comparison-residues.list
NOTE : Only residues that are present in ALL of the input models will be
considered in selecting the best model. Please be aware that a
significant number of missing residues in one or more of the input
models could potentially compromise the model selection process!
NOTE : The average Z-score of the real-space sample correlation coefficient
(ZCCm) over the selected residues for each of the input models are:
average ZCCm = 0.3900, for model results/20210704/1-1w50/refine1/refine.pdb
average ZCCm = 0.5400, for model results/20210704/2-4dh6/refine1/refine.pdb
average ZCCm = 0.4800, for model results/20210704/3-4j0p/refine1/refine.pdb
****************************************************
On the basis of having the highest mean ZCCm score,
over the selected residue range, the model selected
as the best match to the input experimental data is
results/20210704/2-4dh6/refine1/refine.pdb
refined from 4dh6.pdb
Subsequent steps will proceed using this model only!
****************************************************
=================================================================================================
****** BUSTER refinement and unmodelled density elicitation (default protocol - version 2) ******
=================================================================================================
BUSTER refinement
=================
Run_1: Standard refinement, including Rigid Body at big cycle 1
Run_2: adding TLS, 1st and 2nd shell water placement
See Pipedream manual for full details
------------------------------------------------------------------------------------------------------
| Step | R | Rfree | RMS (bonds) | RMS (angles) | Mean B | Wilson B |
------------------------------------------------------------------------------------------------------
| Initial | 0.3549 | 0.3521 | 0.01009 | 0.98686 | | |
| After 1st refinement (Run_1) | 0.3039 | 0.3310 | 0.00816 | 0.98067 | 35.53 | 31.31 |
| Final (Run_2) | 0.2149 | 0.2547 | 0.00853 | 1.01029 | 46.98 | 31.31 |
------------------------------------------------------------------------------------------------------
Waters in final model = 323
For further details please see refine.out
Output files:
model:
refine/refine.pdb
refine/BUSTER_model.cif (deposition-ready)
reflection data and map coefficients:
refine/refine.mtz
refine/BUSTER_refln.cif (deposition-ready)
Unmodelled density elicitation:
===============================
Run_3: TLS, -L, calculation of map coefficients limited to 1.9A resolution
Potential ligand sites identified = 3
Site 1 with (estimated) volume of 147.61 A^3 and contacts <=1.5A: A32(ASP)
Site 3 with (estimated) volume of 77.43 A^3 and contacts <=1.5A: A105(SER) A107(LYS) A111(ASN)
Site 5 with (estimated) volume of 61.10 A^3 and contacts <=1.5A: A58(SER) A349(ARG)
For further details please see refine-L.out
Output files:
refine-L/refine.mtz
==================================================
*********** Ligand Fitting with Rhofit ***********
==================================================
+++++++++++++++++++++++++++++++++++++++++++++++++++++
| Running rhofit with ligand *1R6.grade_PDB_ligand* |
+++++++++++++++++++++++++++++++++++++++++++++++++++++
For output and further details please see rhofit-1R6.grade_PDB_ligand/
rhofit ligand LigProt Poorly
total Correl strain contact fitting LigProt contact to residues
File Chain score coeff score score atoms (% means zero weighted in score)
=================================================================================================
Hit_00_00_000.pdb A -1976.8 0.8237 15.1 0.0 0/41 W|106:HOH% W|238:HOH% W|241:HOH% W|242:HOH% W|245:HOH% W|277:HOH% W|33:HOH% W|37:HOH% W|40:HOH% W|58:HOH%
To view the output solutions from Rhofit in coot use the command:
visualise-rhofit-coot results/20210704/rhofit-1R6.grade_PDB_ligand
Post refinement of "best" solution will be carried out.
Hydrogen atoms will be added to the fit ligand(s) with full occupancy
Output file: rhofit-1R6.grade_PDB_ligand/merged-hydrogenated.pdb
BUSTER post-refinement
======================
------------------------------------------------------------------------------------------------------
| Step | R | Rfree | RMS (bonds) | RMS (angles) | Mean B | Wilson B |
------------------------------------------------------------------------------------------------------
| Initial | 0.2143 | 0.2520 | 0.00833 | 0.99727 | 46.98 | 31.31 |
| Final | 0.2071 | 0.2507 | 0.00809 | 0.98810 | 49.15 | 31.31 |
------------------------------------------------------------------------------------------------------
Waters in final model = 377
For further details please see postrefine-1R6.grade_PDB_ligand.out
Output files:
model:
postrefine-1R6.grade_PDB_ligand/refine.pdb
postrefine-1R6.grade_PDB_ligand/BUSTER_model.cif (deposition-ready)
reflection data and map coefficients:
postrefine-1R6.grade_PDB_ligand/refine.mtz
postrefine-1R6.grade_PDB_ligand/BUSTER_refln.cif (deposition-ready)
==================================================
************* Validation statistics **************
==================================================
-------------------------------------------------------------------------------------------
| Quality metric | Value | Percent | Remark |
-------------------------------------------------------------------------------------------
| Clashscore, all atoms | 0.0000 | | (percentile: 99.4 N=50613, 1.91A+/-0.25A) |
| Poor rotamers | 17 | 5.41 % | Goal: < 0.3% |
| Ramachandran outliers | 0 | 0.00 % | Goal: < 0.2% |
| Ramachandran favored | 352 | 98.05 % | Goal: > 98% |
| Cbeta deviations > 0.25A | 1 | | Goal: 0 |
| Molprobity score | 1.06 | | (percentile: 89.3 N=50034, 1.91A+/-0.25A) |
| RMS (bonds) | 0.0121 | | |
| RMS (angles) | 1.6000 | | |
-------------------------------------------------------------------------------------------
Ligand Refinement Statistics
----------------------------
-----------------------------------------------------------------------------------------------------------------------------
| Ligand | CC(2mFo-DFc) | min(B) | avg(B) | max(B) | min(occupancy) | max(occupancy) |
-----------------------------------------------------------------------------------------------------------------------------
| 1R6 A4000 | 0.930 | 31.92 | 36.11 | 45.99 | 0.82 | 0.82 |
-----------------------------------------------------------------------------------------------------------------------------
Ligand Mogul Statistics
-----------------------
-----------------------------------------------------------------------------------------------------------------------------
| Ligand | 'bad' bonds | 'bad' bond angles | 'unusual' dihedrals | 'bad' rings | bonds rms Z | angles rms Z |
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| 1R6 A4000 | 1/46 | 0/61 | 1/11 | 0/3 | 1.215 | 0.964 |
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For buster-report output see:
report-1R6.grade_PDB_ligand/index.html
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