diff --git a/data/jsonexamples_andrew/1-pipedream_summary.json b/data/jsonexamples_andrew/1-pipedream_summary.json
new file mode 100644
index 0000000000000000000000000000000000000000..ca7eb24eef6b30b21480470ff7230ea330304020
--- /dev/null
+++ b/data/jsonexamples_andrew/1-pipedream_summary.json
@@ -0,0 +1,305 @@
+{
+ "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
+ }
+ ]
+ }
+ ]
+ }
+}
+
diff --git a/data/jsonexamples_andrew/1-summary.out b/data/jsonexamples_andrew/1-summary.out
new file mode 100644
index 0000000000000000000000000000000000000000..50029298d013c825ee950af1d9d6033c86e74c50
--- /dev/null
+++ b/data/jsonexamples_andrew/1-summary.out
@@ -0,0 +1,349 @@
+
+
+##############################################################################
+## [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
+
diff --git a/data/jsonexamples_andrew/2-pipedream_summary.json b/data/jsonexamples_andrew/2-pipedream_summary.json
new file mode 100644
index 0000000000000000000000000000000000000000..19565674e169b1fdec555b9533e0b77193698387
--- /dev/null
+++ b/data/jsonexamples_andrew/2-pipedream_summary.json
@@ -0,0 +1,235 @@
+{
+ "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
+ }
+ ]
+ }
+}
+
diff --git a/data/jsonexamples_andrew/2-summary.out b/data/jsonexamples_andrew/2-summary.out
new file mode 100644
index 0000000000000000000000000000000000000000..67494726959d1de9621a135bfd14732bb5fe83f5
--- /dev/null
+++ b/data/jsonexamples_andrew/2-summary.out
@@ -0,0 +1,278 @@
+
+
+##############################################################################
+## [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
+
diff --git a/data/jsonexamples_andrew/3-pipedream_summary.json b/data/jsonexamples_andrew/3-pipedream_summary.json
new file mode 100644
index 0000000000000000000000000000000000000000..bba779817c318c1d5c5237445429b410133aa06a
--- /dev/null
+++ b/data/jsonexamples_andrew/3-pipedream_summary.json
@@ -0,0 +1,259 @@
+{
+ "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"
+ }
+}
+
diff --git a/data/jsonexamples_andrew/3-summary.out b/data/jsonexamples_andrew/3-summary.out
new file mode 100644
index 0000000000000000000000000000000000000000..0577b98e71857f91ee4046f177034caef8cc28b7
--- /dev/null
+++ b/data/jsonexamples_andrew/3-summary.out
@@ -0,0 +1,355 @@
+
+
+##############################################################################
+## [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
+
diff --git a/data/jsonexamples_andrew/4-pipedream_summary.json b/data/jsonexamples_andrew/4-pipedream_summary.json
new file mode 100644
index 0000000000000000000000000000000000000000..255d3c1b5657b3df75488a4646b0f758f15b439b
--- /dev/null
+++ b/data/jsonexamples_andrew/4-pipedream_summary.json
@@ -0,0 +1,193 @@
+{
+ "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"
+ }
+}
+
diff --git a/data/jsonexamples_andrew/4-summary.out b/data/jsonexamples_andrew/4-summary.out
new file mode 100644
index 0000000000000000000000000000000000000000..17189423606d96c40bafce07bf905a2365718c59
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+
+
+##############################################################################
+## [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 |
+ -----------------------------------------------------------------------------------------------------------------------------
+| 1R6 A4000 | 1/46 | 0/61 | 1/11 | 0/3 | 1.215 | 0.964 |
+ -----------------------------------------------------------------------------------------------------------------------------
+
+
+
+
+ For buster-report output see:
+ report-1R6.grade_PDB_ligand/index.html
+
+ =======================================
+
+
+
+ Successful termination!
+ Run took 01:42:03 h:m:s to complete
+