############################################################################## ## [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 (2011). 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 ============================================================================== ======================================= Processing and Refinement Summary ======================================= Pipedream version: __VERSION__ <__DATE__> Run by asharff on bijvoet at 15:35:56 on Thu Jan 29 2015 Run from /home/asharff/projects/pipedream/multiple-models/bace1 Command run: pipedream -hklin 4ke1/4ke1.mtz -nofreeref -xyzin \ 1w50.pdb,4dh6.pdb,4j0p.pdb -rhofit 1R6.grade_PDB_ligand.cif \ -rhothorough -postref -seqin1 seq.list -d multiple-seqin3 All output in /home/asharff/projects/pipedream/multiple-models/bace1/multiple-seqin3 Reference structure factors (multiple-seqin3/1-1w50_nowater.mtz) have been back calculated from reference model with sfall! ================================================== ************* Input data is MTZ file ************* ================================================== Checking indexing consistency against reference mtz file multiple-seqin3/1-1w50_nowater.mtz. No need to reindex input data. Using Freer column already present in the input mtz file. ================================================== ****************** 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. NOTE: Your Phaser version seems to be newer than the latest that this program was tested with (version 2.5.6) - hopefully it should be OK! 1-1w50: MR solution found with score (TFZ) 52.5 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) 56.7 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) 53.3 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 edstats output for each of the input models, please see: multiple-seqin3/1-1w50/refine1.out multiple-seqin3/1-1w50/refine1/edstats.out multiple-seqin3/2-4dh6/refine1.out multiple-seqin3/2-4dh6/refine1/edstats.out multiple-seqin3/3-4j0p/refine1.out multiple-seqin3/3-4j0p/refine1/edstats.out The residues, as input, 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: multiple-seqin3/comparison-residues.list NOTE: Any residues from the input list that are not present in one (or more) of the input models will be automatically assigned a Z-score of 0 for that particular model. Please be aware that a significant number of "missing" residues could potentially compromise the model selection process! 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 = 5.5000, for model multiple-seqin3/1-1w50/refine1/refine.pdb average ZCCm = 9.1000, for model multiple-seqin3/2-4dh6/refine1/refine.pdb average ZCCm = 5.0875, for model multiple-seqin3/3-4j0p/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 multiple-seqin3/2-4dh6/refine1/refine.pdb refined from 4dh6.pdb Subsequent steps will proceed using this model only! **************************************************** ================================================== ****** BUSTER refinement (default protocol) ****** ================================================== Initial: R = 0.2706, Rfree = 0.2961 After 1st refinement: R = 0.2740, Rfree = 0.3055 Final: R = 0.2210, Rfree = 0.2569 For further details please see refine.out Output files: refine/refine.pdb refine/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 -2260.9 0.8363 28.3 0.0 0/41 BUSTER post-refinement ====================== Initial: R = 0.2524, Rfree = 0.2746 Final: R = 0.1949, Rfree = 0.2330 For further details please see postrefine-1R6.grade_PDB_ligand.out Output files: postrefine-1R6.grade_PDB_ligand/refine.pdb postrefine-1R6.grade_PDB_ligand/refine.mtz buster-report output: report-1R6.grade_PDB_ligand/index.html ======================================= Run took 01:47:02 h:m:s to complete