############################################################################## # This software is licenced to : Global Phasing Ltd (perutz) ############################################################################## ############################################################################## # This software is licenced to : Global Phasing Ltd (perutz) ##############################################################################  ############################################################################## ## [refine] Framework for automatic refinement of macromolecules ############################################################################## Copyright (C) 1992-2011 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: 1.11.1 <2011-02-04 19:10:13> ------------------------------------------------------------------------------ Authors: Bricogne G, Blanc E, Brandl M, Flensburg C, Keller P, Paciorek P, Roversi P, Sharff A, Smart O, Vonrhein C, Womack T (2011). BUSTER version 2.11.1. Cambridge, United Kingdom: Global Phasing Ltd.  External: [TNT] B. Matthews, L. Ten Eyck, D. Tronrud (Univ. Oregon) Partial support by EU projects: VIZIER (LSHG-CT-2004-511960) SILVER (FP7-HEALTH-F3-2010-260644) Contact: buster-develop@GlobalPhasing.com ============================================================================== ################################ Basic checks ################################ NOTE : running with the following command line arguments: "-p inserted-ligand.pdb -l 880.grade_PDB_ligand.cif -m 1pmq.mtz -d first-build-with-ligand -M ShortRunVoid" ######################### Checking PDB and MTZ file ########################## >>> pdbchk >>> >>> pdbchk >>> Extracted from file first-build-with-ligand/pdbchk.2.log : >>> pdbchk >>> >>> pdbchk >>> WARNING : 1 records are shorter than expected - will pad >>> pdbchk >>> with spaces >>> pdbchk >>> >>> pdbchk >>> NOTE : fixed length for 1 records (by padding with spaces) >>> pdbchk >>> >>> pdbchk >>> WARNING : 1 non-standard residues have 35 ATOM records >>> pdbchk >>> (when it should be HETATM) - see below >>> pdbchk >>> ATOM 2975 N1 880 B 1 22.073 11.157 30.880 1.00 10.00 N >>> pdbchk >>> ATOM 2976 C2 880 B 1 22.194 12.466 30.848 1.00 10.00 C >>> pdbchk >>> ATOM 2977 N3 880 B 1 21.359 12.942 31.652 1.00 10.00 N >>> pdbchk >>> ATOM 2978 C4 880 B 1 20.680 11.988 32.249 1.00 10.00 C >>> pdbchk >>> ATOM 2979 C5 880 B 1 21.124 10.776 31.752 1.00 10.00 C >>> pdbchk >>> ATOM 2980 C6 880 B 1 22.853 10.234 30.103 1.00 10.00 C >>> pdbchk >>> ATOM 2981 C7 880 B 1 24.282 10.596 30.407 1.00 10.00 C >>> pdbchk >>> ATOM 2982 C10 880 B 1 24.797 9.754 31.539 1.00 10.00 C >>> pdbchk >>> ATOM 2983 C16 880 B 1 23.144 13.218 29.954 1.00 10.00 C >>> pdbchk >>> ATOM 2984 C17 880 B 1 22.376 13.909 28.841 1.00 10.00 C >>> pdbchk >>> ... and 25 more occurences >>> pdbchk >>> >>> pdbchk >>> NOTE : changed 35 atoms in 1 residues from ATOM to HETATM - >>> pdbchk >>> see residues below: >>> pdbchk >>> WARNING : a check of the input PDB file (/home/twomack/HH/OO/inserted-ligand.pdb) initially gave an error. We applied some fixes to that PDB file and will be using the file first-build-with-ligand/pdbchk.pdb now. For details see above and first-build-with-ligand/pdbchk.2.log. NOTE : using recorded X-ray weight from input PDB file (6.07) as starting value F/SIGF pairs : FP,SIGFP ############################################################################## # refining against FP,SIGFP with: FreeR_flag ############################################################################## NOTE : automatically selected B-factor refinement scheme "individual". It is possible to change this with the -B flag although this default is the recommended strategy. ################################ BIG cycle 1 ################################# NOTE : changed settings at start of BIG cycle 1: mxlcyc="20" TLSfixcycALL="1" running BUSTER in first-build-with-ligand/01-BUSTER/Cycle-1 [extra library /tmp/twomack-BUSTER/twomack-1297787777-refine__11135.elib]: NOTE : if the available wavelength (1.54180 A) is correct, a correction of the used formfactors might be useful ( P:0.2819 S:0.3173 Cl:0.3456). This can be switched on automatically by setting the AutomaticFormfactorCorrection="yes" parameter on the command-line or explicitely with the FormfactorCorrection=":" parameter. You can set/change the wavelength on the command-line with: wavelength=. >>> ab_pdb2tnt >>> >>> ab_pdb2tnt >>> Extracted from file first-build-with-ligand/01-BUSTER/Cycle-1/ab_pdb2tnt.log : >>> ab_pdb2tnt >>> >>> ab_pdb2tnt >>> WARNING : using geometric restraints for ANP from file >>> ab_pdb2tnt >>> /public/xtal/Server-nightly-beta-consortium-darwin/tnt/data/msd/ANP.dic: >>> ab_pdb2tnt >>> this file was generated automatically using >>> ab_pdb2tnt >>> idealised coordinates from EBI/MSD. Although we >>> ab_pdb2tnt >>> believe them to be of good quality, it was not >>> ab_pdb2tnt >>> checked manually. Therefore, it is supplied >>> ab_pdb2tnt >>> without any guarantee - if you prefer your own >>> ab_pdb2tnt >>> geometric restraints dictionary, please create it >>> ab_pdb2tnt >>> with one of the programs in the MakeTNT toolbox >>> ab_pdb2tnt >>> and supply it directly (see documentation). >>> ab_pdb2tnt >>> WARNING : the generation of TNT sequence/restraints from the PDB file produced some warnings - see above and first-build-with-ligand/01-BUSTER/Cycle-1/ab_pdb2tnt.log NOTE : setting solvent content to 0.429 NOTE : rms(bond) = 0.0109 A (details in first-build-with-ligand/01-BUSTER/Cycle-1/geometry.lis) running BUSTER-GELLY-TNT - see first-build-with-ligand/01-BUSTER/Cycle-1/LIST.html ... done NOTE : mean electron density of fragment (should be between 0.42-0.425 e/A^3): 0.420 NOTE : we're going to use the TNT sequence file first-build-with-ligand/01-BUSTER/Cycle-1/TNT.seq from now on NOTE : we're going to use the formfactor file first-build-with-ligand/01-BUSTER/Cycle-1/formfactor.dat from now on Ncyc Total Grms Rfact Rfree LLG Geom_Funct rmsBOND rmsANGLE 0 6.7802e+05 420.6100 0.229 0.252 0.000 3.1175e+04 0.011 1.180 1 6.7041e+05 210.1030 0.218 0.250 0.069 3.2156e+04 0.011 1.220 2 6.6797e+05 231.8270 0.216 0.249 0.086 3.1843e+04 0.011 1.180 3 6.6737e+05 314.9120 0.215 0.249 0.090 3.1729e+04 0.010 1.160 4 6.6664e+05 248.0310 0.215 0.249 0.092 3.1259e+04 0.010 1.120 5 6.6444e+05 144.1780 0.213 0.249 0.105 3.0794e+04 0.010 1.100 6 6.6373e+05 416.0390 0.211 0.249 0.118 3.1626e+04 0.010 1.100 7 6.6254e+05 129.7450 0.211 0.249 0.120 3.0673e+04 0.010 1.090 8 6.6215e+05 81.2597 0.211 0.249 0.122 3.0547e+04 0.010 1.080 9 6.6185e+05 85.0522 0.210 0.249 0.124 3.0494e+04 0.010 1.080 10 6.6139e+05 67.4961 0.210 0.248 0.126 3.0290e+04 0.010 1.070 11 6.6129e+05 100.6400 0.210 0.248 0.126 3.0268e+04 0.010 1.070 12 6.6110e+05 52.8709 0.210 0.248 0.127 3.0154e+04 0.010 1.070 13 6.6097e+05 46.9589 0.210 0.248 0.128 3.0100e+04 0.010 1.060 14 6.6081e+05 73.9478 0.209 0.248 0.129 3.0119e+04 0.010 1.060 15 6.6074e+05 86.1539 0.209 0.248 0.130 3.0217e+04 0.010 1.060 16 6.6066e+05 37.1853 0.209 0.248 0.131 3.0143e+04 0.010 1.060 17 6.6061e+05 30.1607 0.209 0.248 0.131 3.0139e+04 0.010 1.060 18 6.6056e+05 36.0204 0.209 0.248 0.131 3.0157e+04 0.010 1.060 19 6.6046e+05 38.4799 0.208 0.248 0.133 3.0196e+04 0.010 1.060 20 6.6037e+05 77.1533 0.208 0.247 0.134 3.0297e+04 0.010 1.060 NOTE : adjusting X-Ray weight to 5.95 -------------------------------------------------------- NOTE : created PDB file with 14 "atoms" to describe voids Waters present : 142 total : 142 ################################ BIG cycle 2 ################################# NOTE : changed settings at start of BIG cycle 2: mxlcyc="1" running BUSTER in first-build-with-ligand/01-BUSTER/Cycle-2 [extra library first-build-with-ligand/01-BUSTER/my.geom]: NOTE : combining files for BABSLV NOTE : setting solvent content to 0.429 NOTE : rms(bond) = 0.0102 A (details in first-build-with-ligand/01-BUSTER/Cycle-2/geometry.lis) running BUSTER-GELLY-TNT - see first-build-with-ligand/01-BUSTER/Cycle-2/LIST.html ... done NOTE : mean electron density of fragment (should be between 0.42-0.425 e/A^3): 0.420 Ncyc Total Grms Rfact Rfree LLG Geom_Funct rmsBOND rmsANGLE 0 6.4740e+05 78.2371 0.206 0.246 0.000 3.0300e+04 0.010 1.060 1 6.4737e+05 53.3183 0.206 0.246 -0.000 3.0264e+04 0.010 1.060 NOTE : adjusting X-Ray weight to 5.83 Waters present : 142 total : 142 ======================================================================== best refinement in BUSTER-GELLY-TNT reached for FP,SIGFP with R/Rfree 0.2055/0.2460 for resolution range 16.94 - 2.10 A. first-build-with-ligand/01-BUSTER/Cycle-2/BUSTER.pdb first-build-with-ligand/01-BUSTER/Cycle-2/LIST.html first-build-with-ligand/01-BUSTER/Cycle-2/shell.01/mlphas.mtz ======================================================================== Additional files that might be of interest (use 'plotmtv' to visualise *.mtv files): first-build-with-ligand/R-Rfree_vs_cycle.mtv first-build-with-ligand/01-BUSTER/Cycle-2/shell.01/scales.txt first-build-with-ligand/01-BUSTER/Cycle-2/shell.01/R_Rfree.mtv first-build-with-ligand/01-BUSTER/Cycle-2/shell.01/wilson.mtv first-build-with-ligand/01-BUSTER/Cycle-2/shell.01/CCplots/cos_ccoef.001.mtv first-build-with-ligand/01-BUSTER/Cycle-2/shell.01/FOMs/cycle_005.mtv first-build-with-ligand/01-BUSTER/Cycle-2/shell.01/CCplots/R_Rfree.001.mtv NOTE : list of parameters set during this run = first-build-with-ligand/setvar.refine  Normal termination (207 sec) ##############################################################################