
 ##############################################################################
 # This software is licenced to : Global Phasing Ltd (perutz) 
 ##############################################################################

 ##############################################################################
 # This software is licenced to : Global Phasing Ltd (perutz) 
 ##############################################################################
[1m
 ##############################################################################
 ##   [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.
[m
     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 ################################
 
 
 [1mNOTE[m : 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 >>> [1mWARNING[m : 1 records are shorter than expected - will pad
   >>> pdbchk >>>           with spaces
   >>> pdbchk >>>
   >>> pdbchk >>> [1mNOTE[m : fixed length for 1 records (by padding with spaces)
   >>> pdbchk >>>
   >>> pdbchk >>> [1mWARNING[m : 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 >>> [1mNOTE[m : changed 35 atoms in 1 residues from ATOM to HETATM -
   >>> pdbchk >>>        see residues below:
   >>> pdbchk >>>
 
 [1mWARNING[m : 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.
 
 
 [1mNOTE[m : 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 
 ############################################################################## 
 
 
 [1mNOTE[m : 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 #################################
 
 
 [1mNOTE[m : 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]:
 
 [1mNOTE[m : 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="<atom>:<fprime>" parameter. You can
        set/change the wavelength on the command-line with:
        wavelength=<value>.
 
 
   >>> ab_pdb2tnt >>>
   >>> ab_pdb2tnt >>> Extracted from file first-build-with-ligand/01-BUSTER/Cycle-1/ab_pdb2tnt.log : 
   >>> ab_pdb2tnt >>>
   >>> ab_pdb2tnt >>> [1mWARNING[m : 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 >>>
 
 [1mWARNING[m : 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
 
 
 [1mNOTE[m : setting solvent content to 0.429
 
 
 [1mNOTE[m : 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
 
 [1mNOTE[m : mean electron density of fragment (should be between
        0.42-0.425 e/A^3): 0.420
 
 
 [1mNOTE[m : we're going to use the TNT sequence file
        first-build-with-ligand/01-BUSTER/Cycle-1/TNT.seq
        from now on
 
 
 [1mNOTE[m : 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
 
 [1mNOTE[m : adjusting X-Ray weight to 5.95
 
 
 -------------------------------------------------------- 
 
 [1mNOTE[m : created PDB file with 14 "atoms" to describe voids
 
         Waters present  :  142
                total    :  142
 
 
 ################################ BIG cycle 2 #################################
 
 
 [1mNOTE[m : 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]:
 
 [1mNOTE[m : combining files for BABSLV
 
 
 [1mNOTE[m : setting solvent content to 0.429
 
 
 [1mNOTE[m : 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
 
 [1mNOTE[m : 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
 
 [1mNOTE[m : 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
 
 
 [1mNOTE[m : list of parameters set during this run =
        first-build-with-ligand/setvar.refine
 
[1m
 Normal termination (207 sec)

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[m
