BUSTER 2.X: A suite of programs for macromolecular structure refinement by maximum-likelihood and Bayesian methods
Copyright © 1992-2007 Global Phasing Ltd.
All rights reserved.
Authors: G. Bricogne, E. Blanc, M. Brandl, C. Flensburg, P. Keller, W. Paciorek, P. Roversi, O. Smart, C. Vonrhein, T. Womack

Please reference use of the software as:

Version: 2.11.1 for linux-ifort made on Feb 1 2011 at 02:02:52
Licenced to: Global Phasing - temporary key

Today is Tue Feb 8 10:05:35 2011
Software will expire soon : Mon Feb 14 13:27:27 2011


Parsing of the BUSTER cardfile

TITLE : autoBUSTER refinement Cell information (explanation) H lattice: BUSTER assumes hexagonal axes in obverse setting Please make sure that indexing complies with this convention Symmetry information (explanation) Using CCP4 X-ray form factors. Missing structure chemical composition (explanation) Using ATOM block for chemical composition. Shell information

Parsing of the TNT cardfile


Reading observations file

List of rejected reflexions (explanation) Number of reflexions in input: 26994 Number of accepted reflexions: 26956 Number of rejected reflexions: 38 Reflexions in test set: 1352 (explanation) Reflexions in working set: 25604 (explanation)

1. Generating initial model

2.10 * Shannon sampling rate. NX NY NZ: 288 288 180 Effective Shannon rates are: 2.32 2.32 2.65 Allocated BUFFER of size: 57.349 Mb. Initial Geometry Information (explanation) No missing atoms declared Summary of model volumes (explanation) No missing atoms declared: no prior computed Computing bulk solvent model scattering NCSMASK PDB radius for solvent mask: 2.15 Angstrom running PDBSET (setting cell and spacegroup P1) ... done running NCSMASK [1] (creating mask, SMOOTH 1.20779) ... done running MAPDUMP (to check if reduction to unit cell is needed) ... done running MAPMASK (converting mask to map) ... done Generation of babslv by theta-filter (explanation) Electron density in frg mask: 0.420 Å-1 (explanation) FOBS put on rough absolute scale by Wilson plot : K = 0.19847E+01 B = -23.621

Cycle 001: MaxLik scaling and refinement

MaxLik Scaling Cycle 001 (explanation) Wilson plot Statistics in resolution bins just after scaling (explanation) : 
     

   <Log-Likelihood> of null-hypothesis (explanation)

Structure Factor Amplitudes (explanation) Average Figure of Merit (explanation) Switching off refinement of overall temperature factor Added B = -0.8718 Å2 to all atoms in fragment Added B = -0.8718 Å2 to B_SOLV

gelly refinement module
 Developed by O. S. Smart, C. Flensburg,  W. Paciorek, C. Vonrhein, 
              M. Brandl, T. O. Womack and G. Bricogne
 Copyright © 2006, 2007 Global Phasing Ltd. 
 All rights reserved.
 gelly module compilation date Feb 01 2011 02:00:01
 
 gelly uses routines from TNT geometry. References: 
     Tronrud, D. E., Ten Eyck, L. F., Matthews, B. W. (1987)
     "An Efficient General-Purpose Least-Squares Refinement Program 
     for Macromolecular Structures". Acta Crystallogr A, 43:489-501.
     Tronrud, D. E. (1997). "The TNT Refinement Package", 
     in Macromolecular Crystallography, Part B, Eds Charlie Carter 
     and Robert Sweet, Methods in Enzymology, 277:306-319.
 wildcard matching function by Julian Robichaux http://www.nsftools.com
 
 Have -type card that specifies calculation type 'one'
 

 Control flags set to:  -type one \
                     -screen 100 \
                     -screen_sigma 3.0 
 
 Setting up tnt routines including license check:

                   TNT Stereochemistry Program
 Version: 5.23.1.0
 Licence for Global Phasing - temporary key will soon expire
 Expiration date: Mon Feb 14 13:27:27 2011
 
 Using TNT geometry routines to load the tnt control file: gelly.tnt
 Using TNT routines to load initial coordinates from file fragment.cor
 Have copied information for    4551 atoms from TNT to gelly's store 
 
 Have some non-(C,N,O,P,S,H,Se) atom types - listed below.
   You may want to check that the charge states are correct.
   To correct edit the input pdb adding the charge to columns 79 and 80
   of the HETATM record (after element type). For example a chloride ion is set
   HETATM 4798 CL    CL  1015      21.068  14.855  66.797  1.00 13.97          CL-1
          A|940:CL1 (CPB) type: CL  
 
 The TNT WEIGHT cards used this run:
 -----WEIGHT       BOND     2.0
 -----WEIGHT       ANGLE    2.0
 -----WEIGHT       IMPROPER 0.0
 -----WEIGHT       TORSION  2.0
 -----WEIGHT       PSEUDO   0.0
 -----WEIGHT       TRIGONAL 2.0
 -----WEIGHT       PLANE    5.0
 -----WEIGHT       CONTACT  5.0
 -----WEIGHT       BCORREL  20.0
 -----WEIGHT       CHIRAL   5.0
 -----WEIGHT       NCS      50.0
 -----WEIGHT       IDEAL    4.0
 -----WEIGHT       RFACTOR  4
 Dictionary versions picked up from NOTE BUSTER_RESTRAINT_DICT cards as: 
 ------ protgeo_eh99.dat (V1.8) 20110121  STANDARD AMINO ACID DICTIONARY. BONDS AND ANGLES FROM ENGH AND HUBER EH99. OTHER VALUES BASED ON PREVIOUS TNT OR TAKEN FROM CCP4. INCLUDES HYDROGEN ATOMS.
 ------ exoticaa.dat (V1.8) 20100430  COLLECTION OF NON-STANDARD AMINO ACIDS, MAINLY EH91 WITHOUT IDEAL DISTANCE INFO
 ------ nuclgeo.dat (V1.14) 20091104
 ------ bcorrel.dat (V1.15) 20080423
 ------ contact.dat (V1.20) 20101123
 ------ idealdist_contact.dat (V1.7) 20110119  IDEAL-DISTANCE CONTACT TERM DATA AS USED IN PROLSQ. VALUES USED HERE ARE BASED ON THE REFMAC 5.5 IMPLEMENTATION.
 ------ restraints CPB by PDB2TNT2.5.9 from coordinates  NOTE BUSTER_RESTRAINT_INFO Command: PDB2TNT -i /tmp/scifinder-1297159395-ab_pdb2tnt__32757.pdb -n CPB
 ------ assume.dat (V1.10) 20110113
 Have picked up spacegroup name for pdb output as 'H 3       '
 Setting up Chain/Residue arrays
 Setting up BUSTER_SET groups
 No NOTE BUSTER_SET type cards found - just produce automatic definitions
 Now silently applying automatic/dictionary set definitions. For a verbose listing use '-verbose_set' flag.
 Have defined    12 sets: 
      set: 'All' has   4551 atoms in    577 residues - automatically defined
      set: 'Empty' has      0 atoms in      0 residues - automatically defined
      set: 'ExoticAA' has     11 atoms in      1 residues - defined by dictionary file
      set: 'NotHET' has   4476 atoms in    551 residues - automatically defined
      set: 'Chain_A' has   2480 atoms in    315 residues - automatically defined
      set: 'Chain_B' has   2071 atoms in    262 residues - automatically defined
      set: 'Water' has     20 atoms in     20 residues - defined by dictionary file
      set: 'StdProtein' has   4477 atoms in    552 residues - defined by dictionary file
      set: 'Protein' has   4488 atoms in    553 residues - defined by dictionary file
      set: 'Back' has   2209 atoms in    553 residues - defined by dictionary file
      set: 'Side' has   2279 atoms in    530 residues - defined by dictionary file
      set: 'Other' has     43 atoms in      4 residues - defined by dictionary file
 
 Interpreting CONSTANT cards: 
 =====CONSTANT     OCC
 Have found and interpreted      1 CONSTANT cards in the TNT input. 
 Before any COMBINE - Number of atoms with fixed xyz =     0
 Before any COMBINE - Number of atoms with fixed B   =     0
 Before any COMBINE - Number of atoms with fixed OCC =  4551
 Before any COMBINE - Number of atoms with fixed BIJ =  4551
                            cf total number of atoms =  4551
 
 There are no COMBINE cards to be found in the TNT card input 
 
 There are no NOTE BUSTER_COMBINE_RES cards to be found in the TNT card input 
 RANGE allowed for B variables in refinement:   from      3.00000 to    300.00000
 No 'NOTE BUSTER_TARGET' cards or -target?? args found (used to read coordinates files for soft ncs to external)
 No 'NOTE BUSTER_OCCSUM' cards found - so not using sum of occupancy restraints
 No 'NOTE BUSTER_DISTANCE' cards found - so not setting up any additional atom-atom distance restraints
 No 'NOTE BUSTER_UTILANGLE' cards found - so not setting up any additional restraints on any angle
 No 'NOTE BUSTER_UTILTOR' cards found - so not setting up any additional sinusoidal restraints on torsions
 No 'NOTE BUSTER_SIM_DEFINE' cards found - so no similarity restraints will be used
 No 'NOTE BUSTER_TLS_SET' cards found - so no TLS constraints will be used
 Number of parameters to describe molecular conformation  =   18204
 Number of free parameters to be adjusted in refinement   =   18204
 No command line argument '-tnt_fn' so will use gelly to do geometry function calculations
      Getting symmetry operators from TNT. 
          gelly will classify symmetry using pdb-like convention: 
               SYMOP   SYMMETRY
              NNNMMM   OPERATOR
                1555   X,Y,Z
                2555   -Y,X-Y,Z
                3555   -X+Y,-X,Z
                4555   2/3+X,1/3+Y,1/3+Z
                5555   2/3-Y,1/3+X-Y,1/3+Z
                6555   2/3-X+Y,1/3-X,1/3+Z
                7555   1/3+X,2/3+Y,2/3+Z
                8555   1/3-Y,2/3+X-Y,2/3+Z
                9555   1/3-X+Y,2/3-X,2/3+Z
          where NNN -> operator number and MMM -> translation vector
 Ideal-distance contact term setup:
    Restraint function constants (normally values got from NOTE BUSTER_IDEAL_CONTACT_* cards)
    Sigma for general contacts      0.200 Angs
    Sigma for 1-4 contacts          0.200 Angs (contacts across a torsion)
    Sigma for HBOND pairs           0.200 Angs (contacts between HB_types A and D or B's)
    Contact distance increment for each atom in HBOND          -0.150 Angs 
    ContactD for H-bond acceptor to Hydrogen=vdwAccept+         0.100 Angs 
    Contact distance increment for 1-4 with an O atom          -0.100 Angs 
    Contact distance increment for 1-4 with an N atom          -0.100 Angs 
    Contact distance increment for 1-4 with an C atom          -0.150 Angs 
    Contact distance increment for 1-4 with any other atom     -0.150 Angs 
    Have no dictionary entry giving ccp4 atom types for residue types:  TPO CPB
       will use default ccp4 atom types CUNK NUNK OUNK PUNK SUNK .... where possible.
    All atoms matched for ccp4 atom type - so ideal contact will be used for all contacts (rather than TNT short).
    Number of ccp4 atom types used is         29 (H-bound and not H-bound counted separately)
   Using gelly special position handling. (For TNT instead rerun with argument '-special_tnt')
       TERM      weight      number      TNT_fn    Gelly_fn        diff
       BOND       2.000        4633    1121.379    1121.379       0.000
       ANGL       2.000        6291    4684.103    4684.103       0.000
       IMPR       0.000           0       0.000       0.000       0.000
       TORS       2.000        1609    2200.905    2200.906       0.000
       TRIG       2.000         125       4.717       4.717       0.000
       PLAN       5.000         649    5241.355    5241.355       0.000
       CONT       5.000           0      45.757       0.000      45.757
       BCOR      20.000        4633  124076.588  124076.588       0.000

   Switching torsion functionial form to sinusoidal rather than split harmonic functional.
      if you want this not to happen then rerun with '-torsharm'
      Weight for sinusoidal torsion=     2.000
 
 Checking for bonds that do not have a bcorrel restraint defined
 No -bcorrel_missing_sigma found. So will set sigma to    10.0 Ang**2 for any bond with no existing bcorrel
 All bonds have a corresponding bcorrel - so no new added
 A total of       0 planes have been deactivated because they are duplicated hydrogen-free and with-hydrogen forms.
      Torsion angles split into peptide omega and other
         Number of peptide omega angles is       547
         Number of other torsion is             1062
      Peptide omega angles are monitored rather than directly restrained (PLANE used instead).
 Now apply the fix to get correct restraints for cis PRO residues
   Have got       4 bonds records and       8 angles
   from GEOMETRY cards for the special PROC residue
   Apply the fix to cis PRO residue A|319 
   because omega torsion A|318:CA(ASP)=A|318:C(ASP)=A|319:N(PRO)=A|319:CA(PRO) is       -2.83 degrees
     Fix up bond A|319:CA=CB (PRO)
                    ideal from 1.531 to 1.533 actual= 1.537,  sigma from 0.020 to 0.018 Angs
     Fix up bond A|319:CB=CG (PRO)
                    ideal from 1.495 to 1.506 actual= 1.513,  sigma from 0.050 to 0.039 Angs
     Fix up bond A|319:CG=CD (PRO)
                    ideal from 1.502 to 1.512 actual= 1.491,  sigma from 0.033 to 0.027 Angs
     Fix up bond A|319:CD=N (PRO)
                    ideal from 1.474 to 1.474 actual= 1.472,  sigma from 0.014 to 0.014 Angs
     Fix up angle A|318:C(ASP)=A|319:N(PRO)=A|319:CA(PRO)
                    ideal from 119.3 to 127.0 actual= 125.6,  sigma from   1.5 to   2.4 Degs
     Fix up angle A|318:C(ASP)=A|319:N(PRO)=A|319:CD(PRO)
                    ideal from 128.4 to 120.6 actual= 122.2,  sigma from   2.1 to   2.2 Degs
     Fix up angle A|319:N=CA=CB (PRO)
                    ideal from 103.3 to 102.6 actual= 103.5,  sigma from   1.2 to   1.1 Degs
     Fix up angle A|319:CB=CA=C (PRO)
                    ideal from 111.7 to 112.0 actual= 109.3,  sigma from   2.1 to   2.5 Degs
     Fix up angle A|319:CA=CB=CG (PRO)
                    ideal from 104.8 to 104.0 actual= 106.0,  sigma from   1.9 to   1.9 Degs
     Fix up angle A|319:CB=CG=CD (PRO)
                    ideal from 106.5 to 105.4 actual= 106.1,  sigma from   3.9 to   2.3 Degs
     Fix up angle A|319:CG=CD=N (PRO)
                    ideal from 103.2 to 103.8 actual= 102.7,  sigma from   1.5 to   1.2 Degs
     Fix up angle A|319:CA=N=CD (PRO)
                    ideal from 111.7 to 111.5 actual= 112.2,  sigma from   1.4 to   1.4 Degs
   Weight for ideal-distance contact term=     4.000
 No ligand-(fixed protein) contact term will be used

   MaxLik Scaling Cycle 0002 (explanation)
 
 Initial functional value = 6.951561E+05 rms gradient=      652.472
 X-ray contribution to function value = 5.107602E+05
 Geometry contribution (inc ncs)      = 1.843959E+05
 Geometry function summary
     term                           number     weight       rms        GooF      function     fn/numb
     ================================================================================================
     BOND bond lengths (angs)       4633       2.000      0.0070       0.348      1122.11       0.242
     ANGL bond angles (degs)        6291       2.000        0.99       0.607      4637.98       0.737
     TORS split-harmonic tors       1062       0.000       15.86       1.018         0.00       0.000
     SINTOR sinusoidal tors         1062       2.000       15.86                  1785.29       1.681
     TRIG.onal planes (angs)         125       2.000      0.0027       0.137         4.72       0.038
     PLAN general plane (angs)       649       5.000      0.0254       1.271      5241.36       8.076
     BCORrelations (angs*2)         4633      20.000       6.814       1.157    124076.59      26.781
     CONT (bad contacts)               0       5.000                                 0.00
     IDEAL(ideal-dist contact)      5154       4.000                             45579.44
     CHIRAL (gelly semiharmon)       593       5.000                              1948.42
     SIM similarity restraint for NCS and/or TARGET                                  0.00       as none defined
     OCCSUM restraint on sum of occupanies                                           0.00       as none defined
     DISTAN utility restraints interatomic distance                                  0.00       as none defined
     UTILANGLE utility angle restraints                                              0.00       as none defined
     UTILTOR utility restraints on torsion angles                                    0.00       as none defined
     Peptide omega torsion angles                           4.86 degs - monitor only
 
 WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: 
 WARNING:         2 planes.       Worst is     6.5 sigs     0.13 Angs A|176:C=A|176:CA=A|176:O=A|177:N=A|177:CA
 WARNING:        12 Bcorrel.      Worst is    27.2 sigs   120.14 Angs**2 B|48:SD=CE (MET)
 WARNING: (chiral) Have         1 chiral atoms that are inverted:
 WARNING: (chiral)     A|186:CB(TPO)

 Weighted rms      0.0070         0.994  (temporary rms bond and angle for autobuster to pick up!)

 Initial Geometry Sanity Check

 Check for duplicate bonds: no duplicates found
 
 Check for duplicate or missing bond angles: all are OK
 Check for bond between an atom and itself not involving symmetry:  all are OK
   There are not any bad contacts where Delta/sigma is greater than     6.5
   Worst contact dist=   3.006 std=   3.840 sigma=   0.200 abs(Delta/sigma)=    4.169 ats A|198:CG (GLU) A|300:CG (PRO)
   It is likely that the geometry libraries, sequence info and links match the input molecule
 GEOMETRY CHECK OVERALL:  PASS

-type one : simply output final pdb file for compatibitilies with other options


 TLS information. Total number of groups:     0


 Group   Natoms    FixRB   FixTLS   Group Tag    Group Spec

 For final position, Geometry function summary
     term                           number     weight       rms        GooF      function     fn/numb
     ================================================================================================
     BOND bond lengths (angs)       4633       2.000      0.0070       0.348      1122.11       0.242
     ANGL bond angles (degs)        6291       2.000        0.99       0.607      4637.98       0.737
     TORS split-harmonic tors       1062       0.000       15.86       1.018         0.00       0.000
     SINTOR sinusoidal tors         1062       2.000       15.86                  1785.29       1.681
     TRIG.onal planes (angs)         125       2.000      0.0027       0.137         4.72       0.038
     PLAN general plane (angs)       649       5.000      0.0254       1.271      5241.36       8.076
     BCORrelations (angs*2)         4633      20.000       6.814       1.157    124076.59      26.781
     CONT (bad contacts)               0       5.000                                 0.00
     IDEAL(ideal-dist contact)      5154       4.000                             45579.44
     CHIRAL (gelly semiharmon)       593       5.000                              1948.42
     SIM similarity restraint for NCS and/or TARGET                                  0.00       as none defined
     OCCSUM restraint on sum of occupanies                                           0.00       as none defined
     DISTAN utility restraints interatomic distance                                  0.00       as none defined
     UTILANGLE utility angle restraints                                              0.00       as none defined
     UTILTOR utility restraints on torsion angles                                    0.00       as none defined
     Peptide omega torsion angles                           4.86 degs - monitor only
 
 WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: 
 WARNING:         2 planes.       Worst is     6.5 sigs     0.13 Angs A|176:C=A|176:CA=A|176:O=A|177:N=A|177:CA
 WARNING:        12 Bcorrel.      Worst is    27.2 sigs   120.14 Angs**2 B|48:SD=CE (MET)
 WARNING: (chiral) Have         1 chiral atoms that are inverted:
 WARNING: (chiral)     A|186:CB(TPO)

 Weighted rms      0.0070         0.994  (temporary rms bond and angle for autobuster to pick up!)
 s/r gelly normal termination
Final Geometry Information (explanation)

2. Final results

Statistics and scale factors vs. cycle number  (explanation) : 
     

   Average Figure of Merit     (explanation)
   Structure Factor Amplitudes (explanation)


 # normal termination

  Program stopped.



 closesok message: time spent in tree =    43.56 (user)        1.87 (sys)


Normal termination


 Resources usage summary:
     Time spent in client ...................    48.51 (user)        2.00 (system)
     Time spent in scripts (    24 calls) ...     3.15 (user)        0.36 (system)
     Time spent in server ...................     0.00 (user)        0.00 (system)

     Max resident memory used (kb) .......... 0
     Number of page faults .................. 0 (major)    121393 (minor)
     Number of context switches ............. 2028 (niced)    574 (other)