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: 2.8.0 for linux-ifort made on Jul 22 2009 at 02:57:53
Licenced to: Global Phasing Ltd (newton-old)


Parsing of the BUSTER cardfile

TITLE : autoBUSTER refinement Cell information (explanation) 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: 21874 Number of accepted reflexions: 21018 Number of rejected reflexions: 856 Reflexions in test set: 1669 (explanation) Reflexions in working set: 19349 (explanation)

1. Generating initial model

2.10 * Shannon sampling rate. NX NY NZ: 128 240 120 Effective Shannon rates are: 2.13 2.55 2.22 Allocated BUFFER of size: 14.282 Mb. Allocated BUFAUX of size: 14.282 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 1.23848) ... 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 = 0.15726E+02 B = -13.855 Setting starting scale K to value from Wilson scaling: 15.72619 Setting starting scale B to value from Wilson scaling: -13.85451

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)

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 Jul 22 2009 02:55:39
 
 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

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

                   TNT Stereochemistry Program
 Version: 5.20.0.0
 Licence for Global Phasing Ltd (newton-old) is valid
 
 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    4217 atoms from TNT to gelly's store 
 
 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  0.0
 -----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 (V1.6) 20090612  STANDARD AMINO ACID DICTIONARY. BONDS AND ANGLES FROM ENGH AND HUBER EH99. OTHER VALUES BASED ON PREVIOUS TNT OR TAKEN FROM CCP4.
 ------ exoticaa.dat (V1.3.2.1) 20090706  COLLECTION OF NON-STANDARD AMINO ACIDS, MAINLY EH91 WITHOUT IDEAL DISTANCE INFO
 ------ nuclgeo.dat (V1.13) 20090617
 ------ bcorrel.dat (V1.15) 20080423
 ------ contact.dat (V1.15) 20070207
 ------ idealdist_contact.dat (V1.3.2.1) 20090706  IDEAL-DISTANCE CONTACT TERM DATA AS USED IN PROLSQ. VALUES USED HERE ARE BASED ON THE REFMAC 5.5 IMPLEMENTATION.
 ------ assume.dat (V1.9) 20090602
 Have picked up spacegroup name for pdb output as 'P 21 21 2 '
 Setting up Chain/Residue arrays
 
 Have command line specification -autoncs*
     Have found       1 NCS relations
     Pairwise matching residue number and type between chains: 
                    A        B    
          A         .      all   
          B                  .   
       Table key--                                                       
          all   : two chains have 100% match and same number of residues 
         multi  : ditto and they contribute to a multi chain ncs cluster 
          ***%  : two chains have >80% matching residue number/type      
           -    : chains appear to be unrelated                          
      chain A     have identified ncs to     1 other chains. So will weight each autoncs by (       2.000/#)=      2.0000
      chain B     have identified ncs to     1 other chains. So will weight each autoncs by (       2.000/#)=      2.0000
     For .Gelly cards produced see below - after pruning
 
 Setting up BUSTER_SET groups
 Have found    34 BUSTER_SET cards
 Now silently applying automatic/dictionary set definitions. For a verbose listing use '-verbose_set' flag.
 Applying user defined set definitions:
 =====NOTE BUSTER_SET ncsautoXcld = Water --> set 'ncsautoXcld' now has     0 atoms 
 =====NOTE BUSTER_SET ncsautoABset = Chain_A \ ncsautoXcld --> set 'ncsautoABset' now has  2109 atoms 
 Have defined    14 sets: 
      set: 'All' has   4217 atoms in    562 residues - automatically defined
      set: 'Empty' has      0 atoms in      0 residues - automatically defined
      set: 'ExoticAA' has      0 atoms in      0 residues - defined by dictionary file
      set: 'NotHET' has   4215 atoms in    560 residues - automatically defined
      set: 'Chain_A' has   2109 atoms in    281 residues - automatically defined
      set: 'Chain_B' has   2108 atoms in    281 residues - automatically defined
      set: 'Water' has      0 atoms in      0 residues - defined by dictionary file
      set: 'StdProtein' has   4217 atoms in    562 residues - defined by dictionary file
      set: 'Protein' has   4217 atoms in    562 residues - defined by dictionary file
      set: 'Back' has   2241 atoms in    562 residues - defined by dictionary file
      set: 'Side' has   1976 atoms in    532 residues - defined by dictionary file
      set: 'Other' has      0 atoms in      0 residues - defined by dictionary file
      set: 'ncsautoXcld' has      0 atoms in      0 residues - user specified
      set: 'ncsautoABset' has   2109 atoms in    281 residues - user specified
 
 Interpreting CONSTANT cards: 
 =====CONSTANT     B
 =====CONSTANT     OCC
 Have found and interpreted      2 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   =  4217
 Before any COMBINE - Number of atoms with fixed OCC =  4217
 Before any COMBINE - Number of atoms with fixed BIJ =  4217
                            cf total number of atoms =  4217
 
 Have a total of     2 COMBINE and/or NOTE BUSTER_COMBINE cards in TNT input
 
 There are no NOTE BUSTER_COMBINE_RES cards to be found in the TNT card input 
 
 COMBINE groups of type XYZ use rotation method routines from:
     Grassia, F. S. (1998)
     "Practical parameterization of rotations using the exponential map"
     Journal of Graphics Tools, 3:29-48. 
     http://www.acm.org/jgt/papers/Grassia98/
 
 Interpreting COMBINE cards: 
 =====COMBINE XYZ A|*
 =====COMBINE XYZ B|*
 Have    2 COMBINE groups of type XYZ
 xyz combine group number     1 has  2109 atoms in it:
        Residue      A|7   THR  N     CA    C     O     CB    OG1    
        Residue      A|8   SER  N     CA    C     O     CB    OG     
        Residue      A|9   ARG  N     CA    C     O     CB    CG    CD     
        Residue     A|10   PRO  N     CA    C     O     CB    CG     
        Residue     A|11   PRO  N     CA    C     O     CB    CG     
        Residue     A|12   LEU  N     CA    C     O     CB    CG    CD1   CD2    
        Residue     A|13   GLU  N      .......
        (output limited to first 40 atoms '-verbose 4' for longer report) 
 xyz combine group number     2 has  2108 atoms in it:
        Residue      B|7   THR  CA    C     O     CB    OG1    
        Residue      B|8   SER  N     CA    C     O     CB    OG     
        Residue      B|9   ARG  N     CA    C     O     CB    CG    CD     
        Residue     B|10   PRO  N     CA    C     O     CB    CG     
        Residue     B|11   PRO  N     CA    C     O     CB    CG     
        Residue     B|12   LEU  N     CA    C     O     CB    CG    CD1   CD2    
        Residue     B|13   GLU  N     CA     .......
        (output limited to first 40 atoms '-verbose 4' for longer report) 
 Do not have any COMBINE groups of type B
 Do not have any COMBINE groups of type OCC
 Number of atoms with fixed/combined xyz =  4217
 Number of atoms with fixed/combined B   =  4217
 Number of atoms with fixed/combined OCC =  4217
 Number of atoms with fixed/combined BIJ =  4217
                cf total number of atoms =  4217
 
 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
 
 --- Have some similarity definitions 
     Similarity restraints on RMSD use superposition routines from: 
     Coutsias, E.A., Seok, C., Dill, K.A.(2004)
     "Using quaternions to calculate RMSD", J. Comput. Chem., 25:1849-1857 

 Have found    1 'NOTE BUSTER_SIM_DEFINE' cards 
     Maximum number of chains involved in any SIM group (excluding the template)=     1
 Interpreting card: NOTE BUSTER_SIM_DEFINE ncsautoAB ncsautoABset B
     Number of atoms in template set=  2109
     Number of related chains (other than template) in SIM set=    1
     List of chains to be restrained (excluding template)=   B   
     Pairwise RMSD, XYZ in Angstroms, for SIM group: ncsautoAB
                 A         B   
     A         -----     ----- 
     B         0.001     ----- 
     Overall RMSD,XYZ for the SIM group is     0.001 Angstroms
     Pairwise rms deviation of [individual B's minus their set/chain average] in Angs**2
                 A         B         Bavg
     A         -----     -----     20.00
     B          0.00     -----     20.00
     Overall RMSD,B   for the SIM group is     0.000 Angs**2
     The number of common atoms for the above fits:
                 A         B   
     A         -----     ----- 
     B          2108     ----- 
     (compared to the template set that has    2109 atoms in it)
     List of atoms that are absent in one or more chains for this group: 
                                    A    B   
                    N       7       +    -
     (key  +  atom present for this chain 
           -  atom absent  for this chain)
 transforms for each of the superpositions orthogonal matrix r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz (PDBSET syntax): 
TRANS_AB -0.999568 -0.029023 -0.004737  0.029055 -0.999554 -0.006894 -0.004535 -0.007029  0.999965   121.520   255.945   -35.401
 reverse transforms 
TRANS_BA -0.999568  0.029055 -0.004535 -0.029023 -0.999554 -0.007029 -0.004737 -0.006894  0.999965   113.870   259.109    37.739
 
 Setting up LSSR interatomic distance restraints
 Interpreting card: NOTE BUSTER_SIM_RESTRAIN_LSSR ncsautoAB 2.000
        setting up interatomic distance pair restraints with:
        Dmin=         0.00
        Dmax=         5.50
        sigma=        0.20
        Vmax=        10.00
        weight=       2.00
        number of distance pairs defined for this set is      24359
 Have not supplied either '-sim_swap_equiv' or '-sim_swap_equiv_plus' argument 
   so will not try swaping equivalent atoms to improve NCS and/or target agreement.
 
 NCS by LSSR outlier analysis
 -autoncs option automatic NCS prune routine -------- 
 Residues pruned out by gradient condition:
       
 Residues pruned out by function/max condition:
       
 Total number of residues pruned out is        0 out of      561 participating
 Number of LSSR restraints pruned out is         0 this is    0.0% of the total
  
 -autoncs .Gelly cards suitable for adaptation for manual definition/pruning
           (note auto pruning is done in a slightly different way so exact results may differ slightly)
 -autoncs option .Gelly cards also written to file  auto_gelly_cards.txt
NOTE BUSTER_SET ncsautoXcld = Water    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoABset = Chain_A \ ncsautoXcld    # card added - produced by -autoncs
NOTE BUSTER_SIM_DEFINE ncsautoAB ncsautoABset B    # card added - produced by -autoncs
NOTE BUSTER_SIM_RESTRAIN_LSSR ncsautoAB 2.000    # card added - produced by -autoncs

 LSSR function contribution before pruning         1.6
                             after pruning         1.6
 Graph of LSSR function outliers ncs_function_outliers.mtv
 Graph of LSSR gradient outliers ncs_gradient_outliers.mtv
 LSSR - analysis of distance difference distribution for NCS
         DeltaD less than 0.5 Angs:  proportion of population=100.00% average DeltaD of subset     0.000 Angs
 Histogram of LSSR deltaD distribution ncs_histogram.mtv
 
 No 'NOTE BUSTER_TLS_SET' cards found - so no TLS constraints will be used
 Numb parameters added for rigid body rotation/translation=      12
 Number of parameters to describe molecular conformation  =      12
 Number of free parameters to be adjusted in refinement   =      12
 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   -X,-Y,Z
                3555   1/2-X,1/2+Y,-Z
                4555   1/2+X,1/2-Y,-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 
    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 matched       21 residue-type records and will use      20 ccp4 energy atomtypes
    All atoms matched for ccp4 atom type - so ideal contact will be used for all contacts (rather than TNT short).
   Using gelly special position handling. (For TNT instead rerun with argument '-special_tnt')
       TERM      weight      number      TNT_fn    Gelly_fn        diff
       BOND       2.000        4311   18941.486   18941.486       0.000
       ANGL       2.000        5778   18922.969   18922.969       0.000
       IMPR       0.000           0       0.000       0.000       0.000
       TORS       2.000        1400    3054.121    3054.121       0.000
       TRIG       2.000          64       0.283       0.283       0.000
       PLAN       5.000         610     629.638     629.638       0.000
       CONT       0.000           0       0.000       0.000       0.000
       BCOR      20.000        4311   16444.050   16444.050       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
      Torsion angles split into peptide omega and other
         Number of peptide omega angles is       556
         Number of other torsion is              844
      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|102 
   because omega torsion A|101:CA(PRO)=A|101:C(PRO)=A|102:N(PRO)=A|102:CA(PRO) is        0.08 degrees
     Fix up bond A|102:CA=CB (PRO)
                    ideal from 1.531 to 1.533 actual= 1.524,  sigma from 0.020 to 0.018 Angs
     Fix up bond A|102:CB=CG (PRO)
                    ideal from 1.495 to 1.506 actual= 1.495,  sigma from 0.050 to 0.039 Angs
     Fix up bond A|102:CG=CD (PRO)
                    ideal from 1.502 to 1.512 actual= 1.514,  sigma from 0.033 to 0.027 Angs
     Fix up bond A|102:CD=N (PRO)
                    ideal from 1.474 to 1.474 actual= 1.479,  sigma from 0.014 to 0.014 Angs
     Fix up angle A|101:C(PRO)=A|102:N(PRO)=A|102:CA(PRO)
                    ideal from 119.3 to 127.0 actual= 128.8,  sigma from   1.5 to   2.4 Degs
     Fix up angle A|101:C(PRO)=A|102:N(PRO)=A|102:CD(PRO)
                    ideal from 128.4 to 120.6 actual= 119.6,  sigma from   2.1 to   2.2 Degs
     Fix up angle A|102:N=CA=CB (PRO)
                    ideal from 103.3 to 102.6 actual= 103.6,  sigma from   1.2 to   1.1 Degs
     Fix up angle A|102:CB=CA=C (PRO)
                    ideal from 111.7 to 112.0 actual= 111.3,  sigma from   2.1 to   2.5 Degs
     Fix up angle A|102:CA=CB=CG (PRO)
                    ideal from 104.8 to 104.0 actual= 104.4,  sigma from   1.9 to   1.9 Degs
     Fix up angle A|102:CB=CG=CD (PRO)
                    ideal from 106.5 to 105.4 actual= 107.1,  sigma from   3.9 to   2.3 Degs
     Fix up angle A|102:CG=CD=N (PRO)
                    ideal from 103.2 to 103.8 actual= 103.9,  sigma from   1.5 to   1.2 Degs
     Fix up angle A|102:CA=N=CD (PRO)
                    ideal from 111.7 to 111.5 actual= 111.6,  sigma from   1.4 to   1.4 Degs
   Apply the fix to cis PRO residue B|102 
   because omega torsion B|101:CA(PRO)=B|101:C(PRO)=B|102:N(PRO)=B|102:CA(PRO) is       -0.02 degrees
     Fix up bond B|102:CA=CB (PRO)
                    ideal from 1.531 to 1.533 actual= 1.525,  sigma from 0.020 to 0.018 Angs
     Fix up bond B|102:CB=CG (PRO)
                    ideal from 1.495 to 1.506 actual= 1.495,  sigma from 0.050 to 0.039 Angs
     Fix up bond B|102:CG=CD (PRO)
                    ideal from 1.502 to 1.512 actual= 1.514,  sigma from 0.033 to 0.027 Angs
     Fix up bond B|102:CD=N (PRO)
                    ideal from 1.474 to 1.474 actual= 1.478,  sigma from 0.014 to 0.014 Angs
     Fix up angle B|101:C(PRO)=B|102:N(PRO)=B|102:CA(PRO)
                    ideal from 119.3 to 127.0 actual= 128.7,  sigma from   1.5 to   2.4 Degs
     Fix up angle B|101:C(PRO)=B|102:N(PRO)=B|102:CD(PRO)
                    ideal from 128.4 to 120.6 actual= 119.7,  sigma from   2.1 to   2.2 Degs
     Fix up angle B|102:N=CA=CB (PRO)
                    ideal from 103.3 to 102.6 actual= 103.6,  sigma from   1.2 to   1.1 Degs
     Fix up angle B|102:CB=CA=C (PRO)
                    ideal from 111.7 to 112.0 actual= 111.2,  sigma from   2.1 to   2.5 Degs
     Fix up angle B|102:CA=CB=CG (PRO)
                    ideal from 104.8 to 104.0 actual= 104.4,  sigma from   1.9 to   1.9 Degs
     Fix up angle B|102:CB=CG=CD (PRO)
                    ideal from 106.5 to 105.4 actual= 107.1,  sigma from   3.9 to   2.3 Degs
     Fix up angle B|102:CG=CD=N (PRO)
                    ideal from 103.2 to 103.8 actual= 103.9,  sigma from   1.5 to   1.2 Degs
     Fix up angle B|102:CA=N=CD (PRO)
                    ideal from 111.7 to 111.5 actual= 111.6,  sigma from   1.4 to   1.4 Degs
   Weight for ideal-distance contact term=     4.000

   MaxLik Scaling Cycle 0002 (explanation)
 
 Initial functional value = 4.031350E+05 rms gradient=      3685.00
 X-ray contribution to function value = 2.741764E+05
 Geometry contribution (inc ncs)      = 1.289585E+05
 Geometry function summary
     term                           number     weight       rms        GooF      function     fn/numb
     ================================================================================================
     BOND bond lengths (angs)       4311       2.000      0.0293       1.482     18941.80       4.394
     ANGL bond angles (degs)        5778       2.000        2.07       1.272     18701.48       3.237
     TORS split-harmonic tors        844       0.000       20.93       1.345         0.00       0.000
     SINTOR sinusoidal tors          844       2.000       20.93                  2111.76       2.502
     TRIG.onal planes (angs)          64       2.000      0.0009       0.047         0.28       0.004
     PLAN general plane (angs)       610       5.000      0.0091       0.454       629.64       1.032
     BCORrelations (angs*2)         4311      20.000       2.536       0.437     16444.05       3.814
     CONT (bad contacts)               0       0.000                                 0.00
     IDEAL(ideal-dist contact)      4589       4.000                             56851.58
     CHIRAL (gelly semiharmon)       557       5.000                             15276.32
     SIM similarity restraint for NCS and/or TARGET                                  1.62
     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                           1.45 degs - monitor only
 
 WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: 
 WARNING:        80 bond lengths. Worst is    19.0 sigs     1.23 Angs A|151:CG=CD (GLU)
 WARNING:        90 bond angles.  Worst is    16.1 sigs   111.35 degs B|23:CB=CG=CD1 (TYR)
 WARNING:        67 idealD contacts. Worst    16.3 sigs     0.29 Angs A|89:CA(GLU)=A|90:N(PRO) symm: 1555=2675
 WARNING: (chiral) Have         8 chiral atoms that are inverted:
 WARNING: (chiral)     A|57:CB(ILE)    A|105:CB(ILE)    A|204:CB(ILE)    A|252:CB(ILE)    B|57:CB(ILE)    B|105:CB(ILE)    B|204:CB(ILE)    B|252:CB(ILE)

 Weighted rms      0.0293         2.072  (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
   There are at least 20 bad contacts where Delta/sigma is greater than     6.5
   Looking at each one of the first 20 in turn to see whether it is likely to indicate 
   a setup problem with geometry restraints. 

        1 dist=   0.29 idealD=   3.55 sigma=   0.20 abs(Delta/sigma)=   16.30
          Between atoms A|89:CA (GLU) A|90:N (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

        2 dist=   0.94 idealD=   3.50 sigma=   0.20 abs(Delta/sigma)=   12.78
          Between atoms A|89:C (GLU) A|89:C (GLU)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

        3 dist=   1.20 idealD=   3.70 sigma=   0.20 abs(Delta/sigma)=   12.49
          Between atoms A|89:CA (GLU) A|89:C (GLU)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

        4 dist=   1.50 idealD=   3.90 sigma=   0.20 abs(Delta/sigma)=   11.99
          Between atoms A|89:CA (GLU) A|90:CA (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

        5 dist=   1.11 idealD=   3.44 sigma=   0.20 abs(Delta/sigma)=   11.65
          Between atoms A|86:OD2 (ASP) A|87:CG (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

        6 dist=   1.55 idealD=   3.84 sigma=   0.20 abs(Delta/sigma)=   11.45
          Between atoms A|88:CA (GLY) A|90:CG (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

        7 dist=   1.50 idealD=   3.67 sigma=   0.20 abs(Delta/sigma)=   10.85
          Between atoms A|88:C (GLY) A|90:CG (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

        8 dist=   1.44 idealD=   3.52 sigma=   0.20 abs(Delta/sigma)=   10.38
          Between atoms A|89:CB (GLU) A|90:N (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

        9 dist=   1.48 idealD=   3.54 sigma=   0.20 abs(Delta/sigma)=   10.32
          Between atoms B|111:N (LEU) B|111:CD1 (LEU)
          is a contact within a residue - so probably just a distorted residue?

       10 dist=   1.48 idealD=   3.54 sigma=   0.20 abs(Delta/sigma)=   10.32
          Between atoms A|111:N (LEU) A|111:CD1 (LEU)
          is a contact within a residue - so probably just a distorted residue?

       11 dist=   1.48 idealD=   3.54 sigma=   0.20 abs(Delta/sigma)=   10.32
          Between atoms A|215:N (LEU) A|215:CD1 (LEU)
          is a contact within a residue - so probably just a distorted residue?

       12 dist=   1.48 idealD=   3.54 sigma=   0.20 abs(Delta/sigma)=   10.32
          Between atoms B|215:N (LEU) B|215:CD1 (LEU)
          is a contact within a residue - so probably just a distorted residue?

       13 dist=   1.57 idealD=   3.57 sigma=   0.20 abs(Delta/sigma)=   10.02
          Between atoms A|180:CZ2 (TRP) A|184:CZ (ARG)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

       14 dist=   1.45 idealD=   3.44 sigma=   0.20 abs(Delta/sigma)=    9.97
          Between atoms A|86:OD2 (ASP) A|87:CB (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

       15 dist=   1.26 idealD=   3.20 sigma=   0.20 abs(Delta/sigma)=    9.71
          Between atoms A|89:N (GLU) A|90:N (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

       16 dist=   2.07 idealD=   3.87 sigma=   0.20 abs(Delta/sigma)=    9.01
          Between atoms A|89:CB (GLU) A|90:CA (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

       17 dist=   1.85 idealD=   3.55 sigma=   0.20 abs(Delta/sigma)=    8.52
          Between atoms A|89:N (GLU) A|90:CA (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

       18 dist=   2.01 idealD=   3.67 sigma=   0.20 abs(Delta/sigma)=    8.32
          Between atoms A|89:CD (GLU) A|91:CB (SER)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

       19 dist=   1.80 idealD=   3.44 sigma=   0.20 abs(Delta/sigma)=    8.20
          Between atoms A|89:CB (GLU) A|90:O (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.

       20 dist=   1.72 idealD=   3.35 sigma=   0.20 abs(Delta/sigma)=    8.17
          Between atoms A|89:C (GLU) A|90:N (PRO)
          The contact is between two atoms via a symmetry operator,
          hopefully refinement will fix this.
 GEOMETRY CHECK OVERALL:  WARN

 TAO: Toolkit for Advanced Optimization. Reference: 
     Benson, S.J., McInnes, L.C., More, J., Sarich, J. (2005)
     "TAO User Manual (Revision 1.8)", Mathematics and 
     Computer Science Division, Argonne National Laboratory
     ANL/MCS-TM-242, http://www.mcs.anl.gov/tao
 
 Will write writing pdb file every 10 its during opt (overide by -keeppdb value)
 Will apply TAO optimization 
 Maximum number of iterations      100
 Convergence test on Grms       4.0000 (-glim)
 Limit on rms displacement to original position (rmsD2init): NONE test inactive (-dlim)

   MaxLik Scaling Cycle 0003 (explanation)
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init       Opttag_H
       0  4.031350E+05  2.741764E+05  1.289585E+05       3685.00  1.986003E-16  1.776357E-15       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0004 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 001 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       1  4.025817E+05  2.740888E+05  1.284929E+05       3359.65     0.0311868     0.0503035       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0005 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 002 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       2  4.001083E+05  2.749964E+05  1.251119E+05       1164.35      0.377399      0.698268       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0006 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 003 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       3  3.997908E+05  2.748398E+05  1.249511E+05       719.457      0.352214      0.686668       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0007 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 004 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       4  3.994318E+05  2.748681E+05  1.245637E+05       567.204      0.352575      0.776738       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0008 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 005 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       5  3.991609E+05  2.752317E+05  1.239292E+05       460.496      0.408150      0.979634       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0009 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 006 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       6  3.990874E+05  2.754694E+05  1.236180E+05       226.285      0.448487       1.14492       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0010 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 007 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       7  3.990741E+05  2.754536E+05  1.236205E+05       144.849      0.450436       1.11862       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0011 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 008 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       8  3.990697E+05  2.754551E+05  1.236146E+05       33.5594      0.449404       1.11794       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0012 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 009 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       9  3.990691E+05  2.754658E+05  1.236033E+05       27.8057      0.450765       1.12090       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0013 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 010 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      10  3.990677E+05  2.754877E+05  1.235800E+05       30.6357      0.453619       1.12514       Opttag_D
   Writing pdb file to gelly_output_iter000010.pdb
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0014 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 011 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      11  3.990670E+05  2.754793E+05  1.235877E+05       17.2721      0.452553       1.12142       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0015 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 012 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      12  3.990670E+05  2.754788E+05  1.235882E+05       22.6479      0.452666       1.11858       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0016 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 013 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      13  3.990669E+05  2.754768E+05  1.235901E+05       3.81361      0.452311       1.11904       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0017 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 014 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      14  3.990669E+05  2.754763E+05  1.235906E+05       3.17372      0.452254       1.11904       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 


 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)       4311       2.000      0.0293       1.482     18941.80       4.394
     ANGL bond angles (degs)        5778       2.000        2.07       1.272     18701.48       3.237
     TORS split-harmonic tors        844       0.000       20.93       1.345         0.00       0.000
     SINTOR sinusoidal tors          844       2.000       20.93                  2111.76       2.502
     TRIG.onal planes (angs)          64       2.000      0.0009       0.047         0.28       0.004
     PLAN general plane (angs)       610       5.000      0.0091       0.454       629.64       1.032
     BCORrelations (angs*2)         4311      20.000       2.536       0.437     16444.05       3.814
     CONT (bad contacts)               0       0.000                                 0.00
     IDEAL(ideal-dist contact)      4546       4.000                             51483.62
     CHIRAL (gelly semiharmon)       557       5.000                             15276.32
     SIM similarity restraint for NCS and/or TARGET                                  1.62
     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                           1.45 degs - monitor only
 
 WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: 
 WARNING:        80 bond lengths. Worst is    19.0 sigs     1.23 Angs A|151:CG=CD (GLU)
 WARNING:        90 bond angles.  Worst is    16.1 sigs   111.35 degs B|23:CB=CG=CD1 (TYR)
 WARNING:        47 idealD contacts. Worst    14.2 sigs     0.86 Angs A|89:CA=C (GLU) symm: 1555=2675
 WARNING: (chiral) Have         8 chiral atoms that are inverted:
 WARNING: (chiral)     A|57:CB(ILE)    A|105:CB(ILE)    A|204:CB(ILE)    A|252:CB(ILE)    B|57:CB(ILE)    B|105:CB(ILE)    B|204:CB(ILE)    B|252:CB(ILE)

 Weighted rms      0.0293         2.072  (temporary rms bond and angle for autobuster to pick up!)
 Outputing geometry progress graph in plotmtv format to file:Geom_Res.mtv
 s/r gelly normal termination
Statistics and scale factors vs. cycle number  (explanation) : 
     
   Final Geometry Information (explanation)


2. Final results

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

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



Final refined coordinates (explanation)

Final Fourier amplitudes and phases (explanation)

# normal termination Program stopped. closesok message: time spent in tree = 29.39 (user) 1.58 (sys)


Normal termination


 Resources usage summary:
     Time spent in client ...................    47.54 (user)        1.66 (system)
     Time spent in scripts (    50 calls) ...     1.01 (user)        0.20 (system)
     Time spent in server ...................     0.00 (user)        0.01 (system)

     Max resident memory used (kb) .......... 0
     Number of page faults .................. 0 (major)    127708 (minor)
     Number of context switches ............. 5321 (niced)    613 (other)