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: 2.11.5 for linux64-ifort made on Nov 28 2012 at 00:53:37
Licenced to: Global Phasing Ltd (hypatia)


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: 21019 Number of rejected reflexions: 855 Reflexions in test set: 1669 (explanation) Reflexions in working set: 19350 (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. 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 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 = 0.15691E+02 B = -2.573

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 = -0.1551 Å2 to all atoms in fragment Added B = -0.1551 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 Nov 28 2012 00:52:24
 
 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: 5.23.5.0
 Licence for Global Phasing Ltd (hypatia) 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    4710 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  5.0
 -----WEIGHT       BCORREL  20.0
 -----WEIGHT       CHIRAL   5.0
 -----WEIGHT       NCS      50.0
 -----WEIGHT       IDEAL    4.0
 -----WEIGHT       RFACTOR  10.57
 Dictionary versions picked up from NOTE BUSTER_RESTRAINT_DICT cards as: 
 ------ protgeo_eh99.dat (V1.8.2.3) 20120619  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 (V1.8.2.2) 20120418  COLLECTION OF NON-STANDARD AMINO ACIDS, MAINLY EH91 WITHOUT IDEAL DISTANCE INFO
 ------ nuclgeo.dat (V1.14.2.3) 20120611
 ------ bcorrel.dat (V1.15) 20080423
 ------ contact.dat (V1.20.2.3) 20121002
 ------ idealdist_contact.dat (V1.7.2.4) 20121011  IDEAL-DISTANCE CONTACT TERM DATA AS USED IN PROLSQ. VALUES USED HERE ARE BASED ON THE REFMAC 5.5 IMPLEMENTATION.
 ------ restraints for A3P (ADENOSINE-3_-5_-DIPHOSPHATE) from cif dictionary A3P.grade_PDB_ligand.cif using refmacdict2tnt revision 1.23.2.11; generated by GRADE 1.2.0 from mol2 file /tmp/file0RSbRO.mol2 using mogul+qm
 ------ assume.dat (V1.10) 20110113
 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    35 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  2355 atoms 
 Have defined    14 sets: 
      set: 'All' has   4710 atoms in    572 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   4656 atoms in    570 residues - automatically defined
      set: 'Chain_A' has   2355 atoms in    286 residues - automatically defined
      set: 'Chain_B' has   2355 atoms in    286 residues - automatically defined
      set: 'Water' has      0 atoms in      0 residues - defined by dictionary file
      set: 'StdProtein' has   4656 atoms in    570 residues - defined by dictionary file
      set: 'Protein' has   4656 atoms in    570 residues - defined by dictionary file
      set: 'Back' has   2280 atoms in    570 residues - defined by dictionary file
      set: 'Side' has   2376 atoms in    542 residues - defined by dictionary file
      set: 'Other' has     54 atoms in      2 residues - defined by dictionary file
      set: 'ncsautoXcld' has      0 atoms in      0 residues - user specified
      set: 'ncsautoABset' has   2355 atoms in    286 residues - user specified
 No command line arguments '-occ_allhet' or '-occ_restyp' so will not setup automated occcupancy refinement
 
 Interpreting CONSTANT and FREE 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 =  4710
 Before any COMBINE - Number of atoms with fixed BIJ =  4710
                            cf total number of atoms =  4710
 
 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 
WARNING ignoring pseudoCHIRAL centre  A|293:CA(SER) A|293:N(SER) A|293:CB(SER) A|293:C(SER)
WARNING ....  as all three surrounding atoms are equivalent.
WARNING ignoring pseudoCHIRAL centre  B|293:CA(SER) B|293:N(SER) B|293:CB(SER) B|293:C(SER)
WARNING ....  as all three surrounding atoms are equivalent.
 NOTE BUSTER_CHIRAL_ANGLECUT card found - read value=    -31.00 degs from it
 NOTE BUSTER_CHIRAL_SIGMA card found - read value=      1.70 degs from it
 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
 
 --- 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=  2355
     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         0.655     ----- 
     Overall RMSD,XYZ for the SIM group is     0.655 Angstroms
     Pairwise rms deviation of [individual B's minus their set/chain average] in Angs**2
                 A         B         Bavg
     A         -----     -----     37.67
     B          8.20     -----     43.91
     Overall RMSD,B   for the SIM group is     8.196 Angs**2
     All the    2355 atoms in template are matched for each of the above fits
 transforms for each of the superpositions orthogonal matrix r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz (PDBSET syntax): 
TRANS_AB -0.999407 -0.034180 -0.004146  0.034227 -0.999345 -0.011757 -0.003742 -0.011892  0.999922   122.059   255.574   -34.866
 reverse transforms 
TRANS_BA -0.999407  0.034227 -0.003742 -0.034180 -0.999345 -0.011892 -0.004146 -0.011757  0.999922   113.109   259.164    38.374
 
 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      30267
 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:
            A|9      A|21      A|24      A|25      A|27      A|42      A|44
           A|80      A|81      A|82      A|83      A|84      A|85      A|86
           A|91      A|92      A|95      A|96     A|107     A|108     A|125
          A|140     A|145     A|146     A|152     A|159     A|178     A|179
          A|180     A|181     A|182     A|183     A|186     A|187     A|188
          A|189     A|190     A|218     A|225     A|226     A|272     A|273
          A|287     A|289     A|293       B|9      B|21      B|24      B|25
           B|27      B|42      B|44      B|80      B|81      B|82      B|83
           B|84      B|85      B|86      B|91      B|92      B|95      B|96
          B|107     B|108     B|125     B|140     B|145     B|146     B|152
          B|159     B|178     B|179     B|180     B|181     B|182     B|183
          B|186     B|187     B|188     B|189     B|190     B|217     B|218
          B|225     B|226     B|272     B|273     B|287     B|289     B|293
       
 Residues pruned out by function/max condition:
          A|181!    A|217    A|218!    A|222    A|500    B|181!    B|217!
          B|218!    B|222    B|500 
 Total number of residues pruned out is       96 out of      572 participating
 Number of LSSR restraints pruned out is      9431 this is   31.2% 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 ncsautoXcld = ncsautoXcld + { A|9 A|21 A|24 A|25 A|27 A|42 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|44 A|80 A|81 A|82 A|83 A|84 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|85 A|86 A|91 A|92 A|95 A|96 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|107 A|108 A|125 A|140 A|145 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|146 A|152 A|159 A|178 A|179 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|180 A|181 A|182 A|183 A|186 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|187 A|188 A|189 A|190 A|217 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|218 A|222 A|225 A|226 A|272 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|273 A|287 A|289 A|293 A|500 }    # 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     51753.4
                             after pruning      5330.9
 Graph of which residues pruned from LSSR: ncs_pruned.mtv
 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= 99.01% average DeltaD of subset     0.010 Angs
 Histogram of LSSR deltaD distribution ncs_histogram.mtv
 
 No 'NOTE BUSTER_TLS_SET' cards found - so no TLS constraints will be used
 Number of parameters to describe molecular conformation  =   18840
 Number of free parameters to be adjusted in refinement   =   18840
 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           0.100 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 
    All atoms matched for ccp4 atom type.
    Number of ccp4 atom types used is         25 (H-bound and not H-bound counted separately)
 Setting up short/ideal-distance contacts
   Using gelly special position handling. (For TNT instead rerun with argument '-special_tnt')
       TERM      weight      number      TNT_fn    Gelly_fn        diff
       BOND       2.000        4856    2611.540    2611.540       0.000
       ANGL       2.000        6604    6018.239    6018.239       0.000
       IMPR       0.000           0       0.000       0.000       0.000
       TORS       2.000        1664    3961.751    3961.751       0.000
       TRIG       2.000         114      20.466      20.466       0.000
       PLAN       5.000         708    1871.128    1871.128       0.000
       CONT       5.000           0     105.275       0.000     105.275
       BCOR      20.000        4798    6672.114    6672.114       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
    add a default BCOR for bond A|500:P1(A3P) A|500:O1P(A3P)
    add a default BCOR for bond A|500:P1(A3P) A|500:O2P(A3P)
    add a default BCOR for bond A|500:P1(A3P) A|500:O3'(A3P)
    add a default BCOR for bond A|500:P1(A3P) A|500:O3P(A3P)
    add a default BCOR for bond A|500:P2(A3P) A|500:O4P(A3P)
    add a default BCOR for bond A|500:P2(A3P) A|500:O5'(A3P)
    add a default BCOR for bond A|500:P2(A3P) A|500:O5P(A3P)
    add a default BCOR for bond A|500:P2(A3P) A|500:O6P(A3P)
    add a default BCOR for bond A|500:O5'(A3P) A|500:C5'(A3P)
    add a default BCOR for bond A|500:C5'(A3P) A|500:C4'(A3P)
    add a default BCOR for bond A|500:C4'(A3P) A|500:C3'(A3P)
    add a default BCOR for bond A|500:C4'(A3P) A|500:O4'(A3P)
    add a default BCOR for bond A|500:O4'(A3P) A|500:C1'(A3P)
    add a default BCOR for bond A|500:C3'(A3P) A|500:C2'(A3P)
    add a default BCOR for bond A|500:C3'(A3P) A|500:O3'(A3P)
    add a default BCOR for bond A|500:C2'(A3P) A|500:C1'(A3P)
    add a default BCOR for bond A|500:C2'(A3P) A|500:O2'(A3P)
    add a default BCOR for bond A|500:C1'(A3P) A|500:N9(A3P)
    add a default BCOR for bond A|500:N9(A3P) A|500:C4(A3P)
    add a default BCOR for bond A|500:N9(A3P) A|500:C8(A3P)
    add a default BCOR for bond A|500:C8(A3P) A|500:N7(A3P)
    add a default BCOR for bond A|500:N7(A3P) A|500:C5(A3P)
    add a default BCOR for bond A|500:C5(A3P) A|500:C4(A3P)
    add a default BCOR for bond A|500:C5(A3P) A|500:C6(A3P)
    add a default BCOR for bond A|500:C6(A3P) A|500:N1(A3P)
    add a default BCOR for bond A|500:C6(A3P) A|500:N6(A3P)
    add a default BCOR for bond A|500:N1(A3P) A|500:C2(A3P)
    add a default BCOR for bond A|500:C2(A3P) A|500:N3(A3P)
    add a default BCOR for bond A|500:N3(A3P) A|500:C4(A3P)
    add a default BCOR for bond B|500:P1(A3P) B|500:O1P(A3P)
    add a default BCOR for bond B|500:P1(A3P) B|500:O2P(A3P)
    add a default BCOR for bond B|500:P1(A3P) B|500:O3'(A3P)
    add a default BCOR for bond B|500:P1(A3P) B|500:O3P(A3P)
    add a default BCOR for bond B|500:P2(A3P) B|500:O4P(A3P)
    add a default BCOR for bond B|500:P2(A3P) B|500:O5'(A3P)
    add a default BCOR for bond B|500:P2(A3P) B|500:O5P(A3P)
    add a default BCOR for bond B|500:P2(A3P) B|500:O6P(A3P)
    add a default BCOR for bond B|500:O5'(A3P) B|500:C5'(A3P)
    add a default BCOR for bond B|500:C5'(A3P) B|500:C4'(A3P)
    add a default BCOR for bond B|500:C4'(A3P) B|500:C3'(A3P)
    only first 40 added listed here
 Have added a total of        58 bcorrels for bonds which do not already have a bcorrel
 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       568
         Number of other torsion is             1096
      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       -4.48 degrees
     Fix up bond A|102:CA=CB (PRO)
                    ideal from 1.531 to 1.533 actual= 1.536,  sigma from 0.020 to 0.018 Angs
     Fix up bond A|102:CB=CG (PRO)
                    ideal from 1.495 to 1.506 actual= 1.505,  sigma from 0.050 to 0.039 Angs
     Fix up bond A|102:CG=CD (PRO)
                    ideal from 1.502 to 1.512 actual= 1.517,  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= 127.7,  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= 120.3,  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= 103.0,  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= 114.7,  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= 105.3,  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= 106.4,  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= 104.8,  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= 111.8,  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       -2.89 degrees
     Fix up bond B|102:CA=CB (PRO)
                    ideal from 1.531 to 1.533 actual= 1.531,  sigma from 0.020 to 0.018 Angs
     Fix up bond B|102:CB=CG (PRO)
                    ideal from 1.495 to 1.506 actual= 1.522,  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= 1.481,  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= 127.4,  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= 120.3,  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= 103.2,  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= 114.8,  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= 105.1,  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= 107.0,  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= 104.6,  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= 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 = 6.433425E+05 rms gradient=      30.2193
 X-ray contribution to function value = 5.871621E+05
 Geometry contribution (inc ncs)      =      56180.5
 Geometry function summary
     term                           number     weight       rms        GooF      function     fn/numb
     ================================================================================================
     BOND bond lengths (angs)       4856       2.000      0.0101       0.518      2610.60       0.538
     ANGL bond angles (degs)        6604       2.000        1.06       0.665      5834.93       0.884
     TORS split-harmonic tors       1096       0.000       21.25       1.344         0.00       0.000
     SINTOR sinusoidal tors         1096       2.000       21.25                  2786.80       2.543
     TRIG.onal planes (angs)         114       2.000      0.0060       0.300        20.47       0.180
     PLAN general plane (angs)       708       5.000      0.0145       0.727      1871.13       2.643
     BCORrelations (angs*2)         4856      20.000       1.558       0.265      6812.28       1.403
     CONT (bad contacts)               0       5.000                                 0.00
     IDEAL(ideal-dist contact)      5183       4.000                             30846.90
     CHIRAL (gelly semiharmon)       598       5.000                                66.41
     SIM similarity restraint for NCS and/or TARGET                               5330.94
     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                           2.75 degs - monitor only

 Weighted rms      0.0101         1.055  (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=   2.354 std=   3.340 sigma=   0.200 abs(Delta/sigma)=    4.929 ats B|193:OH (TYR) B|500:C2 (A3P)
   It is likely that the geometry libraries, sequence info and links match the input molecule
 GEOMETRY CHECK OVERALL:  PASS

 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        1
 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  6.433425E+05  5.871621E+05       56180.5       30.2193  0.000000E+00  0.000000E+00       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  6.433221E+05  5.871573E+05       56164.8       21.6452  7.797545E-05    0.00220803       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)       4856       2.000      0.0101       0.518      2606.80       0.537
     ANGL bond angles (degs)        6604       2.000        1.05       0.664      5825.48       0.882
     TORS split-harmonic tors       1096       0.000       21.25       1.344         0.00       0.000
     SINTOR sinusoidal tors         1096       2.000       21.25                  2786.77       2.543
     TRIG.onal planes (angs)         114       2.000      0.0060       0.300        20.46       0.180
     PLAN general plane (angs)       708       5.000      0.0145       0.727      1871.09       2.643
     BCORrelations (angs*2)         4856      20.000       1.558       0.265      6810.74       1.403
     CONT (bad contacts)               0       5.000                                 0.00
     IDEAL(ideal-dist contact)      5182       4.000                             30846.66
     CHIRAL (gelly semiharmon)       598       5.000                                66.37
     SIM similarity restraint for NCS and/or TARGET                               5330.44
     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                           2.75 degs - monitor only

 Weighted rms      0.0101         1.055  (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
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 =    20.96 (user)        0.65 (sys)


Normal termination


 Resources usage summary:
     Time spent in client ...................    20.96 (user)        0.66 (system)
     Time spent in scripts (    26 calls) ...     0.95 (user)        0.04 (system)
     Time spent in server ...................     0.00 (user)        0.01 (system)

     Max resident memory used (kb) .......... 150848
     Number of page faults .................. 0 (major)    135104 (minor)
     Number of context switches ............. 2900 (niced)    5697 (other)