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: 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. 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 = 0.14057E+02 B = -8.636

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 = 3.3476 Å2 to all atoms in fragment Added B = 3.3476 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 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  5.0
 -----WEIGHT       BCORREL  20.0
 -----WEIGHT       CHIRAL   5.0
 -----WEIGHT       NCS      50.0
 -----WEIGHT       IDEAL    4.0
 -----WEIGHT       RFACTOR  7.85
 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     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 =  4217
 Before any COMBINE - Number of atoms with fixed BIJ =  4217
                            cf total number of atoms =  4217
 
 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
 
 --- 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         0.367     ----- 
     Overall RMSD,XYZ for the SIM group is     0.367 Angstroms
     Pairwise rms deviation of [individual B's minus their set/chain average] in Angs**2
                 A         B         Bavg
     A         -----     -----     39.96
     B          4.90     -----     44.79
     Overall RMSD,B   for the SIM group is     4.904 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 -0.999720 -0.023077 -0.005186  0.023120 -0.999697 -0.008455 -0.004989 -0.008573  0.999951   120.819   256.319   -35.185
 reverse transforms 
TRANS_BA -0.999720  0.023120 -0.004989 -0.023077 -0.999697 -0.008573 -0.005186 -0.008455  0.999951   114.684   258.728    37.977
 
 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      24370
 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|11      A|12      A|20      A|21      A|22      A|23      A|24
           A|25      A|26      A|27      A|28      A|30      A|81      A|82
           A|83      A|84      A|85      A|86      A|87      A|89      A|90
           A|91      A|92      A|93      A|94      A|95      A|96      A|97
           A|98     A|106     A|107     A|108     A|109     A|145     A|146
          A|147     A|180     A|181     A|182     A|183     A|184     A|185
          A|188     A|246     A|247     A|248      B|11      B|12      B|20
           B|21      B|22      B|23      B|24      B|25      B|26      B|27
           B|28      B|30      B|81      B|82      B|83      B|84      B|85
           B|86      B|87      B|89      B|90      B|91      B|92      B|93
           B|94      B|95      B|96      B|97      B|98     B|106     B|107
          B|108     B|109     B|145     B|146     B|147     B|180     B|181
          B|182     B|183     B|184     B|185     B|188     B|246     B|247
          B|248  
 Residues pruned out by function/max condition:
           A|27!     A|85!     A|86!     A|87!     A|88     A|89!     A|90!
           A|91!     B|27!     B|85!     B|86!     B|87!     B|88     B|89!
           B|90!     B|91! 
 Total number of residues pruned out is       94 out of      561 participating
 Number of LSSR restraints pruned out is      5256 this is   21.6% 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|11 A|12 A|20 A|21 A|22 A|23 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|24 A|25 A|26 A|27 A|28 A|30 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|81 A|82 A|83 A|84 A|85 A|86 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|87 A|88 A|89 A|90 A|91 A|92 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|93 A|94 A|95 A|96 A|97 A|98 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|106 A|107 A|108 A|109 A|145 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|146 A|147 A|180 A|181 A|182 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|183 A|184 A|185 A|188 A|246 }    # card added - produced by -autoncs
NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|247 A|248 }    # 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     20754.3
                             after pruning       110.7
 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=100.00% average DeltaD of subset     0.004 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  =   16868
 Number of free parameters to be adjusted in refinement   =   16868
 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    1349.030    1349.030       0.000
       ANGL       2.000        5778    4499.287    4499.287       0.000
       IMPR       0.000           0       0.000       0.000       0.000
       TORS       2.000        1400    3047.243    3047.214       0.028
       TRIG       2.000          64      11.284      11.284       0.000
       PLAN       5.000         610     741.994     741.994       0.000
       CONT       5.000           0       1.830       0.000       1.830
       BCOR      20.000        4311    2341.126    2341.126       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       -2.23 degrees
     Fix up bond A|102:CA=CB (PRO)
                    ideal from 1.531 to 1.533 actual= 1.535,  sigma from 0.020 to 0.018 Angs
     Fix up bond A|102:CB=CG (PRO)
                    ideal from 1.495 to 1.506 actual= 1.496,  sigma from 0.050 to 0.039 Angs
     Fix up bond A|102:CG=CD (PRO)
                    ideal from 1.502 to 1.512 actual= 1.515,  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= 128.6,  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= 120.0,  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= 103.1,  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= 113.8,  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= 105.1,  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= 106.9,  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= 111.4,  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       -2.02 degrees
     Fix up bond B|102:CA=CB (PRO)
                    ideal from 1.531 to 1.533 actual= 1.534,  sigma from 0.020 to 0.018 Angs
     Fix up bond B|102:CB=CG (PRO)
                    ideal from 1.495 to 1.506 actual= 1.496,  sigma from 0.050 to 0.039 Angs
     Fix up bond B|102:CG=CD (PRO)
                    ideal from 1.502 to 1.512 actual= 1.516,  sigma from 0.033 to 0.027 Angs
     Fix up bond B|102:CD=N (PRO)
                    ideal from 1.474 to 1.474 actual= 1.479,  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= 128.6,  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= 119.9,  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= 113.8,  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= 105.2,  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= 104.7,  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= 111.5,  sigma from   1.4 to   1.4 Degs
   Weight for ideal-distance contact term=     4.000

   MaxLik Scaling Cycle 0002 (explanation)
 
 Initial functional value = 5.325684E+05 rms gradient=      23.5930
 X-ray contribution to function value = 4.999221E+05
 Geometry contribution (inc ncs)      =      32646.2
 Geometry function summary
     term                           number     weight       rms        GooF      function     fn/numb
     ================================================================================================
     BOND bond lengths (angs)       4311       2.000      0.0078       0.395      1348.57       0.313
     ANGL bond angles (degs)        5778       2.000        0.99       0.609      4284.07       0.741
     TORS split-harmonic tors        844       0.000       20.91       1.344         0.00       0.000
     SINTOR sinusoidal tors          844       2.000       20.91                  2185.78       2.590
     TRIG.onal planes (angs)          64       2.000      0.0059       0.297        11.28       0.176
     PLAN general plane (angs)       610       5.000      0.0099       0.493       741.99       1.216
     BCORrelations (angs*2)         4311      20.000       0.957       0.165      2341.13       0.543
     CONT (bad contacts)               0       5.000                                 0.00
     IDEAL(ideal-dist contact)      4292       4.000                             21622.47
     CHIRAL (gelly semiharmon)       557       5.000                                 0.25
     SIM similarity restraint for NCS and/or TARGET                                110.68
     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                           5.46 degs - monitor only

 Weighted rms      0.0078         0.992  (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 not any bad contacts where Delta/sigma is greater than     6.5
   Worst contact dist=   2.761 std=   3.340 sigma=   0.200 abs(Delta/sigma)=    2.894 ats A|24:CD1 (PHE) A|24:CE2 (PHE)
   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      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  5.325684E+05  4.999221E+05       32646.2       23.5930  0.000000E+00  0.000000E+00       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0004 (explanation)

   MaxLik Scaling Cycle 0005 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 001 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       1  5.325374E+05  4.998979E+05       32639.5       16.7606  2.790968E-04    0.00514351       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0006 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 002 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       2  5.325170E+05  4.998730E+05       32644.1       14.8727  4.061870E-04    0.00481672       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0007 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 003 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       3  5.324346E+05  4.996603E+05       32774.3       16.1661    0.00173737     0.0140714       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0008 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 004 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       4  5.324078E+05  4.995099E+05       32897.9       29.9511    0.00270262     0.0204795       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0009 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 005 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       5  5.323659E+05  4.995016E+05       32864.3       16.0110    0.00274784     0.0208533       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0010 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 006 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       6  5.323138E+05  4.994027E+05       32911.1       10.8142    0.00346629     0.0256694       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0011 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 007 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       7  5.322763E+05  4.992651E+05       33011.2       14.8381    0.00452763     0.0327792       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0012 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 008 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       8  5.322575E+05  4.990114E+05       33246.1       40.8089    0.00670398     0.0487719       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0013 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 009 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
       9  5.321963E+05  4.989478E+05       33248.5       15.1188    0.00724295     0.0527484       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0014 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 010 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      10  5.321636E+05  4.989023E+05       33261.2       11.3333    0.00773479     0.0562941       Opttag_D
   Writing pdb file to gelly_output_iter000010.pdb
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0015 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 011 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      11  5.321217E+05  4.988117E+05       33310.0       16.0845    0.00882825     0.0638772       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0016 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 012 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      12  5.320634E+05  4.986776E+05       33385.9       17.0993     0.0105668     0.0749835       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0017 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 013 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      13  5.319958E+05  4.983833E+05       33612.5       40.8280     0.0147304     0.0965307       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0018 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 014 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      14  5.319164E+05  4.981928E+05       33723.6       19.2014     0.0175542      0.114882       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0019 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 015 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      15  5.318786E+05  4.982176E+05       33661.0       12.9842     0.0171607      0.112610       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0020 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 016 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      16  5.318206E+05  4.981618E+05       33658.8       13.1604     0.0180861      0.120294       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0021 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 017 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      17  5.317619E+05  4.980157E+05       33746.2       21.5981     0.0204962      0.138272       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0022 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 018 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      18  5.317013E+05  4.977852E+05       33916.0       26.0775     0.0246837      0.168667       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0023 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 019 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      19  5.316434E+05  4.976851E+05       33958.4       14.5392     0.0266228      0.182289       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0024 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 020 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      20  5.315979E+05  4.975893E+05       34008.6       14.2161     0.0284047      0.194392       Opttag_D
   Writing pdb file to gelly_output_iter000020.pdb
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0025 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 021 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      21  5.315506E+05  4.975012E+05       34049.4       16.0030     0.0301739      0.206290       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0026 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 022 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      22  5.315062E+05  4.972698E+05       34236.3       41.0291     0.0351099      0.239082       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0027 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 023 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      23  5.314267E+05  4.972078E+05       34219.0       16.7296     0.0365200      0.248225       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0028 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 024 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      24  5.313937E+05  4.972066E+05       34187.2       12.7863     0.0366102      0.248609       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0029 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 025 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      25  5.313428E+05  4.971385E+05       34204.2       15.7591     0.0381831      0.258329       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0030 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 026 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      26  5.312807E+05  4.969851E+05       34295.6       24.1038     0.0416541      0.279697       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0031 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 027 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      27  5.312107E+05  4.968241E+05       34386.6       18.1142     0.0455415      0.303223       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0032 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 028 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      28  5.311584E+05  4.966446E+05       34513.8       27.5374     0.0500446      0.329763       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0033 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 029 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      29  5.311040E+05  4.965646E+05       34539.4       15.5363     0.0520355      0.341106       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0034 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 030 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      30  5.310654E+05  4.965406E+05       34524.8       16.0246     0.0527095      0.344145       Opttag_D
   Writing pdb file to gelly_output_iter000030.pdb
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0035 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 031 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      31  5.309839E+05  4.964425E+05       34541.4       17.6893     0.0556684      0.359386       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0036 (explanation)

   MaxLik Scaling Cycle 0037 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 032 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      32  5.309427E+05  4.963403E+05       34602.4       26.5973     0.0586613      0.375826       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0038 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 033 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      33  5.308799E+05  4.962365E+05       34643.4       16.2161     0.0620775      0.394817       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0039 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 034 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      34  5.308245E+05  4.961295E+05       34695.0       15.4760     0.0656627      0.415474       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0040 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 035 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      35  5.307675E+05  4.959929E+05       34774.6       22.3356     0.0699609      0.441016       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0041 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 036 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      36  5.307094E+05  4.959130E+05       34796.4       16.4405     0.0723203      0.455340       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0042 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 037 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      37  5.306329E+05  4.957993E+05       34833.6       15.8893     0.0755743      0.475426       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0043 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 038 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      38  5.305921E+05  4.956673E+05       34924.7       32.2731     0.0795066      0.500152       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0044 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 039 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      39  5.305349E+05  4.956298E+05       34905.1       17.9267     0.0808055      0.508492       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0045 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 040 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      40  5.304798E+05  4.955742E+05       34905.5       15.8593     0.0829547      0.522568       Opttag_D
   Writing pdb file to gelly_output_iter000040.pdb
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0046 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 041 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      41  5.304259E+05  4.954868E+05       34939.1       16.8847     0.0862384      0.544581       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0047 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 042 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      42  5.303381E+05  4.953353E+05       35002.8       18.6041     0.0917451      0.582806       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0048 (explanation)

   MaxLik Scaling Cycle 0049 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 043 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      43  5.302954E+05  4.952387E+05       35056.7       28.4815     0.0953501      0.608718       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0050 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 044 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      44  5.302174E+05  4.951032E+05       35114.2       15.8897      0.100278      0.644365       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0051 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 045 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      45  5.301618E+05  4.950245E+05       35137.3       14.3800      0.102981      0.665102       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0052 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 046 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      46  5.300941E+05  4.949107E+05       35183.5       23.8365      0.106858      0.695787       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0053 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 047 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      47  5.300276E+05  4.948241E+05       35203.6       17.2752      0.109813      0.718732       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0054 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 048 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      48  5.299554E+05  4.947436E+05       35211.8       16.6754      0.112977      0.743843       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0055 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 049 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      49  5.299047E+05  4.946202E+05       35284.5       33.2351      0.118016      0.783072       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0056 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 050 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      50  5.298404E+05  4.945598E+05       35280.7       18.8037      0.120575      0.802366       Opttag_D
   Writing pdb file to gelly_output_iter000050.pdb
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0057 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 051 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      51  5.297784E+05  4.945053E+05       35273.0       18.3614      0.123069      0.821850       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0058 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 052 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      52  5.297008E+05  4.943845E+05       35316.2       20.6681      0.127983      0.859546       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0059 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 053 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      53  5.295909E+05  4.942602E+05       35330.7       21.5641      0.133596      0.904132       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0060 (explanation)

   MaxLik Scaling Cycle 0061 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 054 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      54  5.295416E+05  4.941522E+05       35389.4       32.8015      0.138221      0.939651       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0062 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 055 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      55  5.294409E+05  4.939965E+05       35444.4       16.3966      0.145094      0.991872       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0063 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 056 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      56  5.293801E+05  4.939944E+05       35385.7       14.1976      0.145875      0.999734       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0064 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 057 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      57  5.292906E+05  4.937951E+05       35495.5       18.4965      0.154046       1.05859       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0065 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 058 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      58  5.292419E+05  4.938147E+05       35427.2       38.9812      0.155561       1.07235       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0066 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 059 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      59  5.291601E+05  4.938000E+05       35360.0       16.9525      0.156404       1.07835       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0067 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 060 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      60  5.291128E+05  4.936541E+05       35458.6       13.7058      0.161931       1.11562       Opttag_D
   Writing pdb file to gelly_output_iter000060.pdb
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0068 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 061 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      61  5.290452E+05  4.936283E+05       35416.9       15.5457      0.163784       1.12876       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0069 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 062 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      62  5.289710E+05  4.934528E+05       35518.1       29.6752      0.172957       1.19332       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0070 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 063 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      63  5.289055E+05  4.934296E+05       35475.9       25.9998      0.175407       1.21150       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0071 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 064 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      64  5.288604E+05  4.934608E+05       35399.6       14.0089      0.173975       1.20205       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0072 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 065 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      65  5.288173E+05  4.934309E+05       35386.4       13.6872      0.175384       1.21241       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0073 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 066 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      66  5.287648E+05  4.933898E+05       35375.0       17.2484      0.177333       1.22598       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0074 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 067 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      67  5.287200E+05  4.932115E+05       35508.5       37.5715      0.185364       1.27995       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0075 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 068 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      68  5.286446E+05  4.932260E+05       35418.6       14.5806      0.185214       1.27811       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0076 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 069 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      69  5.286072E+05  4.931991E+05       35408.1       12.6318      0.186668       1.28697       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0077 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 070 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      70  5.285619E+05  4.931567E+05       35405.2       16.6471      0.188629       1.29816       Opttag_D
   Writing pdb file to gelly_output_iter000070.pdb
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0078 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 071 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      71  5.285070E+05  4.930556E+05       35451.4       28.2883      0.193741       1.32926       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0079 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 072 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      72  5.284453E+05  4.929728E+05       35472.5       17.0547      0.197796       1.35245       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0080 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 073 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      73  5.284029E+05  4.929738E+05       35429.1       12.4008      0.197322       1.34718       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0081 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 074 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      74  5.283475E+05  4.928891E+05       35458.4       17.7077      0.201978       1.37595       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0082 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 075 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      75  5.282990E+05  4.928821E+05       35416.9       18.2667      0.201834       1.37008       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0083 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 076 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      76  5.282378E+05  4.928226E+05       35415.2       14.0048      0.204914       1.38468       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0084 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 077 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      77  5.282015E+05  4.926837E+05       35517.8       36.1106      0.213792       1.45998       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0085 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 078 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      78  5.281415E+05  4.926797E+05       35461.8       14.8355      0.213679       1.46309       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0086 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 079 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      79  5.281159E+05  4.926901E+05       35425.7       12.4382      0.212632       1.45583       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0087 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 080 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      80  5.280603E+05  4.926232E+05       35437.1       14.6595      0.216497       1.49216       Opttag_D
   Writing pdb file to gelly_output_iter000080.pdb
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0088 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 081 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      81  5.280151E+05  4.925974E+05       35417.7       21.6156      0.216751       1.50704       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0089 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 082 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      82  5.279676E+05  4.925461E+05       35421.4       14.0232      0.219863       1.53981       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0090 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 083 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      83  5.279113E+05  4.924360E+05       35475.3       12.7087      0.227664       1.61241       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0091 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 084 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      84  5.278793E+05  4.924353E+05       35444.0       23.6257      0.226430       1.61391       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0092 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 085 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      85  5.278383E+05  4.924083E+05       35430.0       15.0587      0.228084       1.62968       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0093 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 086 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      86  5.277884E+05  4.923469E+05       35441.5       12.0460      0.232301       1.66595       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0094 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 087 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      87  5.277522E+05  4.923403E+05       35411.8       14.4942      0.232014       1.67025       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0095 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 088 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      88  5.276947E+05  4.922438E+05       35450.8       22.0181      0.238382       1.73501       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0096 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 089 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      89  5.276476E+05  4.922233E+05       35424.4       13.8951      0.239401       1.75008       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0097 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 090 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      90  5.276140E+05  4.922197E+05       35394.3       11.5535      0.238809       1.74842       Opttag_D
   Writing pdb file to gelly_output_iter000090.pdb
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0098 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 091 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      91  5.275693E+05  4.921715E+05       35397.8       15.3625      0.241607       1.77613       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0099 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 092 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      92  5.275634E+05  4.921000E+05       35463.4       36.0162      0.246545       1.82286       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0100 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 093 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      93  5.275110E+05  4.921211E+05       35390.0       12.0156      0.244675       1.80577       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0101 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 094 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      94  5.274892E+05  4.921136E+05       35375.6       9.85628      0.245543       1.81444       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0102 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 095 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      95  5.274590E+05  4.921016E+05       35357.4       12.6398      0.246595       1.82603       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0103 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 096 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      96  5.274122E+05  4.920584E+05       35353.8       13.6228      0.250339       1.86192       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0104 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 097 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      97  5.274052E+05  4.920373E+05       35367.8       38.9645      0.250940       1.87550       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0105 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 098 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      98  5.273190E+05  4.919795E+05       35339.5       10.7764      0.256178       1.92066       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0106 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 099 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
      99  5.272966E+05  4.919686E+05       35327.9       7.72253      0.256299       1.91995       Opttag_D
   Geometry Restraint Deviations SCREEN Information

 

   MaxLik Scaling Cycle 0107 (explanation)

   Wilson plot

   Statistics in resolution bins after refinement cycle 100 (explanation) : 
  
     
   Iters     Tot_Funct    Xray_Funct    Geom_Funct          Grms     rmsD2init     maxD2init
     100  5.272633E+05  4.919308E+05       35332.5       11.2520      0.258266       1.93556       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      0.0082       0.417      1499.28       0.348
     ANGL bond angles (degs)        5778       2.000        1.04       0.636      4671.90       0.809
     TORS split-harmonic tors        844       0.000       21.74       1.397         0.00       0.000
     SINTOR sinusoidal tors          844       2.000       21.74                  2338.48       2.771
     TRIG.onal planes (angs)          64       2.000      0.0060       0.302        11.67       0.182
     PLAN general plane (angs)       610       5.000      0.0111       0.555       940.93       1.543
     BCORrelations (angs*2)         4311      20.000       1.094       0.188      3060.83       0.710
     CONT (bad contacts)               0       5.000                                 0.00
     IDEAL(ideal-dist contact)      4377       4.000                             22674.71
     CHIRAL (gelly semiharmon)       557       5.000                                 0.22
     SIM similarity restraint for NCS and/or TARGET                                134.47
     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                           5.61 degs - monitor only

 Weighted rms      0.0082         1.036  (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 = 212.37 (user) 8.49 (sys)


Normal termination


 Resources usage summary:
     Time spent in client ...................   392.39 (user)        9.93 (system)
     Time spent in scripts (   224 calls) ...     1.25 (user)        0.62 (system)
     Time spent in server ...................     0.01 (user)        0.00 (system)

     Max resident memory used (kb) .......... 0
     Number of page faults .................. 0 (major)    468107 (minor)
     Number of context switches ............. 40460 (niced)    2553 (other)