#CCP4I VERSION CCP4Interface 1.4.4.2 #CCP4I SCRIPT LOG refmac5 #CCP4I DATE 15 Aug 2007 12:46:54 #CCP4I USER ccp4 #CCP4I PROJECT mao #CCP4I JOB_ID 62 #CCP4I SCRATCH /tmp/ccp4 #CCP4I HOSTNAME dragon.chem.york.ac.uk #CCP4I PID 10234
 
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 ### CCP4 6.0: Refmac_5.3.0037    version 5.3.0037  : 03/29/06##
 ###############################################################
 User: eleanor  Run date: 15/ 8/2007 Run time: 12:47:09 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ comment $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 Data line--- make check NONE
 MAKE
 Data line--- make     hydrogen NO     hout NO     peptide NO     cispeptide YES     ssbridge YES     symmetry YES     sugar YES     connectivity NO     link NO
 MAKE
 Data line--- refi     type REST     resi MLKF     meth CGMAT     bref ISOT
 REFI
 Data line--- ncyc 10
 NCYC
 Data line--- scal     type SIMP     reso 2.260 103.142     LSSC     ANISO     EXPE
 SCAL
 Data line--- solvent YES     VDWProb 1.2     IONProb 0.8     RSHRink 0.8
 SOLV
 Data line--- weight     MATRIX 0.2
 WEIG
 Data line--- monitor MEDIUM     torsion 10.0     distance 10.0     angle 10.0     plane 10.0     chiral 10.0     bfactor 10.0     bsphere 10.0     rbond 10.0     ncsr 10.0
 MONI
 Data line--- labin  FP=FP SIGFP=SIGFP    FREE=FREE
 LABI
 Data line--- labout  FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM
 LABO
 Data line--- PNAME mao
 PNAM
 Data line--- DNAME 2hr0
 DNAM
 Data line--- RSIZE 80
 RSIZ
 Data line--- END
 END 

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /y/work/ccp4/2hr0sf.mtz 


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib

 
    ****           Input and Default parameters#            ****
 
 
Input coordinate file.  Logical name - XYZIN actual file name  - /y/database/brookhaven/pdb/2hr0.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /tmp/ccp4/mao_62_2_pdb_1.tmp
Input reflection file.  Logical name - HKLIN actual file name  - /y/work/ccp4/2hr0sf.mtz
Output reflection file. Logical name - HKLOUT actual file name - /tmp/ccp4/mao_62_3_mtz_1.tmp
 
Cell from mtz :   151.200   142.700   203.700    90.000    98.900    90.000
Space group from mtz: number -    5; name - C 1 2 1
 
  Refinement type                        : Restrained
 
 
    ****                 Makecif parameters                 ****
 
Dictionary files for restraints : /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/ener_lib.cif
User supplied dictionary entries: /y/people/ccp4/projects/mao/mao_61_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will not be written to the output file
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically
 
 
  Residual                               : Rice Maximum Likelihood for Fs
 
    ****          Least-square scaling parameters           ****
 
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800
 
  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0098
  Refinement of individual isotropic Bfactors
  Refinement resln        :   103.1421  2.2600
  Estimated number of reflections :     273145
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.2000
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian
  using working set of reflns and experimental sigmas
 
  Estimation of SigmaA Using 2 Gaussians:
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas
 
  Scaling and SigmaA resln:   103.1420  2.2600
 
  Damping factors:     1.0000  1.0000
 
 
    ****          Geometry restraints and weights           ****
 
 
                                              Sigma:
 Bonding distances
          Weight =  1.00
 
 Bond angles
          Weight =  1.00
 
 Planar groups
          WEIGHT= 1.00
 
 Chiral centers
          Weight= 1.00
 
 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)
 
 TORSION ANGLES
          Weight= 1.00
 
 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)         1.50A**2
     Main chain angle (1-3 neighbour)        2.00A**2
     Side chain bond                         3.00A**2
     Side chain angle                        4.50A**2
 
 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00
 
 RADIUS OF CONFIDENCE
     Positional parameters 0.30A
     Thermal parameters    0.03A**2
     Occupancy parameters  0.50
 
Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------
 
 Input file :/y/database/brookhaven/pdb/2hr0.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      4.30
 _lib_update       02/03/07
  ------------------------------
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      4.30
 _lib_update       02/03/07
  ------------------------------
  WARNING: duplicated name of monomer THC
           Last entry will be used.
  NUMBER OF MONOMERS IN THE LIBRARY          :  2433
                with complete description    :   451
  NUMBER OF MODIFICATIONS                    :    47
  NUMBER OF LINKS                            :    65
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/atomsf.lib


  Number of atoms    :   12958
  Number of residues :    2257
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : link: GLN<-->THC is without link_id
            link will be created with covalent bond only
  WARNING : link:SS       is found dist =     2.041 ideal_dist=     2.031
            ch:AA   res: 605  CYS      at:SG  .->AA   res: 640  CYS      at:SG  .
  INFO:     link is found (not be used) dist=   1.320 ideal_dist=   1.469
            ch:AA   res: 239  TYR      at:OH  .->ch:BB   res: 832  TYR      at:OH  .
  INFO:     link is found (not be used) dist=   1.562 ideal_dist=   1.275
            ch:AA   res: 246  THR      at:O   .->ch:BB   res:1460  TYR      at:OH  .
  INFO:     link is found (not be used) dist=   2.394 ideal_dist=   1.645
            ch:AA   res: 268  ARG      at:NH1 .->ch:BB   res:1378  MET      at:SD  .
  INFO:     link is found (not be used) dist=   2.059 ideal_dist=   1.810
            ch:AA   res: 316  MET      at:SD  .->ch:BB   res:1463  LEU      at:CG  .
  WARNING : link:SS       is found dist =     2.041 ideal_dist=     2.031
            ch:AA   res: 537  CYS      at:SG  .->BB   res: 794  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.023 ideal_dist=     2.031
            ch:BB   res: 851  CYS      at:SG  .->BB   res:1491  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.031 ideal_dist=     2.031
            ch:BB   res:1079  CYS      at:SG  .->BB   res:1136  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.027 ideal_dist=     2.031
            ch:BB   res:1336  CYS      at:SG  .->BB   res:1467  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.032 ideal_dist=     2.031
            ch:BB   res:1367  CYS      at:SG  .->BB   res:1436  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.012 ideal_dist=     2.031
            ch:BB   res:1484  CYS      at:SG  .->BB   res:1489  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.029 ideal_dist=     2.031
            ch:BB   res:1496  CYS      at:SG  .->BB   res:1568  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.033 ideal_dist=     2.031
            ch:BB   res:1515  CYS      at:SG  .->BB   res:1639  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.031 ideal_dist=     2.031
            ch:BB   res:1615  CYS      at:SG  .->BB   res:1624  CYS      at:SG  .
  WARNING : link:GLN-THC  is found dist =     1.462 ideal_dist=     1.330
            ch:BB   res: 991  GLN      at:CD  .->Ba   res:1991  THC      at:OG1 .
  --------------------------------
  --- title of input coord file ---
 
  PDB_code:2HR0
  PDB_name:IMMUNE SYSTEM
  PDB_date:19-JUL-06
  --------------------------------
  ATTENTION: atom:NE2  GLN       991  BB   is missing in the structure
  ATTENTION: atom:O    THC      1991  Ba   is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :    2257
  Number of atoms                   :   12960
  Number of missing atoms           :       2
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
 
  Number of bonds restraints    :   12501
  Number of angles restraints   :   16950
  Number of torsions restraints :    8525
  Number of chiralities         :    1925
  Number of planar groups       :    2186
 
 
 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c
 
 
  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669
 
 
 Number of reflections in file     199279
 Number of reflection read         199278
 
 
     CGMAT cycle number =      1
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A    206 VAL CA    - A    207 LEU CA    mod.= 123.08 id.= 180.00 per.= 1 dev=  56.92 sig.=   5.00
 
 weigth matrix   0.2000000    
 
 
 special position -----------   3.162778    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.386     1.968
Torsion angles, period  1. refined             1541     6.649     5.000
Torsion angles, period  2. refined              566    39.908    24.912
Torsion angles, period  3. refined             2228    20.105    15.000
Torsion angles, period  4. refined               67    17.552    15.000
Chiral centres: refined atoms                  1925     0.103     0.200
Planar groups: refined atoms                   9353     0.005     0.020
VDW repulsions: refined atoms                  6423     0.294     0.200
VDW; torsion: refined atoms                    8371     0.312     0.200
HBOND: refined atoms                            512     0.231     0.200
VDW repulsions; symmetry: refined atoms          15     0.421     0.200
M. chain bond B values: refined atoms          7726     0.650     1.500
M. chain angle B values: refined atoms        12565     1.171     2.000
S. chain bond B values: refined atoms          4775     1.901     3.000
S. chain angle B values: refined atoms         4385     3.090     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =   0.079
Partial structure    1: scale =   -0.006, B  =  88.458
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.005    2205  98.77  3707.1  3661.6  0.12  0.30     121  4032.4  4012.3  0.12  0.29
 0.015    3952  99.90  1885.4  1849.3  0.20  0.61     197  1961.1  1870.8  0.21  0.40
 0.025    5026  99.81  1539.2  1503.8  0.23  0.63     283  1526.5  1476.4  0.26  0.54
 0.034    5988  99.76  1558.8  1532.3  0.23  0.62     307  1585.8  1546.6  0.22  0.43
 0.044    6751  99.79  1483.9  1471.7  0.17  0.42     338  1512.2  1513.6  0.18  0.62
 0.054    7469  99.81  1282.2  1281.2  0.14  0.30     391  1315.2  1327.4  0.15  0.27
 0.064    8078  99.87  1084.2  1079.3  0.16  0.36     465  1069.1  1068.2  0.18  0.43
 0.073    8642  99.84   952.7   949.3  0.15  0.33     488   970.8   978.2  0.16  0.51
 0.083    9255  99.88   845.1   838.1  0.16  0.37     490   835.8   836.2  0.17  0.39
 0.093    9778  99.88   729.3   721.9  0.16  0.37     515   753.9   737.6  0.18  0.38
 0.103   10225  99.86   646.3   639.7  0.17  0.38     547   642.8   634.3  0.19  0.37
 0.113   10768  99.83   582.6   575.5  0.18  0.42     538   578.8   580.7  0.20  0.50
 0.122   11121  99.86   522.4   513.0  0.19  0.48     607   542.5   532.7  0.20  0.47
 0.132   11692  99.85   477.3   470.3  0.19  0.46     607   464.7   458.7  0.23  0.43
 0.142   11999  99.83   442.7   434.3  0.19  0.48     621   444.1   431.8  0.22  0.55
 0.152   12463  99.79   408.9   398.7  0.19  0.44     655   424.6   415.3  0.22  0.53
 0.162   12885  99.78   374.5   365.4  0.20  0.53     632   374.6   367.6  0.22  0.43
 0.171   12698  95.96   348.4   340.2  0.21  0.57     686   345.2   330.4  0.24  0.51
 0.181   11926  87.78   323.9   315.1  0.21  0.66     590   325.2   314.4  0.24  0.57
 0.191   11204  80.39   302.3   291.6  0.22  0.59     600   294.7   288.4  0.26  0.77
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle    1. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0050  1990   0.957   215   0.894  2205   0.951  0.973
  0.0148  3730   0.910   222   0.851  3952   0.907  0.973
  0.0246  4815   0.894   211   0.842  5026   0.892  0.973
  0.0343  5762   0.910   226   0.833  5988   0.907  0.973
  0.0441  6529   0.914   222   0.869  6751   0.913  0.974
  0.0539  7245   0.910   224   0.821  7469   0.908  0.974
  0.0637  7857   0.899   221   0.803  8078   0.896  0.974
  0.0735  8417   0.890   224   0.823  8641   0.888  0.974
  0.0833  9031   0.885   225   0.842  9256   0.884  0.974
  0.0930  9564   0.876   214   0.804  9778   0.875  0.974
  0.1028 10004   0.868   221   0.766 10225   0.866  0.975
  0.1126 10543   0.869   225   0.807 10768   0.867  0.975
  0.1224 10902   0.858   219   0.819 11121   0.857  0.975
  0.1322 11468   0.860   224   0.811 11692   0.859  0.975
  0.1420 11775   0.865   224   0.762 11999   0.863  0.975
  0.1518 12238   0.865   225   0.760 12463   0.863  0.975
  0.1615 12666   0.867   219   0.778 12885   0.866  0.976
  0.1713 12525   0.868   173   0.791 12698   0.867  0.976
  0.1811 11789   0.870   136   0.780 11925   0.869  0.976
  0.1909 11084   0.873   121   0.833 11205   0.872  0.976
 $$
Resolution limits                    =    103.142     2.260
Number of used reflections           =     184125
Percentage observed                  =    97.2531
Percentage of free reflections       =     4.9937
Overall R factor                     =     0.1814
Free R factor                        =     0.1953
Overall weighted R factor            =     0.4466
Free weighted R factor               =     0.4567
Overall correlation coefficient      =     0.9686
Free correlation coefficient         =     0.9717
Cruickshanks DPI for coordinate error=     0.1317
DPI based on free R factor           =     0.1202
Overall figure of merit              =     0.8764
ML based su of positional parameters =     0.0743
ML based su of thermal parameters    =     2.8890
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      2
 
 weigth matrix   0.2000000    
 
 
 special position -----------   3.093260    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.385     1.968
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =  -0.049
Partial structure    1: scale =   -0.006, B  =  88.458
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1802
Free R factor                        =     0.1944
Overall figure of merit              =     0.8772
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      3
 
 weigth matrix   0.2000000    
 
 
 special position -----------   3.045456    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.386     1.968
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =  -0.032
Partial structure    1: scale =   -0.007, B  =  88.588
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1800
Free R factor                        =     0.1943
Overall figure of merit              =     0.8774
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      4
 
 weigth matrix   0.2000000    
 
 
 special position -----------   3.013843    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.388     1.968
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =  -0.032
Partial structure    1: scale =   -0.007, B  =  88.656
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1799
Free R factor                        =     0.1942
Overall figure of merit              =     0.8776
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      5
 
 weigth matrix   0.2000000    
 
 
 special position -----------   2.991957    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.390     1.968
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =  -0.030
Partial structure    1: scale =   -0.007, B  =  88.784
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1798
Free R factor                        =     0.1941
Overall figure of merit              =     0.8778
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      6
 
 weigth matrix   0.2000000    
 
 
 special position -----------   2.976728    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.391     1.968
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =  -0.028
Partial structure    1: scale =   -0.007, B  =  88.964
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1796
Free R factor                        =     0.1940
Overall figure of merit              =     0.8778
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      7
 
 weigth matrix   0.2000000    
 
 
 special position -----------   2.966238    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.392     1.968
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =  -0.027
Partial structure    1: scale =   -0.007, B  =  89.031
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1796
Free R factor                        =     0.1939
Overall figure of merit              =     0.8779
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      8
 
 weigth matrix   0.2000000    
 
 
 special position -----------   2.958910    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.393     1.968
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =  -0.003
Partial structure    1: scale =   -0.007, B  =  89.038
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1795
Free R factor                        =     0.1938
Overall figure of merit              =     0.8779
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      9
 
 weigth matrix   0.2000000    
 
 
 special position -----------   2.953794    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.394     1.968
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =  -0.051
Partial structure    1: scale =   -0.007, B  =  89.098
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.1794
Free R factor                        =     0.1938
Overall figure of merit              =     0.8780
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =     10
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A    206 VAL CA    - A    207 LEU CA    mod.= 122.18 id.= 180.00 per.= 1 dev=  57.82 sig.=   5.00
 
 weigth matrix   0.2000000    
 
 
 special position -----------   2.950405    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.394     1.968
Torsion angles, period  1. refined             1541     6.513     5.000
Torsion angles, period  2. refined              566    39.892    24.912
Torsion angles, period  3. refined             2228    20.256    15.000
Torsion angles, period  4. refined               67    17.846    15.000
Chiral centres: refined atoms                  1925     0.102     0.200
Planar groups: refined atoms                   9353     0.005     0.020
VDW repulsions: refined atoms                  6463     0.304     0.200
VDW; torsion: refined atoms                    8380     0.312     0.200
HBOND: refined atoms                            515     0.232     0.200
VDW repulsions; symmetry: refined atoms          16     0.417     0.200
M. chain bond B values: refined atoms          7881     0.694     1.500
M. chain angle B values: refined atoms        12565     1.156     2.000
S. chain bond B values: refined atoms          5126     2.034     3.000
S. chain angle B values: refined atoms         4385     3.074     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =  -0.029
Partial structure    1: scale =   -0.007, B  =  89.098
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.005    2205  98.77  3709.1  3665.1  0.12  0.30     121  4034.6  4015.6  0.11  0.29
 0.015    3952  99.90  1886.4  1851.5  0.20  0.62     197  1962.2  1870.4  0.21  0.40
 0.025    5026  99.81  1540.0  1505.7  0.23  0.64     283  1527.4  1476.2  0.26  0.55
 0.034    5988  99.76  1559.6  1533.3  0.23  0.62     307  1586.6  1549.7  0.23  0.43
 0.044    6751  99.79  1484.6  1472.4  0.17  0.42     338  1513.1  1514.6  0.18  0.63
 0.054    7469  99.81  1282.9  1282.9  0.14  0.30     391  1315.9  1328.5  0.15  0.27
 0.064    8078  99.87  1084.8  1080.0  0.16  0.36     465  1069.7  1070.7  0.17  0.42
 0.073    8642  99.84   953.3   949.9  0.15  0.33     488   971.3   977.3  0.16  0.50
 0.083    9255  99.88   845.6   838.8  0.16  0.36     490   836.2   836.4  0.17  0.37
 0.093    9778  99.88   729.7   722.7  0.16  0.36     515   754.3   737.8  0.18  0.41
 0.103   10225  99.86   646.7   640.5  0.17  0.37     547   643.1   636.5  0.19  0.37
 0.113   10768  99.83   582.9   576.0  0.18  0.42     538   579.1   581.4  0.20  0.49
 0.122   11121  99.86   522.6   514.0  0.19  0.47     607   542.8   533.5  0.20  0.46
 0.132   11692  99.85   477.5   471.2  0.19  0.46     607   464.9   457.6  0.23  0.42
 0.142   11999  99.83   443.0   435.0  0.19  0.47     621   444.3   432.5  0.22  0.54
 0.152   12463  99.79   409.2   399.2  0.19  0.44     655   424.8   414.9  0.22  0.53
 0.162   12885  99.78   374.7   366.0  0.20  0.52     632   374.8   369.7  0.22  0.42
 0.171   12698  95.96   348.6   340.9  0.20  0.57     686   345.4   331.0  0.24  0.50
 0.181   11926  87.78   324.1   315.6  0.21  0.65     590   325.4   315.3  0.24  0.57
 0.191   11204  80.39   302.4   292.1  0.21  0.59     600   294.9   288.9  0.26  0.78
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle   10. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0050  1990   0.958   215   0.894  2205   0.951  0.974
  0.0148  3730   0.912   222   0.856  3952   0.908  0.974
  0.0246  4815   0.896   211   0.843  5026   0.894  0.974
  0.0343  5762   0.912   226   0.831  5988   0.909  0.974
  0.0441  6529   0.916   222   0.872  6751   0.914  0.974
  0.0539  7245   0.912   224   0.821  7469   0.909  0.974
  0.0637  7857   0.900   221   0.801  8078   0.898  0.975
  0.0735  8417   0.892   224   0.820  8641   0.890  0.975
  0.0833  9031   0.886   225   0.841  9256   0.885  0.975
  0.0930  9564   0.878   214   0.808  9778   0.877  0.975
  0.1028 10004   0.870   221   0.770 10225   0.868  0.975
  0.1126 10543   0.871   225   0.811 10768   0.869  0.975
  0.1224 10902   0.861   219   0.820 11121   0.860  0.975
  0.1322 11468   0.862   224   0.812 11692   0.861  0.975
  0.1420 11775   0.867   224   0.771 11999   0.865  0.976
  0.1518 12238   0.867   225   0.763 12463   0.865  0.976
  0.1615 12666   0.869   219   0.779 12885   0.868  0.976
  0.1713 12525   0.870   173   0.792 12698   0.869  0.976
  0.1811 11789   0.872   136   0.777 11925   0.871  0.976
  0.1909 11084   0.875   121   0.834 11205   0.874  0.976
 $$
Resolution limits                    =    103.142     2.260
Number of used reflections           =     184125
Percentage observed                  =    97.2531
Percentage of free reflections       =     4.9937
Overall R factor                     =     0.1793
Free R factor                        =     0.1937
Overall weighted R factor            =     0.4432
Free weighted R factor               =     0.4542
Overall correlation coefficient      =     0.9693
Free correlation coefficient         =     0.9722
Cruickshanks DPI for coordinate error=     0.1302
DPI based on free R factor           =     0.1192
Overall figure of merit              =     0.8783
ML based su of positional parameters =     0.0733
ML based su of thermal parameters    =     2.8504
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A    206 VAL CA    - A    207 LEU CA    mod.= 122.20 id.= 180.00 per.= 1 dev=  57.80 sig.=   5.00
 

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /tmp/ccp4/mao_62_3_mtz_1.tmp 

 
 
 special position -----------   2.948070    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                 12501     0.012     0.022
Bond angles  : refined atoms                  16950     1.394     1.968
Torsion angles, period  1. refined             1541     6.516     5.000
Torsion angles, period  2. refined              566    39.893    24.912
Torsion angles, period  3. refined             2228    20.258    15.000
Torsion angles, period  4. refined               67    17.856    15.000
Chiral centres: refined atoms                  1925     0.102     0.200
Planar groups: refined atoms                   9353     0.005     0.020
VDW repulsions: refined atoms                  6469     0.305     0.200
VDW; torsion: refined atoms                    8382     0.312     0.200
HBOND: refined atoms                            514     0.232     0.200
VDW repulsions; symmetry: refined atoms          16     0.417     0.200
M. chain bond B values: refined atoms          7881     0.693     1.500
M. chain angle B values: refined atoms        12565     1.154     2.000
S. chain bond B values: refined atoms          5119     2.033     3.000
S. chain angle B values: refined atoms         4385     3.070     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.333, B  =  -0.009
Partial structure    1: scale =   -0.007, B  =  89.098
Overall anisotropic scale factors
   B11 = -0.02 B22 =  0.00 B33 =  0.02 B12 =  0.00 B13 =  0.01 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.005    2205  98.77  3709.1  3665.2  0.12  0.30     121  4034.6  4015.6  0.11  0.29
 0.015    3952  99.90  1886.4  1851.5  0.20  0.62     197  1962.2  1870.2  0.21  0.39
 0.025    5026  99.81  1540.0  1505.7  0.23  0.64     283  1527.3  1476.1  0.26  0.55
 0.034    5988  99.76  1559.6  1533.1  0.23  0.62     307  1586.6  1549.9  0.23  0.43
 0.044    6751  99.79  1484.6  1472.1  0.17  0.42     338  1513.1  1514.4  0.18  0.63
 0.054    7469  99.81  1282.9  1282.6  0.14  0.30     391  1315.9  1328.1  0.15  0.27
 0.064    8078  99.87  1084.8  1079.6  0.16  0.36     465  1069.7  1070.6  0.17  0.42
 0.073    8642  99.84   953.3   949.6  0.15  0.33     488   971.3   977.1  0.16  0.50
 0.083    9255  99.88   845.6   838.6  0.16  0.36     490   836.2   836.1  0.17  0.37
 0.093    9778  99.88   729.7   722.5  0.16  0.36     515   754.3   737.6  0.18  0.41
 0.103   10225  99.86   646.7   640.2  0.17  0.37     547   643.1   636.2  0.19  0.37
 0.113   10768  99.83   582.9   575.8  0.18  0.42     538   579.1   581.1  0.20  0.49
 0.122   11121  99.86   522.6   513.8  0.19  0.47     607   542.8   533.1  0.20  0.46
 0.132   11692  99.85   477.5   471.0  0.19  0.46     607   464.9   457.3  0.23  0.42
 0.142   11999  99.83   443.0   434.8  0.19  0.47     621   444.3   432.2  0.22  0.54
 0.152   12463  99.79   409.2   399.0  0.19  0.44     655   424.8   414.6  0.22  0.53
 0.162   12885  99.78   374.7   365.7  0.20  0.52     632   374.8   369.5  0.22  0.42
 0.171   12698  95.96   348.6   340.6  0.20  0.57     686   345.4   330.8  0.24  0.50
 0.181   11926  87.78   324.1   315.4  0.21  0.65     590   325.4   315.1  0.24  0.57
 0.191   11204  80.39   302.4   291.9  0.21  0.59     600   294.9   288.7  0.26  0.78
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle   11. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0050  1990   0.958   215   0.894  2205   0.952  0.974
  0.0148  3730   0.912   222   0.856  3952   0.909  0.974
  0.0246  4815   0.896   211   0.844  5026   0.894  0.975
  0.0343  5762   0.912   226   0.831  5988   0.909  0.975
  0.0441  6529   0.916   222   0.872  6751   0.914  0.975
  0.0539  7245   0.912   224   0.821  7469   0.909  0.975
  0.0637  7857   0.901   221   0.801  8078   0.898  0.975
  0.0735  8417   0.892   224   0.820  8641   0.890  0.975
  0.0833  9031   0.886   225   0.841  9256   0.885  0.975
  0.0930  9564   0.879   214   0.809  9778   0.877  0.976
  0.1028 10004   0.870   221   0.770 10225   0.868  0.976
  0.1126 10543   0.871   225   0.811 10768   0.870  0.976
  0.1224 10902   0.861   219   0.820 11121   0.860  0.976
  0.1322 11468   0.862   224   0.813 11692   0.861  0.976
  0.1420 11775   0.867   224   0.771 11999   0.865  0.976
  0.1518 12238   0.867   225   0.763 12463   0.865  0.976
  0.1615 12666   0.869   219   0.779 12885   0.868  0.977
  0.1713 12525   0.870   173   0.792 12698   0.869  0.977
  0.1811 11789   0.872   136   0.778 11925   0.871  0.977
  0.1909 11084   0.875   121   0.834 11205   0.874  0.977
 $$
Resolution limits                    =    103.142     2.260
Number of used reflections           =     184125
Percentage observed                  =    97.2531
Percentage of free reflections       =     4.9937
Overall R factor                     =     0.1792
Free R factor                        =     0.1936
Overall weighted R factor            =     0.4429
Free weighted R factor               =     0.4538
Overall correlation coefficient      =     0.9693
Free correlation coefficient         =     0.9722
Cruickshanks DPI for coordinate error=     0.1302
DPI based on free R factor           =     0.1192
Overall figure of merit              =     0.8785
ML based su of positional parameters =     0.0733
ML based su of thermal parameters    =     2.8504
-----------------------------------------------------------------------------
  Time in seconds: CPU =       377.35
             Elapsed =         380.00
 
    **** Things for loggraph, R factor and others vs cycle  ****
 
 
$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LLG vs cycle :N:1,5:
:Geometry vs cycle:N:1,6,7,8:
$$
      Ncyc   Rfact   Rfree     FOM         LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
$$
         0   0.181   0.195    0.876     1234483.4    0.012    1.386    0.103
         1   0.180   0.194    0.877     1233018.5    0.012    1.385    0.100
         2   0.180   0.194    0.877     1232907.0    0.012    1.386    0.100
         3   0.180   0.194    0.878     1232713.8    0.012    1.388    0.100
         4   0.180   0.194    0.878     1232577.4    0.012    1.390    0.100
         5   0.180   0.194    0.878     1232501.4    0.012    1.391    0.101
         6   0.180   0.194    0.878     1232398.8    0.012    1.392    0.101
         7   0.179   0.194    0.878     1232350.4    0.012    1.393    0.101
         8   0.179   0.194    0.878     1232268.9    0.012    1.394    0.101
         9   0.179   0.194    0.878     1232157.4    0.012    1.394    0.102
        10   0.179   0.194    0.878     1232070.1    0.012    1.394    0.102
 $$

 Refmac_5.3.0037:  End of Refmac_5.3.0037
Times: User:     391.5s System:   13.5s Elapsed:     6:48  
*************************************************************************** * Information from CCP4Interface script *************************************************************************** Writing final coordinates (XYZOUT) to /y/work/ccp4/2hr0_refmac1.pdb *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Writing final phases (HKLOUT) to /y/work/ccp4/2hr0sf_refmac1.mtz *************************************************************************** #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 15 Aug 2007 12:53:59 #CCP4I TERMINATION OUTPUT_FILES /y/people/ccp4/projects/mao/mao_62_2hr0.refmac.cif mao #CCP4I MESSAGE Task completed successfully