#CCP4I VERSION CCP4Interface 1.5.3 #CCP4I SCRIPT LOG refmac5 #CCP4I DATE 06 Feb 2008 14:00:14 #CCP4I USER ccp4 #CCP4I PROJECT buccaneer #CCP4I JOB_ID 286 #CCP4I SCRATCH /tmp/ccp4 #CCP4I HOSTNAME dragon.chem.york.ac.uk #CCP4I PID 19417 
 
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 ### CCP4 6.0: Refmac_5.4.0065    version 5.4.0065  : 12/02/07##
 ###############################################################
 User: ccp4  Run date:  6/ 2/2008 Run time: 14:00:21 


 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
 Data line ---> 
 make     hydrogen YES     hout NO     peptide NO     cispeptide YES     ssbridg
 e YES     symmetry YES     sugar YES     connectivity NO     link NO
 Data line ---> refi     type REST     resi MLKF     meth CGMAT     bref ISOT
 Data line ---> ncyc 10
 Data line ---> blim 2.0 200.0
 Data line ---> 
 scal     type SIMP     reso 2.193 60.412     LSSC     ANISO     EXPE
 Data line ---> solvent YES     VDWProb 1.2     IONProb 0.8     RSHRink 0.8
 Data line ---> weight     AUTO
 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
 Data line ---> labin  FP=F_ip SIGFP=SIGF_ip    FREE=FreeR_flag
 Data line ---> 
 labout  FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM
 Data line ---> PNAME gp2
 Data line ---> DNAME fsfsfs
 Data line ---> RSIZE 80
 Data line ---> END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /y/people/ccp4/projects/buccaneer/oleg/v1.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/people/ccp4/projects/buccaneer/oleg/v1-phic_pirate1_buccaneer3a-coot-3.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /tmp/ccp4/buccaneer_286_2_pdb_1.tmp
Input reflection file.  Logical name - HKLIN actual file name  - /y/people/ccp4/projects/buccaneer/oleg/v1.mtz
Output reflection file. Logical name - HKLOUT actual file name - /tmp/ccp4/buccaneer_286_3_mtz_1.tmp
 
Cell from mtz :    69.795    69.795    72.458    90.000    90.000   120.000
Space group from mtz: number -  154; name - P 32 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
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens in input coordinate file will be kept
    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       0.0104
  Refinement of individual isotropic Bfactors
  Refinement resln        :    60.4122  2.1931
  Estimated number of reflections :      16247
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  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:    60.4120  2.1930
 
  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)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**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/people/ccp4/projects/buccaneer/oleg/v1-phic_pirate1_buccaneer3a
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      4.13
 _lib_update       18/01/08
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          :  2436
                with complete description    :   455
  NUMBER OF MODIFICATIONS                    :    47
  NUMBER OF LINKS                            :    64
  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    :    1519
  Number of residues :     191
  Number of chains   :       2
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : CIS peptide bond is found, angle =      2.35
            ch:AA   res: 174  ASP      --> 175  LYS
  --------------------------------
  --- title of input coord file ---
 
  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-9-
  --------------------------------
  ATTENTION: atom:CB   UNK       206  AA   is missing in the structure
  ATTENTION: atom:O    TRP       211  AA   is missing in the structure
  Number of chains                  :       2
  Total number of monomers          :     191
  Number of atoms                   :    1521
  Number of missing atoms           :       2
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
 
  Number of bonds restraints    :    1514
  Number of angles restraints   :    2042
  Number of torsions restraints :    1036
  Number of chiralities         :     216
  Number of planar groups       :     271
 
 
 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
 
 
 We are here
 Bonds before and after        1514        1514
 Angles before and after        2042        2042
 Chirals before and after         216         216
 planes before and after         271         271
 Torsions before and after        1036        1036
 Number of reflections in file      10792
 Number of reflection read          10714
 
 
     CGMAT cycle number =      1
 Starting restraints
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
A    170 ASP C   . - A    171 TYR N   . mod.= 0.927 id.= 1.329 dev=  0.402 sig.= 0.014
A    171 TYR C   . - A    171 TYR O   . mod.= 0.000 id.= 1.231 dev=  1.231 sig.= 0.020
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A     28 PRO CB    - A     28 PRO C     mod.=  89.41 id.= 110.10 dev= 20.687 sig.=  1.900
A     74 LYS N     - A     74 LYS CB    mod.=  86.77 id.= 110.50 dev= 23.729 sig.=  1.700
A    171 TYR CA    - A    171 TYR O     mod.=  90.00 id.= 120.80 dev= 30.800 sig.=  1.700
A    171 TYR O     - A    172 GLN N     mod.=  90.00 id.= 123.00 dev= 33.000 sig.=  1.600
A    171 TYR CA    - A    172 GLN N     mod.=  93.31 id.= 116.20 dev= 22.890 sig.=  2.000
A    182 ARG CB    - A    182 ARG C     mod.=  84.34 id.= 110.10 dev= 25.757 sig.=  1.900
A    183 LEU N     - A    183 LEU CB    mod.=  90.62 id.= 110.50 dev= 19.875 sig.=  1.700
A    200 ARG CB    - A    200 ARG C     mod.=  83.67 id.= 110.10 dev= 26.434 sig.=  1.900
A    201 ASP N     - A    201 ASP CB    mod.= 137.55 id.= 110.50 dev=-27.045 sig.=  1.700
 
    ****               Chiral volume outliers               ****
 
Chiral volume deviations from the ideal >10.000Sigma will be monitored
 
A     29 PHE CA    mod.=  -0.29 id.=  -2.50 dev= -2.215 sig.=  0.200
A     49 ASN CA    mod.=   2.19 id.=  -2.47 dev= -4.656 sig.=  0.200
 
    ****                  B-value outliers                  ****
 
B-value differences >  10.00Sigma will be monitored
A    171 TYR N     - A    170 ASP CA       ABS(DELTA)= 28.320   Sigma=  2.000
A    171 TYR N     - A    170 ASP C        ABS(DELTA)= 29.880   Sigma=  1.500
A    171 TYR CA    - A    170 ASP C        ABS(DELTA)= 29.880   Sigma=  2.000
A    171 TYR N     - A    170 ASP O        ABS(DELTA)= 29.860   Sigma=  2.000
A    172 GLN O     - A    172 GLN CA       ABS(DELTA)= 44.240   Sigma=  2.000
A    173 THR N     - A    172 GLN CA       ABS(DELTA)= 47.360   Sigma=  2.000
A    172 GLN O     - A    172 GLN C        ABS(DELTA)= 44.240   Sigma=  1.500
A    173 THR N     - A    172 GLN C        ABS(DELTA)= 47.360   Sigma=  1.500
A    173 THR CA    - A    172 GLN C        ABS(DELTA)= 49.750   Sigma=  2.000
 
 weigth matrix   2.2369964E-04
 
 
 Before reporting
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.038     0.022
Bond angles  : refined atoms                   2042     2.814     1.954
Torsion angles, period  1. refined              179     9.251     5.000
Torsion angles, period  2. refined               84    39.204    23.810
Torsion angles, period  3. refined              268    19.726    15.000
Torsion angles, period  4. refined               16    16.242    15.000
Chiral centres: refined atoms                   216     0.407     0.200
Planar groups: refined atoms                   1171     0.007     0.021
VDW repulsions: refined_atoms                   684     0.288     0.200
VDW; torsion: refined_atoms                    1013     0.332     0.200
HBOND: refined_atoms                             37     0.254     0.200
VDW repulsions: symmetry: refined_atoms          53     0.377     0.200
HBOND: symmetry: refined_atoms                    5     0.351     0.200
M. chain bond B values: refined atoms           903     2.588     1.500
M. chain angle B values: refined atoms         1459     3.090     2.000
S. chain bond B values: refined atoms           611     2.368     3.000
S. chain angle B values: refined atoms          583     3.525     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.786, B  =   3.320
Partial structure    1: scale =    0.349, B  =  23.054
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.005     134  92.76   413.5   389.7  0.27  0.50       7   447.0   330.0  0.37  0.38
 0.016     230 100.00   349.4   342.9  0.25  0.40      10   384.9   342.1  0.17  0.21
 0.026     291 100.00   252.1   250.7  0.31  0.43      10   225.4   213.6  0.49  0.80
 0.036     336  99.72   273.1   274.3  0.27  0.36      15   272.6   247.3  0.38  0.64
 0.047     365 100.00   303.0   285.9  0.23  0.30      18   305.0   247.6  0.35  0.41
 0.057     414 100.00   292.2   266.6  0.25  0.33      13   414.7   363.7  0.24  0.42
 0.067     451 100.00   251.6   230.4  0.25  0.30      25   275.0   227.5  0.35  0.45
 0.078     470 100.00   210.1   183.2  0.28  0.35      19   178.1   138.0  0.41  0.49
 0.088     494 100.00   164.2   150.8  0.31  0.36      28   180.7   179.8  0.35  0.41
 0.098     536 100.00   130.2   122.3  0.33  0.38      31   136.2   103.9  0.40  0.46
 0.109     537 100.00   114.5   105.5  0.32  0.36      29   109.8    86.1  0.38  0.39
 0.119     581  99.84    86.6    84.3  0.35  0.37      33    87.9    92.5  0.49  0.50
 0.129     600 100.00    75.5    72.9  0.36  0.36      24    78.9    73.9  0.49  0.49
 0.139     616  99.69    61.9    61.2  0.37  0.35      37    51.2    59.0  0.59  0.54
 0.150     636  99.26    54.9    54.5  0.34  0.34      34    50.7    57.6  0.45  0.41
 0.160     641  98.53    49.5    50.1  0.34  0.32      31    48.6    49.8  0.44  0.39
 0.170     654  96.67    43.0    43.7  0.36  0.32      42    45.7    53.0  0.48  0.42
 0.181     669  92.38    39.3    39.2  0.34  0.31      22    34.1    38.0  0.44  0.38
 0.191     636  90.65    33.4    34.0  0.37  0.33      33    31.6    30.0  0.50  0.47
 0.201     627  84.12    31.4    31.1  0.34  0.29      30    35.1    37.4  0.33  0.24
$$
 
    ****            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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0054    78   0.682    56   0.525   134   0.616  0.980
  0.0157   163   0.692    67   0.496   230   0.635  0.970
  0.0260   224   0.560    67   0.564   291   0.561  0.959
  0.0364   267   0.703    69   0.548   336   0.671  0.948
  0.0467   301   0.753    64   0.716   365   0.747  0.937
  0.0570   348   0.767    66   0.690   414   0.755  0.926
  0.0673   383   0.772    68   0.733   451   0.766  0.915
  0.0776   403   0.727    67   0.622   470   0.712  0.905
  0.0879   434   0.708    60   0.666   494   0.703  0.894
  0.0982   463   0.700    73   0.518   536   0.675  0.884
  0.1085   472   0.693    65   0.557   537   0.677  0.874
  0.1188   511   0.636    70   0.598   581   0.631  0.864
  0.1292   535   0.642    65   0.538   600   0.630  0.854
  0.1395   559   0.608    57   0.507   616   0.599  0.844
  0.1498   569   0.621    67   0.544   636   0.613  0.834
  0.1601   578   0.638    63   0.601   641   0.634  0.825
  0.1704   603   0.637    51   0.612   654   0.635  0.816
  0.1807   625   0.671    44   0.604   669   0.666  0.806
  0.1910   592   0.665    44   0.611   636   0.661  0.797
  0.2013   589   0.702    38   0.689   627   0.701  0.788
 $$
Resolution limits                    =     60.412     2.201
Number of used reflections           =       9918
Percentage observed                  =    97.1623
Percentage of free reflections       =     4.7171
Overall R factor                     =     0.2920
Free R factor                        =     0.3766
Overall weighted R factor            =     0.3475
Free weighted R factor               =     0.4525
Overall correlation coefficient      =     0.9112
Free correlation coefficient         =     0.8639
Cruickshanks DPI for coordinate error=     0.4046
DPI based on free R factor           =     0.3296
Overall figure of merit              =     0.6641
ML based su of positional parameters =     0.2870
ML based su of thermal parameters    =    10.9532
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Trying gamma equal   5.0000001E-02
 Gamma decreased to   3.9999999E-02
 average, maximum and rms   4.9283175E-04  0.3419545      3.7318300E-02
 average, maximum and rms B shifts    2.658017       20.56914       2.108098    
 
 
     CGMAT cycle number =      2
 Starting restraints
 
 weigth matrix   5.1245122E-04
 
 
 Before reporting
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.036     0.022
Bond angles  : refined atoms                   2042     2.001     1.954
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.789, B  =   0.288
Partial structure    1: scale =    0.351, B  =  26.836
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2807
Free R factor                        =     0.3642
Overall figure of merit              =     0.6837
-----------------------------------------------------------------------------
 Trying gamma equal   3.9999999E-02
 Gamma decreased to   3.0909089E-02
 average, maximum and rms  -2.8158716E-04  0.2924476      2.0419937E-02
 average, maximum and rms B shifts   0.1588902       10.96816       1.107507    
 
 
     CGMAT cycle number =      3
 Starting restraints
 
 weigth matrix   4.5648916E-04
 
 
 Before reporting
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.036     0.022
Bond angles  : refined atoms                   2042     1.921     1.954
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.790, B  =  -0.030
Partial structure    1: scale =    0.350, B  =  27.055
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2761
Free R factor                        =     0.3589
Overall figure of merit              =     0.6927
-----------------------------------------------------------------------------
 Trying gamma equal   3.0909089E-02
 Gamma decreased to   2.2644626E-02
 average, maximum and rms  -4.0951351E-04  0.2375915      1.5768522E-02
 average, maximum and rms B shifts  -3.8357090E-02   9.031544      0.8933601    
 
 
     CGMAT cycle number =      4
 Starting restraints
 
 weigth matrix   5.9690105E-04
 
 
 Before reporting
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.036     0.022
Bond angles  : refined atoms                   2042     1.911     1.954
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.789, B  =  -0.158
Partial structure    1: scale =    0.350, B  =  27.634
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2741
Free R factor                        =     0.3560
Overall figure of merit              =     0.6986
-----------------------------------------------------------------------------
 Trying gamma equal   2.2644626E-02
 Gamma decreased to   1.5131478E-02
 average, maximum and rms  -5.5713055E-04  0.1857136      1.4150417E-02
 average, maximum and rms B shifts  -0.1234790       6.658434      0.6994349    
 
 
     CGMAT cycle number =      5
 Starting restraints
 
 weigth matrix   8.0769148E-04
 
 
 Before reporting
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.036     0.022
Bond angles  : refined atoms                   2042     1.908     1.954
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.788, B  =  -0.102
Partial structure    1: scale =    0.349, B  =  27.647
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2730
Free R factor                        =     0.3543
Overall figure of merit              =     0.7012
-----------------------------------------------------------------------------
 Trying gamma equal   1.5131478E-02
 Gamma decreased to   8.3013438E-03
 average, maximum and rms  -6.5700186E-04  0.1836041      1.3638957E-02
 average, maximum and rms B shifts  -7.8261055E-02   5.588721      0.5268544    
 
 
     CGMAT cycle number =      6
 Starting restraints
 
 weigth matrix   1.5111472E-03
 
 
 Before reporting
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.036     0.022
Bond angles  : refined atoms                   2042     1.897     1.954
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.788, B  =  -0.089
Partial structure    1: scale =    0.349, B  =  27.930
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2722
Free R factor                        =     0.3540
Overall figure of merit              =     0.7060
-----------------------------------------------------------------------------
 Trying gamma equal   8.3013438E-03
 Gamma decreased to   2.0921309E-03
 average, maximum and rms  -7.1817444E-04  0.2031246      1.3585337E-02
 average, maximum and rms B shifts  -3.1476162E-02   3.818484      0.3863178    
 
 
     CGMAT cycle number =      7
 Starting restraints
 
 weigth matrix   5.8069970E-03
 
 
 Before reporting
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.036     0.022
Bond angles  : refined atoms                   2042     1.900     1.954
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.788, B  =  -0.062
Partial structure    1: scale =    0.349, B  =  27.874
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2717
Free R factor                        =     0.3541
Overall figure of merit              =     0.7069
-----------------------------------------------------------------------------
 Trying gamma equal   2.0921309E-03
 Gamma decreased to   0.0000000E+00
 average, maximum and rms  -7.5822714E-04  0.2308955      1.3668665E-02
 average, maximum and rms B shifts  -2.2930350E-02   2.567143      0.2701696    
 
 
     CGMAT cycle number =      8
 Starting restraints
 
 weigth matrix   0.1138975    
 
 
 Before reporting
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.035     0.022
Bond angles  : refined atoms                   2042     1.888     1.954
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.788, B  =  -0.024
Partial structure    1: scale =    0.349, B  =  27.873
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2711
Free R factor                        =     0.3549
Overall figure of merit              =     0.7102
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Gamma decreased to   0.0000000E+00
 average, maximum and rms  -5.6689919E-04  0.5951940      2.0209249E-02
 average, maximum and rms B shifts   2.7340256E-02   1.562113      0.2008526    
 
 
     CGMAT cycle number =      9
 Starting restraints
 
 weigth matrix   0.1239944    
 
 
 Before reporting
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.019     0.022
Bond angles  : refined atoms                   2042     1.965     1.954
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.789, B  =  -0.041
Partial structure    1: scale =    0.349, B  =  28.129
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2710
Free R factor                        =     0.3548
Overall figure of merit              =     0.7114
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Gamma decreased to   0.0000000E+00
 average, maximum and rms  -7.3918171E-04  0.3196759      1.4909632E-02
 average, maximum and rms B shifts  -6.7073233E-02   1.427452      0.1570524    
 
 
     CGMAT cycle number =     10
 Starting restraints
 
 weigth matrix   0.1263151    
 
 
 Before reporting
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.018     0.022
Bond angles  : refined atoms                   2042     1.871     1.954
Torsion angles, period  1. refined              179     8.494     5.000
Torsion angles, period  2. refined               84    40.503    23.810
Torsion angles, period  3. refined              268    19.979    15.000
Torsion angles, period  4. refined               16    16.068    15.000
Chiral centres: refined atoms                   216     0.131     0.200
Planar groups: refined atoms                   1171     0.010     0.021
VDW repulsions: refined_atoms                   668     0.247     0.200
VDW; torsion: refined_atoms                    1007     0.321     0.200
HBOND: refined_atoms                             37     0.185     0.200
VDW repulsions: symmetry: refined_atoms          59     0.200     0.200
HBOND: symmetry: refined_atoms                    5     0.341     0.200
M. chain bond B values: refined atoms           903     1.072     1.500
M. chain angle B values: refined atoms         1459     1.891     2.000
S. chain bond B values: refined atoms           611     2.654     3.000
S. chain angle B values: refined atoms          583     3.973     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.790, B  =   0.035
Partial structure    1: scale =    0.348, B  =  27.807
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.005     134  92.76   411.4   387.7  0.26  0.49       7   444.8   311.8  0.39  0.37
 0.016     230 100.00   347.6   343.7  0.25  0.41      10   383.0   372.1  0.16  0.26
 0.026     291 100.00   250.8   248.8  0.31  0.42      10   224.3   215.5  0.44  0.72
 0.036     336  99.72   271.7   269.4  0.25  0.33      15   271.3   257.3  0.35  0.59
 0.047     365 100.00   301.5   283.3  0.22  0.28      18   303.5   243.7  0.39  0.47
 0.057     414 100.00   290.7   268.2  0.23  0.31      13   412.6   357.9  0.29  0.46
 0.067     451 100.00   250.3   230.7  0.23  0.29      25   273.7   220.4  0.32  0.46
 0.078     470 100.00   209.1   186.7  0.27  0.33      19   177.2   138.3  0.37  0.47
 0.088     494 100.00   163.4   150.0  0.29  0.34      28   179.8   181.7  0.37  0.40
 0.098     536 100.00   129.6   124.0  0.31  0.35      31   135.5   107.4  0.36  0.41
 0.109     537 100.00   113.9   107.4  0.30  0.33      29   109.2    90.1  0.35  0.35
 0.119     581  99.84    86.2    83.9  0.32  0.33      33    87.5    93.2  0.46  0.44
 0.129     600 100.00    75.1    73.9  0.33  0.33      24    78.5    77.5  0.42  0.43
 0.139     616  99.69    61.6    61.2  0.32  0.32      37    51.0    57.4  0.56  0.50
 0.150     636  99.26    54.6    55.4  0.30  0.30      34    50.4    56.2  0.41  0.37
 0.160     641  98.53    49.3    50.8  0.29  0.28      31    48.4    52.0  0.36  0.33
 0.170     654  96.67    42.7    44.1  0.30  0.27      42    45.4    49.8  0.36  0.32
 0.181     669  92.38    39.1    40.1  0.28  0.24      22    34.0    36.0  0.27  0.22
 0.191     636  90.65    33.2    33.5  0.29  0.25      33    31.5    29.2  0.42  0.40
 0.201     627  84.12    31.2    31.8  0.25  0.21      30    34.9    36.6  0.24  0.19
$$
 
    ****            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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0054    78   0.634    56   0.482   134   0.570  0.945
  0.0157   163   0.657    67   0.462   230   0.600  0.941
  0.0260   224   0.524    67   0.538   291   0.527  0.937
  0.0364   267   0.678    69   0.530   336   0.648  0.932
  0.0467   301   0.738    64   0.696   365   0.730  0.928
  0.0570   348   0.763    66   0.700   414   0.753  0.924
  0.0673   383   0.775    68   0.734   451   0.768  0.920
  0.0776   403   0.736    67   0.673   470   0.727  0.916
  0.0879   434   0.723    60   0.682   494   0.718  0.912
  0.0982   463   0.733    73   0.532   536   0.706  0.908
  0.1085   472   0.735    65   0.601   537   0.718  0.903
  0.1188   511   0.681    70   0.599   581   0.671  0.899
  0.1292   535   0.705    65   0.622   600   0.696  0.895
  0.1395   559   0.675    57   0.588   616   0.667  0.891
  0.1498   569   0.699    67   0.608   636   0.689  0.887
  0.1601   578   0.724    63   0.711   641   0.723  0.883
  0.1704   603   0.731    51   0.695   654   0.728  0.879
  0.1807   625   0.770    44   0.725   669   0.767  0.875
  0.1910   592   0.755    44   0.728   636   0.753  0.871
  0.2013   589   0.812    38   0.843   627   0.814  0.867
 $$
Resolution limits                    =     60.412     2.201
Number of used reflections           =       9918
Percentage observed                  =    97.1623
Percentage of free reflections       =     4.7171
Overall R factor                     =     0.2706
Free R factor                        =     0.3557
Overall weighted R factor            =     0.3181
Free weighted R factor               =     0.4151
Overall correlation coefficient      =     0.9205
Free correlation coefficient         =     0.8647
Cruickshanks DPI for coordinate error=     0.3749
DPI based on free R factor           =     0.3113
Overall figure of merit              =     0.7128
ML based su of positional parameters =     0.2224
ML based su of thermal parameters    =     8.2325
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Gamma decreased to   0.0000000E+00
 average, maximum and rms  -7.0030265E-04  0.3393906      1.3038892E-02
 average, maximum and rms B shifts   5.3676289E-02   1.224760      0.1411436    
 Starting restraints
 

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /tmp/ccp4/buccaneer_286_3_mtz_1.tmp 

 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1514     0.018     0.022
Bond angles  : refined atoms                   2042     1.855     1.954
Torsion angles, period  1. refined              179     8.482     5.000
Torsion angles, period  2. refined               84    40.479    23.810
Torsion angles, period  3. refined              268    20.052    15.000
Torsion angles, period  4. refined               16    16.374    15.000
Chiral centres: refined atoms                   216     0.129     0.200
Planar groups: refined atoms                   1171     0.009     0.021
VDW repulsions: refined_atoms                   670     0.245     0.200
VDW; torsion: refined_atoms                    1007     0.322     0.200
HBOND: refined_atoms                             37     0.172     0.200
VDW repulsions: symmetry: refined_atoms          58     0.198     0.200
HBOND: symmetry: refined_atoms                    5     0.339     0.200
M. chain bond B values: refined atoms           903     1.076     1.500
M. chain angle B values: refined atoms         1459     1.895     2.000
S. chain bond B values: refined atoms           611     2.670     3.000
S. chain angle B values: refined atoms          583     3.993     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.790, B  =  -0.016
Partial structure    1: scale =    0.349, B  =  27.654
Overall anisotropic scale factors
   B11 =  1.10 B22 =  1.10 B33 = -1.65 B12 =  0.55 B13 =  0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.005     134  92.76   411.3   388.1  0.26  0.49       7   444.6   314.3  0.38  0.36
 0.016     230 100.00   347.5   343.5  0.25  0.40      10   382.8   371.4  0.16  0.26
 0.026     291 100.00   250.7   248.9  0.31  0.42      10   224.2   213.6  0.43  0.70
 0.036     336  99.72   271.6   268.9  0.25  0.33      15   271.2   258.4  0.36  0.59
 0.047     365 100.00   301.4   283.3  0.22  0.28      18   303.4   243.2  0.40  0.48
 0.057     414 100.00   290.6   268.2  0.23  0.31      13   412.4   357.9  0.29  0.47
 0.067     451 100.00   250.2   230.5  0.23  0.29      25   273.6   219.3  0.33  0.47
 0.078     470 100.00   209.0   186.9  0.27  0.33      19   177.1   138.5  0.38  0.47
 0.088     494 100.00   163.3   150.0  0.29  0.34      28   179.7   180.9  0.37  0.41
 0.098     536 100.00   129.5   124.1  0.31  0.35      31   135.5   107.8  0.36  0.41
 0.109     537 100.00   113.9   107.5  0.30  0.33      29   109.2    89.7  0.35  0.35
 0.119     581  99.84    86.1    83.9  0.32  0.33      33    87.5    93.4  0.45  0.44
 0.129     600 100.00    75.1    73.9  0.33  0.33      24    78.5    77.4  0.42  0.44
 0.139     616  99.69    61.6    61.2  0.32  0.32      37    51.0    57.4  0.57  0.50
 0.150     636  99.26    54.6    55.4  0.30  0.29      34    50.4    56.2  0.40  0.36
 0.160     641  98.53    49.3    50.7  0.29  0.28      31    48.3    51.8  0.35  0.32
 0.170     654  96.67    42.7    44.1  0.30  0.27      42    45.4    49.5  0.36  0.32
 0.181     669  92.38    39.1    40.0  0.27  0.24      22    34.0    36.0  0.26  0.21
 0.191     636  90.65    33.2    33.5  0.28  0.25      33    31.5    29.3  0.41  0.38
 0.201     627  84.12    31.2    31.8  0.25  0.21      30    34.9    36.5  0.24  0.20
$$
 
    ****            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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0054    78   0.631    56   0.480   134   0.568  0.943
  0.0157   163   0.655    67   0.459   230   0.598  0.939
  0.0260   224   0.522    67   0.536   291   0.525  0.935
  0.0364   267   0.676    69   0.527   336   0.645  0.931
  0.0467   301   0.736    64   0.697   365   0.729  0.927
  0.0570   348   0.763    66   0.700   414   0.753  0.924
  0.0673   383   0.774    68   0.731   451   0.767  0.920
  0.0776   403   0.736    67   0.674   470   0.727  0.916
  0.0879   434   0.724    60   0.683   494   0.719  0.912
  0.0982   463   0.734    73   0.535   536   0.707  0.908
  0.1085   472   0.735    65   0.603   537   0.719  0.904
  0.1188   511   0.682    70   0.601   581   0.673  0.901
  0.1292   535   0.706    65   0.624   600   0.697  0.897
  0.1395   559   0.677    57   0.591   616   0.669  0.893
  0.1498   569   0.701    67   0.609   636   0.692  0.889
  0.1601   578   0.726    63   0.715   641   0.725  0.886
  0.1704   603   0.734    51   0.700   654   0.731  0.882
  0.1807   625   0.773    44   0.727   669   0.770  0.878
  0.1910   592   0.758    44   0.730   636   0.756  0.875
  0.2013   589   0.815    38   0.847   627   0.817  0.871
 $$
Resolution limits                    =     60.412     2.201
Number of used reflections           =       9918
Percentage observed                  =    97.1623
Percentage of free reflections       =     4.7171
Overall R factor                     =     0.2701
Free R factor                        =     0.3563
Overall weighted R factor            =     0.3174
Free weighted R factor               =     0.4152
Overall correlation coefficient      =     0.9208
Free correlation coefficient         =     0.8643
Cruickshanks DPI for coordinate error=     0.3741
DPI based on free R factor           =     0.3118
Overall figure of merit              =     0.7139
ML based su of positional parameters =     0.2224
ML based su of thermal parameters    =     8.2325
-----------------------------------------------------------------------------
  Time in seconds: CPU =        20.67
             Elapsed =          20.00
 
    **** 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:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2920   0.3766   0.664     49212.    2491.6   0.0380  1.916   2.814  1.406   0.407
       1   0.2807   0.3642   0.684     48766.    2476.6   0.0357  1.736   2.001  0.925   0.281
       2   0.2761   0.3589   0.693     48589.    2470.4   0.0358  1.732   1.921  0.875   0.237
       3   0.2741   0.3560   0.699     48507.    2466.9   0.0359  1.736   1.911  0.873   0.208
       4   0.2730   0.3543   0.701     48453.    2463.6   0.0360  1.739   1.908  0.875   0.185
       5   0.2722   0.3540   0.706     48413.    2461.9   0.0360  1.738   1.897  0.873   0.168
       6   0.2717   0.3541   0.707     48379.    2459.6   0.0362  1.743   1.900  0.876   0.157
       7   0.2711   0.3549   0.710     48338.    2457.9   0.0348  1.670   1.888  0.873   0.146
       8   0.2710   0.3548   0.711     48297.    2455.6   0.0193  0.840   1.965  0.934   0.137
       9   0.2706   0.3557   0.713     48269.    2454.3   0.0180  0.755   1.871  0.867   0.131
      10   0.2701   0.3563   0.714     48242.    2453.3   0.0180  0.757   1.855  0.857   0.129
 $$

 Refmac_5.4.0065:  End of Refmac_5.4.0065 
Times: User:      23.8s System:    1.4s Elapsed:     0:25
*************************************************************************** * Information from CCP4Interface script *************************************************************************** Writing final coordinates (XYZOUT) to /y/people/ccp4/projects/buccaneer/v1-phic_pirate1_buccaneer3a-coot-3_refmac1.pdb *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Writing final phases (HKLOUT) to /y/people/ccp4/projects/buccaneer/v1_refmac2.mtz *************************************************************************** #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 06 Feb 2008 14:00:47 #CCP4I TERMINATION OUTPUT_FILES /y/people/ccp4/projects/buccaneer/buccaneer_286_fsfsfs.refmac.cif buccaneer #CCP4I MESSAGE Task completed successfully