#CCP4I VERSION CCP4Interface 7.0.009
#CCP4I SCRIPT LOG refmac5
#CCP4I DATE 11 Apr 2016  10:22:02
#CCP4I USER andrey
#CCP4I PROJECT peru
#CCP4I JOB_ID 10
#CCP4I SCRATCH /tmp/andrey
#CCP4I HOSTNAME kaftino.local
#CCP4I PID 3632

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 ### CCP4 7.0.009: Refmac_5.8.0135 version 5.8.0135 : 01/10/15##
 ###############################################################
 User: andrey  Run date: 11/ 4/2016 Run time: 10:22:02 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

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

 $TEXT:Reference2: $$ Secondary reference $$ 
   "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

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make check NONE
  Data line--- 
 make     hydrogen ALL     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--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  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_FROMDIALS SIGFP=SIGF_FROMDIALS    FREE=FreeR_flag
  Data line--- 
 labout  FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM
  Data line--- NOHARVEST
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /Users/andrey/Desktop/Brazil/04_Piramide/combined_scaled_C2.mtz 


    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - /Users/andrey/Desktop/Brazil/04_Piramide/3alt_A_molrep2_shelxe4mr_soln1x_refmac7.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /Users/andrey/Desktop/Brazil/04_Piramide/combined_scaled_C2_refmac1.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /Users/andrey/Desktop/Brazil/04_Piramide/combined_scaled_C2.mtz
Output reflection file. Logical name - HKLOUT actual file name - /Users/andrey/Desktop/Brazil/04_Piramide/combined_scaled_C2_refmac1.mtz

Cell from mtz :    84.768    56.161    74.465    90.000   119.758    90.000
Space group from mtz: number -    5; name - C 1 2 1

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /Applications/Xtal70/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /Applications/Xtal70/ccp4-7.0/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 will be restored in their riding positions
    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


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed
 
  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0173
  Refinement of individual isotropic Bfactors
  Refinement resln        :    64.6456  1.7000
  Estimated number of reflections :      52360
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    64.6456  1.7000

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 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 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

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 :/Users/andrey/Desktop/Brazil/04_Piramide/3alt_A_molrep2_shelxe4mr_
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.44
 _lib_update       30/05/14
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 13409
                with complete description    : 13409
  NUMBER OF MODIFICATIONS                    :    63
  NUMBER OF LINKS                            :    73
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: ATOMSF, Filename: /Applications/Xtal70/ccp4-7.0/lib/data/atomsf.lib
<!--SUMMARY_END--></FONT></B>

  Number of atoms    :    1548
  Number of residues :     240
  Number of chains   :       3
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---
 
  PDB_code:xxxx
  PDB_name:----
  PDB_date:11-APR-16
  --------------------------------
  ATTENTION: atom:N    ALA                 1  BB   is missing in the structure
  ATTENTION: atom:CB   ALA                 1  BB   is missing in the structure
  ATTENTION: atom:CB   ALA                51  BB   is missing in the structure
  ATTENTION: atom:C    ALA                51  BB   is missing in the structure
  ATTENTION: atom:O    ALA                51  BB   is missing in the structure
  ATTENTION: atom:N    ALA                 1  CC   is missing in the structure
  ATTENTION: atom:CB   ALA                 1  CC   is missing in the structure
  ATTENTION: atom:CB   ALA                68  CC   is missing in the structure
  ATTENTION: atom:C    ALA                68  CC   is missing in the structure
  ATTENTION: atom:O    ALA                68  CC   is missing in the structure
  Number of chains                  :       3
  Total number of monomers          :     240
  Number of atoms                   :    3033
  Number of missing atoms           :       4
  Number of rebuilt atoms           :    1457
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0


 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
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   1.1842
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      3033         0      3033
               Angles:      5434         0      5434
              Chirals:       247         0       247
               Planes:       521         0       521
             Torsions:      1264         0      1264
            Intervals:         0         0         0
--------------------------------------------------------------------------------
 
 
  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------
 

    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections       1620
Number of   all  reflections      33541
--------------------------------------------------------------------------------
 Number of reflections in file      33541
 Number of reflections read          33541


######  TLS Group Definitions ######



     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   176  120  154
 Maximuum H,K,L                 :    50   34   44
 Minimum acceptable grid spacing:   116   77  102
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   176  120  154
 Maximuum H,K,L                 :    50   34   44
 Minimum acceptable grid spacing:   116   77  102
 Weight matrix   0.4032824    
 Actual weight    10.00000      is applied to the X-ray term
Norm of X_ray positional gradient                59.2
Norm of Geom. positional gradient                54.8
Norm of X_ray B-factor gradient                  159.
Norm of Geom. B-factor gradient                 0.191E+04
Product of X_ray and Geom posit. gradients     -0.102E+08
 Cosine of angle between them                      -0.350
Product of X_ray and Geom B-fact gradients     -0.194E+08
 Cosine of angle between them                      -0.021


Residuals: XRAY=     0.1704E+07 GEOM=     0.1456E+05 TOTAL=     0.1719E+07
 function value    1718918.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.020     0.019
Bond distances: others                         1434     0.000     0.020
Bond angles  : refined atoms                   2210     1.806     1.833
Bond angles  : others                          3224     4.321     3.000
Torsion angles, period  1. refined              236     8.433     5.000
Torsion angles, period  2. refined               42    35.825    21.905
Torsion angles, period  3. refined              117    11.744    15.000
Chiral centres: refined atoms                   247     0.135     0.200
Planar groups: refined atoms                   1976     0.009     0.020
Planar groups: others                           412     0.018     0.020
VDW repulsions: refined_atoms                   600     0.216     0.200
VDW repulsions.others                          2302     0.270     0.200
VDW; torsion: refined_atoms                    1466     0.182     0.200
VDW; torsion.others                            1322     0.111     0.200
HBOND: refined_atoms                             38     0.075     0.200
HBOND.others                                      2     0.050     0.200
VDW repulsions: symmetry: refined_atoms           2     0.139     0.200
VDW repulsions: symmetry: others                 17     0.142     0.200
HBOND: symmetry: refined_atoms                    1     0.043     0.200
M. chain bond B values: refined atoms           950     2.010     2.295
M. chain bond B values: others                  951     2.009     2.297
M. chain angle B values: refined atoms         1182     2.587     3.428
M. chain angle B values: others                1183     2.586     3.431
S. chain bond B values: refined atoms           649     2.449     2.185
S. chain bond B values: others                  650     2.447     2.189
S. chain angle B values: refined atoms         1028     2.842     3.289
S. chain angle B values: others                1029     2.841     3.292
Long range B values: refined atoms             1692     3.337    18.754
Long range B values: others                    1692     3.337    18.754
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.269, B  =  -1.437
Partial structure    1: scale =    0.429, B  =  56.619
Overall anisotropic scale factors
   B11 =  0.26 B22 = -2.03 B33 =  0.22 B12 =  0.00 B13 =  1.24 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle    1. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.009     396  99.76   484.7   486.1  0.38  0.43      19   445.1   531.9  0.33  0.40
 0.026     685 100.00   382.5   448.5  0.41  0.45      30   415.1   485.9  0.42  0.44
 0.043     868 100.00   502.2   514.8  0.29  0.33      35   548.2   565.2  0.30  0.34
 0.061    1015 100.00   552.5   488.4  0.29  0.31      52   578.8   477.0  0.34  0.35
 0.078    1099 100.00   487.1   392.1  0.34  0.35      93   496.3   391.1  0.36  0.39
 0.095    1259 100.00   398.0   331.1  0.35  0.35      77   409.8   322.8  0.38  0.38
 0.113    1359 100.00   326.3   289.2  0.33  0.33      74   322.0   309.0  0.32  0.33
 0.130    1462 100.00   267.1   248.8  0.32  0.32      92   294.5   281.4  0.33  0.33
 0.147    1543 100.00   239.3   230.3  0.31  0.30      83   230.9   210.8  0.31  0.31
 0.164    1674  99.94   216.8   208.8  0.31  0.30      78   209.1   189.3  0.33  0.31
 0.182    1707 100.00   202.1   192.4  0.31  0.30     108   196.6   198.4  0.36  0.34
 0.199    1830  99.95   192.2   176.9  0.32  0.30      77   190.8   169.5  0.29  0.29
 0.216    1893 100.00   182.5   164.0  0.30  0.29      97   174.1   155.4  0.31  0.30
 0.234    1947 100.00   165.1   148.1  0.29  0.27      81   155.6   139.2  0.31  0.28
 0.251    2000 100.00   146.6   133.8  0.30  0.28     109   161.3   147.7  0.27  0.26
 0.268    2162 100.00   130.1   122.9  0.28  0.26      78   118.6   115.7  0.34  0.31
 0.286    2153 100.00   115.1   110.1  0.29  0.27     117   113.9   101.1  0.29  0.27
 0.303    2242 100.00   104.6    98.2  0.30  0.28      88   108.4   104.4  0.28  0.26
 0.320    2273 100.00    90.9    86.2  0.32  0.30     125    83.5    84.2  0.34  0.31
 0.337    2350 100.00    83.6    79.5  0.33  0.32     107    80.7    68.5  0.36  0.34
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0089    323   0.764     73   0.562    396   0.727  0.697  0.8014  0.8490  0.8680  0.6592
  0.0262    614   0.639     71   0.586    685   0.633  0.669  0.7594  0.7855  0.5817  0.6609
  0.0435    796   0.772     72   0.633    868   0.760  0.860  0.8959  0.8772  0.8060  0.7802
  0.0608    940   0.746     75   0.610   1015   0.736  0.961  0.8347  0.8655  0.6624  0.7846
  0.0780   1033   0.724     66   0.639   1099   0.719  1.028  0.8370  0.8373  0.7211  0.7316
  0.0953   1193   0.700     66   0.571   1259   0.693  0.985  0.8034  0.8167  0.6562  0.6963
  0.1126   1288   0.710     71   0.645   1359   0.706  0.932  0.8271  0.8181  0.7137  0.7005
  0.1299   1390   0.723     72   0.509   1462   0.712  0.904  0.8351  0.8299  0.7328  0.7178
  0.1472   1469   0.776     73   0.633   1542   0.769  0.919  0.8426  0.8598  0.7054  0.7419
  0.1645   1602   0.771     72   0.546   1674   0.762  0.912  0.8503  0.8584  0.7552  0.7408
  0.1818   1630   0.742     77   0.606   1707   0.736  0.906  0.8217  0.8452  0.7220  0.7408
  0.1991   1760   0.758     70   0.658   1830   0.754  0.943  0.8502  0.8538  0.7737  0.7442
  0.2164   1819   0.791     74   0.722   1893   0.789  0.973  0.8652  0.8697  0.7468  0.7523
  0.2336   1878   0.798     69   0.694   1947   0.795  0.973  0.8654  0.8793  0.8061  0.7763
  0.2509   1928   0.770     73   0.671   2001   0.767  0.948  0.8824  0.8587  0.7957  0.7579
  0.2682   2084   0.764     77   0.706   2161   0.762  0.908  0.8371  0.8585  0.7990  0.7905
  0.2855   2084   0.762     69   0.607   2153   0.757  0.892  0.8400  0.8472  0.7407  0.7827
  0.3028   2171   0.746     72   0.674   2243   0.744  0.878  0.8466  0.8345  0.8109  0.7827
  0.3201   2198   0.722     74   0.662   2272   0.720  0.838  0.7989  0.8083  0.7030  0.7452
  0.3374   2278   0.649     73   0.500   2351   0.645  0.773  0.7010  0.7472  0.7151  0.7020
 $$
Resolution limits                    =     64.646     1.700
Number of used reflections           =      31916
Percentage observed                  =    99.9911
Percentage of free reflections       =     4.8306
Overall R factor                     =     0.3170
Free R factor                        =     0.3321
Average Fourier shell correlation    =     0.8390
AverageFree Fourier shell correlation=     0.8297
Overall weighted R factor            =     0.3171
Free weighted R factor               =     0.3334
Overall weighted R2 factor           =     0.3849
Free weighted R2 factor              =     0.3962
Average correlation coefficient      =     0.7465
Overall correlation coefficient      =     0.8478
Free correlation coefficient         =     0.8364
Cruickshanks DPI for coordinate error=     0.1344
DPI based on free R factor           =     0.1264
Overall figure of merit              =     0.7382
ML based su of positional parameters =     0.0969
ML based su of thermal parameters    =     2.8570
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Trying gamma equal   5.0000001E-02
 Gamma decreased to   3.9999999E-02


 fvalues    170798.2       14556.01       1708622.       1722538.    


     CGMAT cycle number =      2

 Weight matrix   0.3626472    
 Actual weight    10.00000      is applied to the X-ray term


 function value    1710537.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.023     0.019
Bond distances: others                         1434     0.008     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.265, B  =  -0.108
Partial structure    1: scale =    0.428, B  =  53.210
Overall anisotropic scale factors
   B11 =  0.28 B22 = -2.06 B33 =  0.21 B12 =  0.00 B13 =  1.26 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3123
Free R factor                        =     0.3409
Average Fourier shell correlation    =     0.8349
AverageFree Fourier shell correlation=     0.8183
Average correlation coefficient      =     0.7581
Overall figure of merit              =     0.7253
-----------------------------------------------------------------------------
 Trying gamma equal   3.9999999E-02
 Gamma decreased to   3.0909089E-02


 fvalues    170127.3       9227.613       1708391.       1710500.    


     CGMAT cycle number =      3

 Weight matrix   0.3110518    
 Actual weight    9.090909      is applied to the X-ray term


 function value    1555085.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.022     0.019
Bond distances: others                         1434     0.003     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.261, B  =  -0.235
Partial structure    1: scale =    0.429, B  =  49.329
Overall anisotropic scale factors
   B11 =  0.28 B22 = -2.08 B33 =  0.21 B12 =  0.00 B13 =  1.27 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3117
Free R factor                        =     0.3457
Average Fourier shell correlation    =     0.8314
AverageFree Fourier shell correlation=     0.8121
Average correlation coefficient      =     0.7597
Overall figure of merit              =     0.7180
-----------------------------------------------------------------------------
 Trying gamma equal   3.0909089E-02
 Gamma decreased to   2.2644628E-02


 fvalues    170208.3       7744.341       1554404.       1555093.    


     CGMAT cycle number =      4

 Weight matrix   0.2974449    
 Actual weight    9.090909      is applied to the X-ray term


 function value    1554650.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.020     0.019
Bond distances: others                         1434     0.003     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.261, B  =  -0.108
Partial structure    1: scale =    0.429, B  =  49.352
Overall anisotropic scale factors
   B11 =  0.28 B22 = -2.10 B33 =  0.21 B12 =  0.00 B13 =  1.28 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3120
Free R factor                        =     0.3483
Average Fourier shell correlation    =     0.8286
AverageFree Fourier shell correlation=     0.8080
Average correlation coefficient      =     0.7595
Overall figure of merit              =     0.7127
-----------------------------------------------------------------------------
 Trying gamma equal   2.2644628E-02
 Gamma decreased to   1.5131480E-02


 fvalues    170240.8       6994.313       1554409.       1554638.    


     CGMAT cycle number =      5

 Weight matrix   0.2923563    
 Actual weight    9.090909      is applied to the X-ray term


 function value    1555300.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.020     0.019
Bond distances: others                         1434     0.003     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.259, B  =  -0.189
Partial structure    1: scale =    0.429, B  =  49.551
Overall anisotropic scale factors
   B11 =  0.28 B22 = -2.09 B33 =  0.21 B12 =  0.00 B13 =  1.28 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3121
Free R factor                        =     0.3501
Average Fourier shell correlation    =     0.8274
AverageFree Fourier shell correlation=     0.8060
Average correlation coefficient      =     0.7593
Overall figure of merit              =     0.7104
-----------------------------------------------------------------------------
 Trying gamma equal   1.5131480E-02
 Gamma decreased to   8.3013456E-03


 fvalues    170343.3       6717.703       1555201.       1555294.    


     CGMAT cycle number =      6

 Weight matrix   0.2888786    
 Actual weight    9.090909      is applied to the X-ray term


 function value    1555699.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.019     0.019
Bond distances: others                         1434     0.003     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.258, B  =  -0.174
Partial structure    1: scale =    0.429, B  =  49.526
Overall anisotropic scale factors
   B11 =  0.28 B22 = -2.08 B33 =  0.20 B12 =  0.00 B13 =  1.28 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3122
Free R factor                        =     0.3512
Average Fourier shell correlation    =     0.8266
AverageFree Fourier shell correlation=     0.8045
Average correlation coefficient      =     0.7591
Overall figure of merit              =     0.7087
-----------------------------------------------------------------------------
 Trying gamma equal   8.3013456E-03
 Gamma decreased to   2.0921328E-03


 fvalues    170398.4       6609.375       1555632.       1555686.    


     CGMAT cycle number =      7

 Weight matrix   0.2850770    
 Actual weight    9.090909      is applied to the X-ray term


 function value    1555379.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.019     0.019
Bond distances: others                         1434     0.003     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.260, B  =  -0.113
Partial structure    1: scale =    0.429, B  =  49.328
Overall anisotropic scale factors
   B11 =  0.28 B22 = -2.08 B33 =  0.20 B12 =  0.00 B13 =  1.28 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3123
Free R factor                        =     0.3522
Average Fourier shell correlation    =     0.8257
AverageFree Fourier shell correlation=     0.8031
Average correlation coefficient      =     0.7591
Overall figure of merit              =     0.7071
-----------------------------------------------------------------------------
 Trying gamma equal   2.0921328E-03
 Gamma decreased to   9.9999997E-05


 fvalues    170372.0       6529.811       1555351.       1555366.    


     CGMAT cycle number =      8

 Weight matrix   0.2844366    
 Actual weight    9.090909      is applied to the X-ray term


 function value    1555882.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.019     0.019
Bond distances: others                         1434     0.004     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.259, B  =  -0.207
Partial structure    1: scale =    0.429, B  =  49.305
Overall anisotropic scale factors
   B11 =  0.28 B22 = -2.08 B33 =  0.20 B12 =  0.00 B13 =  1.28 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3124
Free R factor                        =     0.3531
Average Fourier shell correlation    =     0.8255
AverageFree Fourier shell correlation=     0.8025
Average correlation coefficient      =     0.7589
Overall figure of merit              =     0.7065
-----------------------------------------------------------------------------
 Trying gamma equal   9.9999997E-05
 Trying gamma equal   2.5757903E-02
 Gamma decreased to   2.0626321E-02


 fvalues    170433.5       6472.319       1555826.       1555868.    


     CGMAT cycle number =      9

 Weight matrix   0.2835051    
 Actual weight    9.090909      is applied to the X-ray term


 function value    1556307.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.019     0.019
Bond distances: others                         1434     0.003     0.020
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.257, B  =  -0.209
Partial structure    1: scale =    0.429, B  =  49.412
Overall anisotropic scale factors
   B11 =  0.28 B22 = -2.08 B33 =  0.20 B12 =  0.00 B13 =  1.28 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3124
Free R factor                        =     0.3536
Average Fourier shell correlation    =     0.8252
AverageFree Fourier shell correlation=     0.8020
Average correlation coefficient      =     0.7589
Overall figure of merit              =     0.7060
-----------------------------------------------------------------------------
 Trying gamma equal   2.0626321E-02
 Gamma decreased to   1.5961248E-02


 $$
 $SUMMARY :Reference2:  $$ Refmac: $$

 fvalues    170486.0       6428.256       1556271.       1556301.    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   176  120  154
 Maximuum H,K,L                 :    50   34   44
 Minimum acceptable grid spacing:   116   77  102
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :   176  120  154
 Maximuum H,K,L                 :    50   34   44
 Minimum acceptable grid spacing:   116   77  102
 Weight matrix   0.2816837    
 Actual weight    9.090909      is applied to the X-ray term
Norm of X_ray positional gradient                32.9
Norm of Geom. positional gradient                33.0
Norm of X_ray B-factor gradient                  87.1
Norm of Geom. B-factor gradient                  89.8
Product of X_ray and Geom posit. gradients     -0.970E+07
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.224E+08
 Cosine of angle between them                      -0.960


Residuals: XRAY=     0.1549E+07 GEOM=      6405.     TOTAL=     0.1556E+07
 function value    1555756.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.019     0.019
Bond distances: others                         1434     0.003     0.020
Bond angles  : refined atoms                   2210     1.763     1.833
Bond angles  : others                          3224     1.078     3.000
Torsion angles, period  1. refined              236     8.348     5.000
Torsion angles, period  2. refined               42    36.552    21.905
Torsion angles, period  3. refined              117    11.355    15.000
Chiral centres: refined atoms                   247     0.123     0.200
Planar groups: refined atoms                   1976     0.010     0.020
Planar groups: others                           412     0.002     0.020
VDW repulsions: refined_atoms                   604     0.212     0.200
VDW repulsions.others                          2392     0.183     0.200
VDW; torsion: refined_atoms                    1498     0.186     0.200
VDW; torsion.others                            1588     0.083     0.200
HBOND: refined_atoms                             30     0.082     0.200
VDW repulsions: symmetry: refined_atoms           4     0.096     0.200
VDW repulsions: symmetry: others                 21     0.087     0.200
HBOND: symmetry: refined_atoms                    1     0.001     0.200
M. chain bond B values: refined atoms           950     1.852     2.146
M. chain bond B values: others                  951     1.851     2.148
M. chain angle B values: refined atoms         1182     2.474     3.208
M. chain angle B values: others                1183     2.473     3.210
S. chain bond B values: refined atoms           649     2.113     2.063
S. chain bond B values: others                  650     2.112     2.066
S. chain angle B values: refined atoms         1028     2.563     3.099
S. chain angle B values: others                1029     2.562     3.102
Long range B values: refined atoms             1702     3.218    17.638
Long range B values: others                    1702     3.221    17.636
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.259, B  =  -0.148
Partial structure    1: scale =    0.429, B  =  49.459
Overall anisotropic scale factors
   B11 =  0.28 B22 = -2.08 B33 =  0.20 B12 =  0.00 B13 =  1.28 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   10. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.009     396  99.76   488.7   487.7  0.38  0.43      19   448.7   530.7  0.31  0.36
 0.026     685 100.00   385.6   447.3  0.41  0.45      30   418.5   489.1  0.44  0.46
 0.043     868 100.00   506.3   516.8  0.29  0.33      35   552.7   566.2  0.31  0.35
 0.061    1015 100.00   557.0   492.1  0.29  0.31      52   583.5   485.2  0.35  0.36
 0.078    1099 100.00   491.1   395.3  0.33  0.35      93   500.3   396.2  0.36  0.39
 0.095    1259 100.00   401.2   334.2  0.34  0.35      77   413.1   325.5  0.39  0.39
 0.113    1359 100.00   329.0   291.3  0.33  0.33      74   324.6   317.4  0.35  0.36
 0.130    1462 100.00   269.3   250.9  0.33  0.32      92   296.9   281.2  0.35  0.35
 0.147    1543 100.00   241.2   232.1  0.31  0.30      83   232.8   214.3  0.35  0.34
 0.164    1674  99.94   218.5   210.6  0.31  0.30      78   210.8   193.6  0.35  0.33
 0.182    1707 100.00   203.8   194.4  0.30  0.29     108   198.2   199.6  0.39  0.37
 0.199    1830  99.95   193.8   179.4  0.30  0.29      77   192.4   173.4  0.33  0.32
 0.216    1893 100.00   183.9   166.2  0.30  0.29      97   175.5   153.7  0.35  0.34
 0.234    1947 100.00   166.4   149.9  0.28  0.27      81   156.9   141.3  0.35  0.33
 0.251    2000 100.00   147.8   135.0  0.29  0.27     109   162.6   149.6  0.31  0.29
 0.268    2162 100.00   131.2   124.5  0.28  0.26      78   119.6   117.0  0.37  0.35
 0.286    2153 100.00   116.1   111.7  0.28  0.26     117   114.8   103.9  0.32  0.30
 0.303    2242 100.00   105.4    99.0  0.28  0.26      88   109.3   106.0  0.31  0.29
 0.320    2273 100.00    91.6    87.6  0.29  0.27     125    84.2    86.9  0.37  0.34
 0.337    2350 100.00    84.2    81.2  0.32  0.31     107    81.4    70.8  0.34  0.33
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0089    323   0.789     73   0.599    396   0.754  0.715  0.8126  0.8601  0.8725  0.6635
  0.0262    614   0.687     71   0.620    685   0.680  0.696  0.7795  0.8105  0.5533  0.6572
  0.0435    796   0.775     72   0.634    868   0.763  0.865  0.8910  0.8782  0.7838  0.7800
  0.0608    940   0.738     75   0.603   1015   0.728  0.961  0.8230  0.8617  0.6206  0.7866
  0.0780   1033   0.724     66   0.637   1099   0.719  1.027  0.8356  0.8385  0.7162  0.7372
  0.0953   1193   0.678     66   0.557   1259   0.672  0.968  0.7783  0.8055  0.6040  0.7004
  0.1126   1288   0.676     71   0.609   1359   0.672  0.912  0.7973  0.7993  0.6593  0.7025
  0.1299   1390   0.693     72   0.486   1462   0.683  0.889  0.8099  0.8105  0.6930  0.7069
  0.1472   1469   0.741     73   0.593   1542   0.734  0.906  0.8102  0.8431  0.6452  0.7423
  0.1645   1602   0.737     72   0.501   1674   0.727  0.894  0.8227  0.8415  0.7044  0.7414
  0.1818   1630   0.715     77   0.596   1707   0.710  0.891  0.7959  0.8351  0.6831  0.7591
  0.1991   1760   0.727     70   0.626   1830   0.723  0.932  0.8156  0.8451  0.7051  0.7678
  0.2164   1819   0.742     74   0.688   1893   0.740  0.952  0.8176  0.8494  0.6779  0.7616
  0.2336   1878   0.741     69   0.637   1947   0.737  0.947  0.8157  0.8526  0.7147  0.7772
  0.2509   1928   0.734     73   0.625   2001   0.730  0.932  0.8534  0.8464  0.7336  0.7722
  0.2682   2084   0.727     77   0.662   2161   0.724  0.890  0.8078  0.8428  0.7515  0.7992
  0.2855   2084   0.714     69   0.552   2153   0.709  0.871  0.8006  0.8279  0.6671  0.8004
  0.3028   2171   0.695     72   0.620   2243   0.693  0.858  0.8096  0.8128  0.7596  0.8013
  0.3201   2198   0.697     74   0.632   2272   0.695  0.829  0.7754  0.8052  0.6474  0.7901
  0.3374   2278   0.597     73   0.445   2351   0.592  0.732  0.6631  0.7181  0.7240  0.7354
 $$
Resolution limits                    =     64.646     1.700
Number of used reflections           =      31916
Percentage observed                  =    99.9911
Percentage of free reflections       =     4.8306
Overall R factor                     =     0.3125
Free R factor                        =     0.3538
Average Fourier shell correlation    =     0.8248
AverageFree Fourier shell correlation=     0.8015
Overall weighted R factor            =     0.3131
Free weighted R factor               =     0.3547
Overall weighted R2 factor           =     0.3822
Free weighted R2 factor              =     0.4164
Average correlation coefficient      =     0.7591
Overall correlation coefficient      =     0.8503
Free correlation coefficient         =     0.8184
Cruickshanks DPI for coordinate error=     0.1325
DPI based on free R factor           =     0.1347
Overall figure of merit              =     0.7053
ML based su of positional parameters =     0.1104
ML based su of thermal parameters    =     3.2629
-----------------------------------------------------------------------------
 Trying gamma equal   1.5961248E-02
 Gamma decreased to   1.1720273E-02


 fvalues    170426.8       6405.359       1555716.       1555740.    


 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /Users/andrey/Desktop/Brazil/04_Piramide/combined_scaled_C2_refmac1.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1599     0.019     0.019
Bond distances: others                         1434     0.003     0.020
Bond angles  : refined atoms                   2210     1.759     1.833
Bond angles  : others                          3224     1.075     3.000
Torsion angles, period  1. refined              236     8.338     5.000
Torsion angles, period  2. refined               42    36.577    21.905
Torsion angles, period  3. refined              117    11.346    15.000
Chiral centres: refined atoms                   247     0.123     0.200
Planar groups: refined atoms                   1976     0.010     0.020
Planar groups: others                           412     0.002     0.020
VDW repulsions: refined_atoms                   604     0.212     0.200
VDW repulsions.others                          2398     0.182     0.200
VDW; torsion: refined_atoms                    1496     0.187     0.200
VDW; torsion.others                            1590     0.083     0.200
HBOND: refined_atoms                             30     0.082     0.200
VDW repulsions: symmetry: refined_atoms           4     0.095     0.200
VDW repulsions: symmetry: others                 21     0.087     0.200
HBOND: symmetry: refined_atoms                    1     0.001     0.200
M. chain bond B values: refined atoms           950     1.846     2.149
M. chain bond B values: others                  951     1.845     2.151
M. chain angle B values: refined atoms         1182     2.468     3.213
M. chain angle B values: others                1183     2.467     3.215
S. chain bond B values: refined atoms           649     2.106     2.067
S. chain bond B values: others                  650     2.104     2.070
S. chain angle B values: refined atoms         1028     2.556     3.104
S. chain angle B values: others                1029     2.554     3.107
Long range B values: refined atoms             1702     3.214    17.680
Long range B values: others                    1702     3.217    17.678
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    1.258, B  =  -0.185
Partial structure    1: scale =    0.429, B  =  49.184
Overall anisotropic scale factors
   B11 =  0.28 B22 = -2.09 B33 =  0.20 B12 =  0.00 B13 =  1.29 B23 =  0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   11. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.009     396  99.76   488.9   487.7  0.38  0.43      19   448.9   529.7  0.31  0.36
 0.026     685 100.00   385.8   447.2  0.41  0.45      30   418.7   488.5  0.44  0.46
 0.043     868 100.00   506.6   516.7  0.29  0.33      35   552.9   566.2  0.31  0.36
 0.061    1015 100.00   557.3   492.2  0.29  0.31      52   583.8   485.0  0.35  0.36
 0.078    1099 100.00   491.3   395.4  0.33  0.35      93   500.6   396.3  0.36  0.39
 0.095    1259 100.00   401.4   334.4  0.34  0.35      77   413.3   325.7  0.39  0.39
 0.113    1359 100.00   329.2   291.5  0.33  0.33      74   324.8   317.7  0.35  0.36
 0.130    1462 100.00   269.4   251.1  0.33  0.32      92   297.0   281.3  0.35  0.35
 0.147    1543 100.00   241.4   232.3  0.31  0.30      83   232.9   214.4  0.35  0.34
 0.164    1674  99.94   218.6   210.9  0.31  0.30      78   211.0   193.7  0.35  0.33
 0.182    1707 100.00   203.9   194.7  0.30  0.29     108   198.3   199.8  0.39  0.37
 0.199    1830  99.95   193.9   179.6  0.30  0.29      77   192.5   173.5  0.33  0.32
 0.216    1893 100.00   184.0   166.3  0.30  0.29      97   175.6   153.9  0.35  0.34
 0.234    1947 100.00   166.5   150.0  0.29  0.27      81   156.9   141.4  0.35  0.33
 0.251    2000 100.00   147.9   135.1  0.29  0.27     109   162.7   149.7  0.31  0.29
 0.268    2162 100.00   131.2   124.6  0.28  0.26      78   119.7   117.2  0.37  0.35
 0.286    2153 100.00   116.1   111.8  0.28  0.26     117   114.9   104.0  0.32  0.30
 0.303    2242 100.00   105.5    99.1  0.28  0.26      88   109.3   106.1  0.31  0.29
 0.320    2273 100.00    91.7    87.6  0.29  0.27     125    84.2    87.0  0.37  0.34
 0.337    2350 100.00    84.3    81.2  0.32  0.31     107    81.4    71.0  0.34  0.33
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0089    323   0.789     73   0.599    396   0.754  0.715  0.8127  0.8600  0.8729  0.6635
  0.0262    614   0.686     71   0.619    685   0.679  0.696  0.7787  0.8101  0.5524  0.6569
  0.0435    796   0.774     72   0.633    868   0.762  0.865  0.8905  0.8778  0.7829  0.7798
  0.0608    940   0.738     75   0.603   1015   0.728  0.961  0.8226  0.8615  0.6198  0.7867
  0.0780   1033   0.724     66   0.636   1099   0.719  1.027  0.8353  0.8383  0.7158  0.7373
  0.0953   1193   0.678     66   0.558   1259   0.671  0.968  0.7781  0.8055  0.6032  0.7005
  0.1126   1288   0.676     71   0.609   1359   0.672  0.912  0.7974  0.7992  0.6596  0.7025
  0.1299   1390   0.693     72   0.486   1462   0.683  0.889  0.8097  0.8105  0.6928  0.7070
  0.1472   1469   0.740     73   0.591   1542   0.733  0.900  0.8091  0.8424  0.6445  0.7423
  0.1645   1602   0.734     72   0.496   1674   0.724  0.889  0.8213  0.8400  0.7030  0.7412
  0.1818   1630   0.713     77   0.595   1707   0.708  0.891  0.7948  0.8342  0.6823  0.7589
  0.1991   1760   0.727     70   0.625   1830   0.723  0.932  0.8150  0.8449  0.7040  0.7680
  0.2164   1819   0.742     74   0.687   1893   0.739  0.952  0.8169  0.8490  0.6766  0.7613
  0.2336   1878   0.740     69   0.636   1947   0.737  0.947  0.8152  0.8523  0.7137  0.7769
  0.2509   1928   0.733     73   0.624   2001   0.729  0.932  0.8530  0.8462  0.7331  0.7721
  0.2682   2084   0.726     77   0.662   2161   0.724  0.890  0.8075  0.8425  0.7513  0.7991
  0.2855   2084   0.713     69   0.551   2153   0.708  0.871  0.8001  0.8275  0.6663  0.8005
  0.3028   2171   0.695     72   0.618   2243   0.692  0.858  0.8089  0.8124  0.7586  0.8012
  0.3201   2198   0.697     74   0.632   2272   0.695  0.829  0.7750  0.8050  0.6462  0.7903
  0.3374   2278   0.597     73   0.445   2351   0.592  0.732  0.6636  0.7183  0.7247  0.7357
 $$
Resolution limits                    =     64.646     1.700
Number of used reflections           =      31916
Percentage observed                  =    99.9911
Percentage of free reflections       =     4.8306
Overall R factor                     =     0.3125
Free R factor                        =     0.3541
Average Fourier shell correlation    =     0.8245
AverageFree Fourier shell correlation=     0.8010
Overall weighted R factor            =     0.3131
Free weighted R factor               =     0.3550
Overall weighted R2 factor           =     0.3823
Free weighted R2 factor              =     0.4167
Average correlation coefficient      =     0.7590
Overall correlation coefficient      =     0.8503
Free correlation coefficient         =     0.8181
Cruickshanks DPI for coordinate error=     0.1325
DPI based on free R factor           =     0.1348
Overall figure of merit              =     0.7047
ML based su of positional parameters =     0.1104
ML based su of thermal parameters    =     3.2629
-----------------------------------------------------------------------------
  Time in seconds: CPU =        72.68
             Elapsed =         128.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> 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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.3170   0.3321   0.738      170436.    8763.1   0.0197  0.987   1.806  0.934   0.135
       1   0.3123   0.3409   0.725      170131.    8808.0   0.0226  1.140   1.859  0.974   0.142
       2   0.3117   0.3457   0.718      170208.    8831.4   0.0217  1.093   1.862  0.974   0.139
       3   0.3120   0.3483   0.713      170242.    8841.0   0.0202  1.018   1.824  0.949   0.132
       4   0.3121   0.3501   0.710      170344.    8852.2   0.0197  0.991   1.801  0.935   0.129
       5   0.3122   0.3512   0.709      170400.    8859.1   0.0194  0.978   1.788  0.927   0.127
       6   0.3123   0.3522   0.707      170373.    8860.8   0.0192  0.969   1.778  0.921   0.126
       7   0.3124   0.3531   0.707      170435.    8866.7   0.0191  0.961   1.770  0.916   0.125
       8   0.3124   0.3536   0.706      170487.    8870.8   0.0190  0.957   1.767  0.914   0.124
       9   0.3125   0.3538   0.705      170429.    8869.0   0.0190  0.954   1.763  0.912   0.123
      10   0.3125   0.3541   0.705      170439.    8870.4   0.0189  0.951   1.759  0.910   0.123
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.3170   0.3125
             R free    0.3321   0.3541
     Rms BondLength    0.0197   0.0189
      Rms BondAngle    1.8063   1.7592
     Rms ChirVolume    0.1349   0.1230
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac_5.8.0135:  End of Refmac_5.8.0135  
Times: User:      75.6s System:    1.3s Elapsed:     1:17  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
Writing final coordinates (XYZOUT) to /Users/andrey/Desktop/Brazil/04_Piramide/combined_scaled_C2_refmac1.pdb
***************************************************************************

***************************************************************************
* Information from CCP4Interface script
***************************************************************************
Writing final phases (HKLOUT) to /Users/andrey/Desktop/Brazil/04_Piramide/combined_scaled_C2_refmac1.mtz
***************************************************************************


#CCP4I TERMINATION STATUS 1 
#CCP4I TERMINATION TIME 11 Apr 2016  10:23:19
#CCP4I MESSAGE Task completed successfully

