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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 21:23:38 


 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.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

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

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "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

 $$
 $SUMMARY :Reference3:  $$ 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

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.42     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 11
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R11_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R11_1-42A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R11_1-42A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/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
    Standard sugar links 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:     4       0.1240
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4200
  Estimated number of reflections :      51186
  Free R exclusion - flag equals:    11
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  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:    41.9635  1.4200

  Damping factors:     1.0000  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
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R11_1-50A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.048 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.178 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.834 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.211 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.385 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.392 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.076 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 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     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 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:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


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

FreeR flag                           11
Number of "free" reflections       1980
Number of   all  reflections      39817
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          39817

   Current auto weighting coefficient =    6.0498405    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.903 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.24727581    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                38.7
Norm of Geom. positional gradient                80.2
Norm of X_ray B-factor gradient                  102.
Norm of Geom. B-factor gradient                 0.236E+05
Product of X_ray and Geom posit. gradients     -0.137E+08
 Cosine of angle between them                      -0.458
Product of X_ray and Geom B-fact gradients     -0.296E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1068E+07 GEOM=     0.2694E+05 TOTAL=     0.1095E+07
 function value    1094506.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.769     1.644
Bond angles  : others                          3242     2.345     1.582
Torsion angles, period  1. refined              184     6.866     5.000
Torsion angles, period  2. refined               90    35.642    22.778
Torsion angles, period  3. refined              268    13.370    15.000
Torsion angles, period  4. refined                9    10.572    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   304     0.264     0.200
VDW repulsions.others                          1344     0.230     0.200
VDW; torsion: refined_atoms                     717     0.173     0.200
VDW; torsion.others                             723     0.080     0.200
HBOND: refined_atoms                            216     0.199     0.200
HBOND.others                                      2     0.084     0.200
VDW repulsions: symmetry: refined_atoms           9     0.212     0.200
VDW repulsions: symmetry: others                 26     0.181     0.200
HBOND: symmetry: refined_atoms                   20     0.290     0.200
M. chain bond B values: refined atoms           745     1.775     1.619
M. chain bond B values: others                  745     1.772     1.619
M. chain angle B values: refined atoms          926     2.754     2.417
M. chain angle B values: others                 927     2.753     2.417
S. chain bond B values: refined atoms           811     3.133     2.029
S. chain bond B values: others                  810     3.127     2.029
S. chain angle B values: refined atoms         1177     4.818     2.874
S. chain angle B values: others                1178     4.816     2.874
Long range B values: refined atoms             1843     7.636    22.339
Long range B values: others                    1753     7.339    20.865
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.8146
Partial structure    1: scale =     0.3938, B  =   46.8679
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5076 100.00   379.7   389.1  0.17  0.18     253   380.8   402.2  0.21  0.21
 0.186    8702  99.98   206.1   181.9  0.19  0.17     441   200.9   175.7  0.22  0.20
 0.310   11051 100.00    92.0    88.6  0.23  0.20     596    88.9    88.2  0.27  0.24
 0.434   12813  98.63    38.7    48.1  0.47  0.46     682    38.1    47.7  0.50  0.50
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3847   0.902   1229   0.792   5076   0.875  0.948  0.9626  0.9660  0.9164  0.9348
  0.1863   7462   0.868   1240   0.773   8702   0.855  1.097  0.9486  0.9589  0.8986  0.9387
  0.3102   9809   0.792   1242   0.718  11051   0.784  0.946  0.9113  0.9293  0.8584  0.9108
  0.4340  11558   0.349   1255   0.314  12813   0.346  0.346  0.5756  0.6061  0.5829  0.6485
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37642
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9780
Overall R factor                     =     0.2183
Free R factor                        =     0.2571
Average Fourier shell correlation    =     0.8311
AverageFree Fourier shell correlation=     0.8101
Overall weighted R factor            =     0.1819
Free weighted R factor               =     0.2152
Overall weighted R2 factor           =     0.2101
Free weighted R2 factor              =     0.2441
Average correlation coefficient      =     0.8312
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9455
Cruickshanks DPI for coordinate error=     0.0777
DPI based on free R factor           =     0.0822
Overall figure of merit              =     0.6635
ML based su of positional parameters =     0.0758
ML based su of thermal parameters    =     2.2104
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176461.27       26943.855       1094506.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31770822    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1069188.1    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0610
Partial structure    1: scale =     0.3938, B  =   46.3998
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2185
Free R factor                        =     0.2581
Average Fourier shell correlation    =     0.8506
AverageFree Fourier shell correlation=     0.8301
Average correlation coefficient      =     0.8302
Overall figure of merit              =     0.6962
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175073.06       10023.950       1069188.1       1094506.4    


     CGMAT cycle number =      3

 Weight matrix   0.32627976    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066702.9    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0142
Partial structure    1: scale =     0.3942, B  =   42.6414
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2173
Free R factor                        =     0.2573
Average Fourier shell correlation    =     0.8551
AverageFree Fourier shell correlation=     0.8343
Average correlation coefficient      =     0.8315
Overall figure of merit              =     0.7017
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174790.83       9246.1934       1066702.9       1069188.1    


     CGMAT cycle number =      4

 Weight matrix   0.32904634    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065989.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0052
Partial structure    1: scale =     0.3940, B  =   39.6962
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2170
Free R factor                        =     0.2568
Average Fourier shell correlation    =     0.8568
AverageFree Fourier shell correlation=     0.8359
Average correlation coefficient      =     0.8321
Overall figure of merit              =     0.7040
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174722.30       8947.0264       1065989.0       1066702.9    


     CGMAT cycle number =      5

 Weight matrix   0.29508266    
 Actual weight    5.4998550      is applied to the X-ray term


 function value    970069.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0001
Partial structure    1: scale =     0.3942, B  =   39.5808
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2169
Free R factor                        =     0.2564
Average Fourier shell correlation    =     0.8531
AverageFree Fourier shell correlation=     0.8320
Average correlation coefficient      =     0.8323
Overall figure of merit              =     0.6973
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    174758.42       8923.2441       970069.25       1065989.0    


     CGMAT cycle number =      6

 Weight matrix   0.27130285    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    882408.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0000
Partial structure    1: scale =     0.3942, B  =   39.5788
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2172
Free R factor                        =     0.2564
Average Fourier shell correlation    =     0.8561
AverageFree Fourier shell correlation=     0.8353
Average correlation coefficient      =     0.8319
Overall figure of merit              =     0.7029
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    174757.27       8644.9688       882408.25       970069.25    


     CGMAT cycle number =      7

 Weight matrix   0.27280959    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    882393.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0020
Partial structure    1: scale =     0.3943, B  =   39.3810
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2176
Free R factor                        =     0.2564
Average Fourier shell correlation    =     0.8577
AverageFree Fourier shell correlation=     0.8372
Average correlation coefficient      =     0.8314
Overall figure of merit              =     0.7059
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    174820.13       8316.3486       882393.94       882408.25    


     CGMAT cycle number =      8

 Weight matrix   0.26812994    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    882822.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0018
Partial structure    1: scale =     0.3944, B  =   39.2957
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2177
Free R factor                        =     0.2563
Average Fourier shell correlation    =     0.8531
AverageFree Fourier shell correlation=     0.8324
Average correlation coefficient      =     0.8313
Overall figure of merit              =     0.6976
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    174873.47       8251.7764       882617.88       882393.94    

 fvalues    174873.47       8251.7764       882580.50       882596.00    
 fvalues    174873.47       8251.7764       882580.50       882596.00    


     CGMAT cycle number =      9

 Weight matrix   0.27156493    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    882565.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0001
Partial structure    1: scale =     0.3944, B  =   39.2640
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2177
Free R factor                        =     0.2563
Average Fourier shell correlation    =     0.8567
AverageFree Fourier shell correlation=     0.8361
Average correlation coefficient      =     0.8312
Overall figure of merit              =     0.7040
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    174871.48       8230.9033       882565.19       882596.00    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.924 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.27216989    
 Actual weight    4.9998679      is applied to the X-ray term
Norm of X_ray positional gradient                37.9
Norm of Geom. positional gradient                38.0
Norm of X_ray B-factor gradient                  93.8
Norm of Geom. B-factor gradient                  94.0
Product of X_ray and Geom posit. gradients     -0.139E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.285E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8744E+06 GEOM=      8219.     TOTAL=     0.8826E+06
 function value    882574.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.757     1.644
Bond angles  : others                          3242     1.488     1.582
Torsion angles, period  1. refined              184     6.861     5.000
Torsion angles, period  2. refined               90    35.558    22.778
Torsion angles, period  3. refined              268    13.467    15.000
Torsion angles, period  4. refined                9    10.660    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   308     0.261     0.200
VDW repulsions.others                          1364     0.203     0.200
VDW; torsion: refined_atoms                     721     0.172     0.200
VDW; torsion.others                             786     0.083     0.200
HBOND: refined_atoms                            212     0.199     0.200
HBOND.others                                      2     0.086     0.200
VDW repulsions: symmetry: refined_atoms           8     0.221     0.200
VDW repulsions: symmetry: others                 29     0.159     0.200
HBOND: symmetry: refined_atoms                   20     0.288     0.200
M. chain bond B values: refined atoms           745     1.807     1.698
M. chain bond B values: others                  745     1.802     1.698
M. chain angle B values: refined atoms          926     2.791     2.535
M. chain angle B values: others                 927     2.789     2.534
S. chain bond B values: refined atoms           811     3.177     2.112
S. chain bond B values: others                  810     3.172     2.112
S. chain angle B values: refined atoms         1177     4.881     2.998
S. chain angle B values: others                1178     4.879     2.997
Long range B values: refined atoms             1844     7.579    23.341
Long range B values: others                    1754     7.332    21.845
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0026
Partial structure    1: scale =     0.3945, B  =   39.2640
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5076 100.00   380.3   389.5  0.17  0.18     253   381.4   402.1  0.21  0.21
 0.186    8702  99.98   206.4   182.3  0.19  0.17     441   201.3   176.2  0.22  0.20
 0.310   11051 100.00    92.2    88.8  0.23  0.20     596    89.1    88.5  0.27  0.24
 0.434   12813  98.63    38.8    48.1  0.47  0.46     682    38.2    47.7  0.50  0.49
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3847   0.925   1229   0.833   5076   0.903  0.951  0.9685  0.9724  0.9167  0.9351
  0.1863   7462   0.892   1240   0.798   8702   0.879  1.102  0.9549  0.9646  0.8990  0.9386
  0.3102   9809   0.819   1242   0.745  11051   0.811  0.953  0.9194  0.9369  0.8580  0.9114
  0.4340  11558   0.420   1255   0.384  12813   0.417  0.386  0.6388  0.6699  0.5853  0.6481
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37642
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9780
Overall R factor                     =     0.2177
Free R factor                        =     0.2563
Average Fourier shell correlation    =     0.8572
AverageFree Fourier shell correlation=     0.8366
Overall weighted R factor            =     0.1813
Free weighted R factor               =     0.2146
Overall weighted R2 factor           =     0.2093
Free weighted R2 factor              =     0.2428
Average correlation coefficient      =     0.8312
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9457
Cruickshanks DPI for coordinate error=     0.0776
DPI based on free R factor           =     0.0819
Overall figure of merit              =     0.7048
ML based su of positional parameters =     0.0656
ML based su of thermal parameters    =     1.9052
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    174937.13       8218.8525       882630.69       882565.19    
 fvalues    174937.13       8218.8525       882630.69       882881.38    

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.925 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS
          28          24          36  0.70425701      2.37302221E-02  0.70425248    
          36           8          36  0.70425701      2.37302221E-02  0.70425248    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R11_1-42A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.756     1.644
Bond angles  : others                          3242     1.487     1.582
Torsion angles, period  1. refined              184     6.860     5.000
Torsion angles, period  2. refined               90    35.553    22.778
Torsion angles, period  3. refined              268    13.471    15.000
Torsion angles, period  4. refined                9    10.652    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   307     0.261     0.200
VDW repulsions.others                          1365     0.203     0.200
VDW; torsion: refined_atoms                     721     0.172     0.200
VDW; torsion.others                             786     0.083     0.200
HBOND: refined_atoms                            212     0.199     0.200
HBOND.others                                      2     0.086     0.200
VDW repulsions: symmetry: refined_atoms           8     0.221     0.200
VDW repulsions: symmetry: others                 29     0.159     0.200
HBOND: symmetry: refined_atoms                   20     0.288     0.200
M. chain bond B values: refined atoms           745     1.806     1.698
M. chain bond B values: others                  745     1.801     1.698
M. chain angle B values: refined atoms          926     2.790     2.535
M. chain angle B values: others                 927     2.788     2.535
S. chain bond B values: refined atoms           811     3.175     2.112
S. chain bond B values: others                  810     3.169     2.112
S. chain angle B values: refined atoms         1177     4.878     2.997
S. chain angle B values: others                1178     4.876     2.997
Long range B values: refined atoms             1843     7.578    23.335
Long range B values: others                    1753     7.330    21.838
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0009
Partial structure    1: scale =     0.3945, B  =   39.2611
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5076 100.00   380.4   389.5  0.17  0.18     253   381.5   402.2  0.21  0.21
 0.186    8702  99.98   206.4   182.3  0.19  0.17     441   201.3   176.2  0.22  0.20
 0.310   11051 100.00    92.2    88.8  0.23  0.20     596    89.1    88.5  0.27  0.24
 0.434   12813  98.63    38.8    48.1  0.47  0.46     682    38.2    47.8  0.50  0.49
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3847   0.925   1229   0.833   5076   0.903  0.951  0.9685  0.9724  0.9167  0.9351
  0.1863   7462   0.892   1240   0.798   8702   0.879  1.102  0.9549  0.9646  0.8990  0.9385
  0.3102   9809   0.819   1242   0.745  11051   0.811  0.953  0.9194  0.9369  0.8579  0.9113
  0.4340  11558   0.416   1255   0.380  12813   0.412  0.383  0.6363  0.6675  0.5852  0.6482
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37642
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9780
Overall R factor                     =     0.2178
Free R factor                        =     0.2564
Average Fourier shell correlation    =     0.8564
AverageFree Fourier shell correlation=     0.8357
Overall weighted R factor            =     0.1813
Free weighted R factor               =     0.2146
Overall weighted R2 factor           =     0.2092
Free weighted R2 factor              =     0.2428
Average correlation coefficient      =     0.8312
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9456
Cruickshanks DPI for coordinate error=     0.0776
DPI based on free R factor           =     0.0819
Overall figure of merit              =     0.7034
ML based su of positional parameters =     0.0656
ML based su of thermal parameters    =     1.9052
-----------------------------------------------------------------------------
  Time in seconds: CPU =        26.65
             Elapsed =           0.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2183   0.2571   0.664      176461.    9338.9   0.0124  0.928   1.769  1.028   0.088
       1   0.2185   0.2581   0.696      175073.    9299.4   0.0120  0.903   1.744  1.014   0.088
       2   0.2173   0.2573   0.702      174791.    9290.9   0.0133  0.999   1.803  1.049   0.090
       3   0.2170   0.2568   0.704      174722.    9288.1   0.0134  1.009   1.824  1.061   0.091
       4   0.2169   0.2564   0.697      174758.    9289.1   0.0135  1.014   1.835  1.067   0.092
       5   0.2172   0.2564   0.703      174757.    9287.5   0.0129  0.969   1.809  1.051   0.090
       6   0.2176   0.2564   0.706      174820.    9287.9   0.0122  0.924   1.771  1.029   0.087
       7   0.2177   0.2563   0.698      174919.    9291.7   0.0122  0.921   1.760  1.023   0.087
       8   0.2177   0.2563   0.704      174871.    9289.6   0.0122  0.920   1.759  1.022   0.087
       9   0.2177   0.2563   0.705      174876.    9290.0   0.0122  0.920   1.757  1.021   0.087
      10   0.2178   0.2564   0.703      174891.    9290.3   0.0122  0.920   1.756  1.021   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2183   0.2178
             R free    0.2571   0.2564
     Rms BondLength    0.0124   0.0122
      Rms BondAngle    1.7690   1.7564
     Rms ChirVolume    0.0876   0.0871
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      58.9s System:    0.2s Elapsed:     0:59