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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: 21:17:59 


 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 10
  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_R10_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R10_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_R10_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:    10
  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_R10_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=   2.070 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=   2.196 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=   1.830 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=   2.193 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=   2.417 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=   2.383 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=   2.071 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                           10
Number of "free" reflections       2002
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.= 0.897 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   0.25532180    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                38.6
Norm of Geom. positional gradient                80.4
Norm of X_ray B-factor gradient                  98.5
Norm of Geom. B-factor gradient                 0.243E+05
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.459
Product of X_ray and Geom B-fact gradients     -0.293E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1066E+07 GEOM=     0.2736E+05 TOTAL=     0.1093E+07
 function value    1092913.1    

-------------------------------------------------------------------------------
             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     1.790     1.644
Bond angles  : others                          3242     2.345     1.582
Torsion angles, period  1. refined              184     6.767     5.000
Torsion angles, period  2. refined               90    35.202    22.778
Torsion angles, period  3. refined              268    12.720    15.000
Torsion angles, period  4. refined                9    11.507    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   303     0.269     0.200
VDW repulsions.others                          1321     0.234     0.200
VDW; torsion: refined_atoms                     725     0.171     0.200
VDW; torsion.others                             714     0.081     0.200
HBOND: refined_atoms                            227     0.188     0.200
HBOND.others                                      1     0.053     0.200
VDW repulsions: symmetry: refined_atoms          10     0.193     0.200
VDW repulsions: symmetry: others                 24     0.190     0.200
HBOND: symmetry: refined_atoms                   24     0.182     0.200
M. chain bond B values: refined atoms           745     1.737     1.621
M. chain bond B values: others                  745     1.733     1.621
M. chain angle B values: refined atoms          926     2.684     2.419
M. chain angle B values: others                 927     2.683     2.418
S. chain bond B values: refined atoms           811     3.025     2.017
S. chain bond B values: others                  810     3.019     2.017
S. chain angle B values: refined atoms         1177     4.654     2.863
S. chain angle B values: others                1178     4.652     2.863
Long range B values: refined atoms             1856     6.837    22.426
Long range B values: others                    1761     6.556    20.894
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.7572
Partial structure    1: scale =     0.3944, B  =   44.9331
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5051 100.00   379.7   390.3  0.18  0.18     278   372.1   376.6  0.21  0.22
 0.186    8680  99.98   205.8   182.2  0.19  0.17     463   202.3   179.3  0.22  0.19
 0.310   11062 100.00    91.7    88.6  0.23  0.20     585    92.6    88.5  0.26  0.23
 0.434   12827  98.63    38.6    48.0  0.47  0.46     668    38.5    48.3  0.49  0.48
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3810   0.897   1241   0.775   5051   0.867  0.945  0.9539  0.9643  0.8904  0.9323
  0.1863   7430   0.873   1250   0.778   8680   0.859  1.096  0.9512  0.9600  0.9137  0.9384
  0.3102   9820   0.795   1242   0.721  11062   0.787  0.946  0.9212  0.9328  0.8774  0.9148
  0.4340  11583   0.393   1244   0.347  12827   0.389  0.378  0.6073  0.6134  0.6199  0.6453
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37620
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0336
Overall R factor                     =     0.2192
Free R factor                        =     0.2509
Average Fourier shell correlation    =     0.8344
AverageFree Fourier shell correlation=     0.8276
Overall weighted R factor            =     0.1843
Free weighted R factor               =     0.2134
Overall weighted R2 factor           =     0.2156
Free weighted R2 factor              =     0.2601
Average correlation coefficient      =     0.8307
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9428
Cruickshanks DPI for coordinate error=     0.0781
DPI based on free R factor           =     0.0802
Overall figure of merit              =     0.6785
ML based su of positional parameters =     0.0746
ML based su of thermal parameters    =     2.1700
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176129.27       27359.127       1092913.1      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31952575    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1069066.8    

-------------------------------------------------------------------------------
             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  =   -0.0656
Partial structure    1: scale =     0.3938, B  =   44.6521
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                     =     0.2191
Free R factor                        =     0.2505
Average Fourier shell correlation    =     0.8466
AverageFree Fourier shell correlation=     0.8397
Average correlation coefficient      =     0.8301
Overall figure of merit              =     0.6985
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175038.75       10110.229       1069066.8       1092913.1    


     CGMAT cycle number =      3

 Weight matrix   0.32344353    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066863.3    

-------------------------------------------------------------------------------
             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  =   -0.0239
Partial structure    1: scale =     0.3942, B  =   41.3743
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2183
Free R factor                        =     0.2505
Average Fourier shell correlation    =     0.8477
AverageFree Fourier shell correlation=     0.8404
Average correlation coefficient      =     0.8314
Overall figure of merit              =     0.6979
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174831.23       9162.0693       1066863.3       1069066.8    


     CGMAT cycle number =      4

 Weight matrix   0.32139975    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066363.4    

-------------------------------------------------------------------------------
             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  =   -0.0133
Partial structure    1: scale =     0.3943, B  =   38.2328
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2181
Free R factor                        =     0.2505
Average Fourier shell correlation    =     0.8463
AverageFree Fourier shell correlation=     0.8390
Average correlation coefficient      =     0.8318
Overall figure of merit              =     0.6946
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174810.17       8789.7578       1066363.4       1066863.3    


     CGMAT cycle number =      5

 Weight matrix   0.31951633    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066406.6    

-------------------------------------------------------------------------------
             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  =   -0.0091
Partial structure    1: scale =     0.3945, B  =   37.9818
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2181
Free R factor                        =     0.2505
Average Fourier shell correlation    =     0.8448
AverageFree Fourier shell correlation=     0.8377
Average correlation coefficient      =     0.8320
Overall figure of merit              =     0.6912
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    174834.81       8727.0469       1066420.5       1066363.4    
 fvalues    174834.81       8727.0469       1066420.5       1066449.8    


     CGMAT cycle number =      6

 Weight matrix   0.31973776    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066425.9    

-------------------------------------------------------------------------------
             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  =   -0.0024
Partial structure    1: scale =     0.3946, B  =   37.9269
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2180
Free R factor                        =     0.2505
Average Fourier shell correlation    =     0.8448
AverageFree Fourier shell correlation=     0.8377
Average correlation coefficient      =     0.8320
Overall figure of merit              =     0.6909
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    174830.16       8731.3682       1066425.9       1066449.8    


     CGMAT cycle number =      7

 Weight matrix   0.32057741    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066428.5    

-------------------------------------------------------------------------------
             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  =   -0.0229
Partial structure    1: scale =     0.3946, B  =   37.8873
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2180
Free R factor                        =     0.2505
Average Fourier shell correlation    =     0.8451
AverageFree Fourier shell correlation=     0.8380
Average correlation coefficient      =     0.8319
Overall figure of merit              =     0.6912
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05

 fvalues    174829.33       8729.5352       1066419.0       1066425.9    


     CGMAT cycle number =      8

 Weight matrix   0.32123175    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066457.5    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0195
Partial structure    1: scale =     0.3946, B  =   37.7991
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2180
Free R factor                        =     0.2504
Average Fourier shell correlation    =     0.8451
AverageFree Fourier shell correlation=     0.8380
Average correlation coefficient      =     0.8319
Overall figure of merit              =     0.6913
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    174837.33       8740.9590       1066478.8       1066419.0    
 fvalues    174837.33       8740.9590       1066478.8       1066479.0    


     CGMAT cycle number =      9

 Weight matrix   0.32124537    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066459.1    

-------------------------------------------------------------------------------
             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  =   -0.0169
Partial structure    1: scale =     0.3947, B  =   37.7945
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2180
Free R factor                        =     0.2504
Average Fourier shell correlation    =     0.8451
AverageFree Fourier shell correlation=     0.8381
Average correlation coefficient      =     0.8319
Overall figure of merit              =     0.6913
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    174834.58       8737.8672       1066459.1       1066479.0    


     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.= 0.908 id.= 3.000 dev= -2.09 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   0.32129374    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                43.7
Norm of Geom. positional gradient                43.7
Norm of X_ray B-factor gradient                  102.
Norm of Geom. B-factor gradient                  102.
Product of X_ray and Geom posit. gradients     -0.185E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.336E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.1058E+07 GEOM=      8741.     TOTAL=     0.1066E+07
 function value    1066466.8    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.844     1.644
Bond angles  : others                          3242     1.504     1.582
Torsion angles, period  1. refined              184     6.749     5.000
Torsion angles, period  2. refined               90    34.998    22.778
Torsion angles, period  3. refined              268    12.650    15.000
Torsion angles, period  4. refined                9    11.500    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.270     0.200
VDW repulsions.others                          1361     0.206     0.200
VDW; torsion: refined_atoms                     726     0.172     0.200
VDW; torsion.others                             779     0.085     0.200
HBOND: refined_atoms                            232     0.187     0.200
HBOND.others                                      1     0.032     0.200
VDW repulsions: symmetry: refined_atoms          10     0.193     0.200
VDW repulsions: symmetry: others                 25     0.174     0.200
HBOND: symmetry: refined_atoms                   24     0.176     0.200
M. chain bond B values: refined atoms           745     1.856     1.694
M. chain bond B values: others                  745     1.851     1.694
M. chain angle B values: refined atoms          926     2.814     2.527
M. chain angle B values: others                 927     2.812     2.527
S. chain bond B values: refined atoms           811     3.241     2.111
S. chain bond B values: others                  810     3.234     2.110
S. chain angle B values: refined atoms         1177     4.938     2.995
S. chain angle B values: others                1178     4.936     2.994
Long range B values: refined atoms             1861     7.055    23.400
Long range B values: others                    1765     6.773    21.851
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0170
Partial structure    1: scale =     0.3946, B  =   37.7912
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5051 100.00   380.1   390.3  0.18  0.18     278   372.5   377.0  0.21  0.22
 0.186    8680  99.98   206.0   182.5  0.19  0.16     463   202.6   179.2  0.22  0.19
 0.310   11062 100.00    91.8    88.8  0.23  0.20     585    92.7    88.9  0.26  0.23
 0.434   12827  98.63    38.7    48.1  0.47  0.46     668    38.5    48.3  0.49  0.48
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3810   0.912   1241   0.800   5051   0.884  0.948  0.9585  0.9687  0.8908  0.9330
  0.1863   7430   0.895   1250   0.800   8680   0.881  1.100  0.9565  0.9652  0.9145  0.9400
  0.3102   9820   0.822   1242   0.749  11062   0.813  0.955  0.9302  0.9415  0.8784  0.9155
  0.4340  11583   0.386   1244   0.344  12827   0.382  0.369  0.6252  0.6322  0.6204  0.6469
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37620
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0336
Overall R factor                     =     0.2180
Free R factor                        =     0.2503
Average Fourier shell correlation    =     0.8452
AverageFree Fourier shell correlation=     0.8381
Overall weighted R factor            =     0.1832
Free weighted R factor               =     0.2131
Overall weighted R2 factor           =     0.2140
Free weighted R2 factor              =     0.2596
Average correlation coefficient      =     0.8319
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9431
Cruickshanks DPI for coordinate error=     0.0777
DPI based on free R factor           =     0.0800
Overall figure of merit              =     0.6913
ML based su of positional parameters =     0.0665
ML based su of thermal parameters    =     1.9251
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    174835.55       8741.2305       1066512.4       1066459.1    

 fvalues    174835.55       8741.2305       1066491.3       1066468.4    
 fvalues    174835.55       8741.2305       1066491.3       1066468.4    

    ****                              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.= 0.908 id.= 3.000 dev= -2.09 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_R10_1-42A.mtz 




-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.844     1.644
Bond angles  : others                          3242     1.504     1.582
Torsion angles, period  1. refined              184     6.749     5.000
Torsion angles, period  2. refined               90    34.994    22.778
Torsion angles, period  3. refined              268    12.649    15.000
Torsion angles, period  4. refined                9    11.499    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.270     0.200
VDW repulsions.others                          1361     0.206     0.200
VDW; torsion: refined_atoms                     726     0.172     0.200
VDW; torsion.others                             780     0.085     0.200
HBOND: refined_atoms                            232     0.187     0.200
HBOND.others                                      1     0.032     0.200
VDW repulsions: symmetry: refined_atoms          10     0.193     0.200
VDW repulsions: symmetry: others                 25     0.174     0.200
HBOND: symmetry: refined_atoms                   24     0.176     0.200
M. chain bond B values: refined atoms           745     1.856     1.694
M. chain bond B values: others                  745     1.851     1.694
M. chain angle B values: refined atoms          926     2.814     2.527
M. chain angle B values: others                 927     2.813     2.527
S. chain bond B values: refined atoms           811     3.241     2.111
S. chain bond B values: others                  810     3.234     2.110
S. chain angle B values: refined atoms         1177     4.938     2.995
S. chain angle B values: others                1178     4.936     2.994
Long range B values: refined atoms             1861     7.055    23.400
Long range B values: others                    1765     6.773    21.851
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0125
Partial structure    1: scale =     0.3946, B  =   37.8224
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5051 100.00   380.2   390.3  0.18  0.18     278   372.5   376.9  0.21  0.22
 0.186    8680  99.98   206.0   182.4  0.19  0.16     463   202.6   179.2  0.22  0.19
 0.310   11062 100.00    91.8    88.8  0.23  0.20     585    92.7    88.9  0.26  0.23
 0.434   12827  98.63    38.7    48.0  0.47  0.46     668    38.5    48.3  0.49  0.48
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3810   0.911   1241   0.800   5051   0.884  0.948  0.9585  0.9687  0.8907  0.9330
  0.1863   7430   0.895   1250   0.800   8680   0.881  1.100  0.9565  0.9652  0.9144  0.9400
  0.3102   9820   0.821   1242   0.749  11062   0.813  0.955  0.9302  0.9415  0.8784  0.9155
  0.4340  11583   0.386   1244   0.344  12827   0.382  0.369  0.6251  0.6320  0.6204  0.6470
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37620
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0336
Overall R factor                     =     0.2180
Free R factor                        =     0.2503
Average Fourier shell correlation    =     0.8451
AverageFree Fourier shell correlation=     0.8380
Overall weighted R factor            =     0.1832
Free weighted R factor               =     0.2132
Overall weighted R2 factor           =     0.2140
Free weighted R2 factor              =     0.2597
Average correlation coefficient      =     0.8319
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9431
Cruickshanks DPI for coordinate error=     0.0777
DPI based on free R factor           =     0.0800
Overall figure of merit              =     0.6912
ML based su of positional parameters =     0.0665
ML based su of thermal parameters    =     1.9251
-----------------------------------------------------------------------------
  Time in seconds: CPU =        35.13
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2192   0.2509   0.679      176129.    9521.1   0.0120  0.910   1.790  1.043   0.088
       1   0.2191   0.2505   0.699      175039.    9490.6   0.0118  0.892   1.760  1.024   0.087
       2   0.2183   0.2505   0.698      174831.    9488.2   0.0128  0.974   1.810  1.054   0.090
       3   0.2181   0.2505   0.695      174810.    9488.4   0.0129  0.979   1.827  1.064   0.090
       4   0.2181   0.2505   0.691      174828.    9489.4   0.0129  0.981   1.834  1.068   0.091
       5   0.2180   0.2505   0.691      174830.    9489.6   0.0129  0.981   1.838  1.070   0.091
       6   0.2180   0.2505   0.691      174831.    9489.7   0.0129  0.981   1.840  1.071   0.091
       7   0.2180   0.2504   0.691      174834.    9489.3   0.0129  0.982   1.842  1.073   0.091
       8   0.2180   0.2504   0.691      174835.    9489.2   0.0129  0.982   1.843  1.073   0.091
       9   0.2180   0.2503   0.691      174835.    9489.3   0.0129  0.982   1.844  1.074   0.091
      10   0.2180   0.2503   0.691      174842.    9489.5   0.0129  0.983   1.844  1.074   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2192   0.2180
             R free    0.2509   0.2503
     Rms BondLength    0.0120   0.0129
      Rms BondAngle    1.7902   1.8443
     Rms ChirVolume    0.0877   0.0910
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      67.6s System:    0.6s Elapsed:     1:08