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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: 21:29:05 


 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 12
  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_R12_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R12_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_R12_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:    12
  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_R12_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=   2.062 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=   2.199 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=   1.801 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=   2.195 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=   2.353 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=   2.387 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=   2.086 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                           12
Number of "free" reflections       2024
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.= 0.867 id.= 3.000 dev= -2.13 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   0.25141406    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                38.0
Norm of Geom. positional gradient                79.8
Norm of X_ray B-factor gradient                  101.
Norm of Geom. B-factor gradient                 0.229E+05
Product of X_ray and Geom posit. gradients     -0.134E+08
 Cosine of angle between them                      -0.456
Product of X_ray and Geom B-fact gradients     -0.298E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1067E+07 GEOM=     0.2635E+05 TOTAL=     0.1093E+07
 function value    1093466.5    

-------------------------------------------------------------------------------
             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     1.767     1.644
Bond angles  : others                          3242     2.341     1.582
Torsion angles, period  1. refined              184     6.818     5.000
Torsion angles, period  2. refined               90    35.710    22.778
Torsion angles, period  3. refined              268    12.962    15.000
Torsion angles, period  4. refined                9    11.112    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   302     0.267     0.200
VDW repulsions.others                          1337     0.231     0.200
VDW; torsion: refined_atoms                     718     0.172     0.200
VDW; torsion.others                             716     0.080     0.200
HBOND: refined_atoms                            223     0.196     0.200
VDW repulsions: symmetry: refined_atoms          10     0.189     0.200
VDW repulsions: symmetry: others                 27     0.179     0.200
HBOND: symmetry: refined_atoms                   20     0.276     0.200
M. chain bond B values: refined atoms           745     1.752     1.615
M. chain bond B values: others                  745     1.748     1.615
M. chain angle B values: refined atoms          926     2.710     2.410
M. chain angle B values: others                 927     2.709     2.410
S. chain bond B values: refined atoms           811     3.051     2.017
S. chain bond B values: others                  810     3.046     2.016
S. chain angle B values: refined atoms         1177     4.706     2.860
S. chain angle B values: others                1178     4.704     2.859
Long range B values: refined atoms             1848     7.935    22.314
Long range B values: others                    1754     7.725    20.790
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =    0.8040
Partial structure    1: scale =     0.3944, B  =   46.1713
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5068 100.00   380.6   389.4  0.18  0.18     261   384.7   391.8  0.21  0.21
 0.186    8695  99.98   206.4   182.1  0.19  0.17     448   205.9   183.3  0.23  0.20
 0.310   11019 100.00    92.2    88.8  0.23  0.20     628    91.1    89.0  0.27  0.23
 0.434   12814  98.63    38.8    48.3  0.47  0.46     681    38.0    47.6  0.50  0.50
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.895   1222   0.793   5068   0.871  0.946  0.9551  0.9647  0.8953  0.9338
  0.1863   7447   0.865   1248   0.762   8695   0.850  1.095  0.9440  0.9564  0.8872  0.9365
  0.3102   9772   0.795   1247   0.721  11019   0.787  0.947  0.9214  0.9333  0.8794  0.9137
  0.4340  11570   0.398   1244   0.351  12814   0.393  0.382  0.5650  0.6178  0.5744  0.6458
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37596
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0942
Overall R factor                     =     0.2199
Free R factor                        =     0.2569
Average Fourier shell correlation    =     0.8354
AverageFree Fourier shell correlation=     0.8105
Overall weighted R factor            =     0.1837
Free weighted R factor               =     0.2172
Overall weighted R2 factor           =     0.2111
Free weighted R2 factor              =     0.2464
Average correlation coefficient      =     0.8304
Overall correlation coefficient      =     0.9593
Free correlation coefficient         =     0.9416
Cruickshanks DPI for coordinate error=     0.0784
DPI based on free R factor           =     0.0822
Overall figure of merit              =     0.6785
ML based su of positional parameters =     0.0752
ML based su of thermal parameters    =     2.1679
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176386.84       26354.223       1093466.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31427187    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1070384.3    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0639
Partial structure    1: scale =     0.3944, B  =   45.8563
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                     =     0.2199
Free R factor                        =     0.2567
Average Fourier shell correlation    =     0.8472
AverageFree Fourier shell correlation=     0.8220
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.6984
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175284.09       9943.4863       1070384.3       1093466.5    


     CGMAT cycle number =      3

 Weight matrix   0.31937125    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068309.8    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0148
Partial structure    1: scale =     0.3946, B  =   41.8397
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                     =     0.2189
Free R factor                        =     0.2560
Average Fourier shell correlation    =     0.8485
AverageFree Fourier shell correlation=     0.8232
Average correlation coefficient      =     0.8314
Overall figure of merit              =     0.7000
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    175077.92       9116.2168       1068309.8       1070384.3    


     CGMAT cycle number =      4

 Weight matrix   0.31920308    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067749.0    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0064
Partial structure    1: scale =     0.3942, B  =   39.0513
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                     =     0.2188
Free R factor                        =     0.2560
Average Fourier shell correlation    =     0.8481
AverageFree Fourier shell correlation=     0.8226
Average correlation coefficient      =     0.8318
Overall figure of merit              =     0.6989
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    175039.94       8785.2617       1067749.0       1068309.8    


     CGMAT cycle number =      5

 Weight matrix   0.32268906    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067514.0    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0021
Partial structure    1: scale =     0.3943, B  =   38.8087
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                     =     0.2187
Free R factor                        =     0.2559
Average Fourier shell correlation    =     0.8504
AverageFree Fourier shell correlation=     0.8254
Average correlation coefficient      =     0.8319
Overall figure of merit              =     0.7034
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    175007.80       8744.7656       1067514.0       1067749.0    


     CGMAT cycle number =      6

 Weight matrix   0.32198378    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067658.0    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0094
Partial structure    1: scale =     0.3940, B  =   38.5297
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                     =     0.2188
Free R factor                        =     0.2559
Average Fourier shell correlation    =     0.8498
AverageFree Fourier shell correlation=     0.8247
Average correlation coefficient      =     0.8320
Overall figure of merit              =     0.7022
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    175036.58       8755.0098       1067700.3       1067514.0    

 fvalues    175036.58       8755.0098       1067714.6       1067698.4    
 fvalues    175036.58       8755.0098       1067714.6       1067698.4    


     CGMAT cycle number =      7

 Weight matrix   0.32074645    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067719.8    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0004
Partial structure    1: scale =     0.3940, B  =   38.4858
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                     =     0.2187
Free R factor                        =     0.2559
Average Fourier shell correlation    =     0.8492
AverageFree Fourier shell correlation=     0.8240
Average correlation coefficient      =     0.8320
Overall figure of merit              =     0.7011
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    175040.63       8756.3984       1067705.1       1067698.4    
 fvalues    175040.63       8756.3984       1067705.1       1067724.3    


     CGMAT cycle number =      8

 Weight matrix   0.32077512    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067715.6    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0045
Partial structure    1: scale =     0.3940, B  =   38.4219
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                     =     0.2188
Free R factor                        =     0.2560
Average Fourier shell correlation    =     0.8490
AverageFree Fourier shell correlation=     0.8236
Average correlation coefficient      =     0.8319
Overall figure of merit              =     0.7006
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    175039.64       8753.6904       1067715.6       1067724.3    


     CGMAT cycle number =      9

 Weight matrix   0.32076588    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067727.5    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0013
Partial structure    1: scale =     0.3940, B  =   38.4030
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                     =     0.2187
Free R factor                        =     0.2560
Average Fourier shell correlation    =     0.8489
AverageFree Fourier shell correlation=     0.8235
Average correlation coefficient      =     0.8319
Overall figure of merit              =     0.7004
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    175015.20       8756.9268       1067570.9       1067715.6    


     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.= 0.878 id.= 3.000 dev= -2.12 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   0.32422295    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                43.5
Norm of Geom. positional gradient                43.4
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                  103.
Product of X_ray and Geom posit. gradients     -0.183E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.341E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.1059E+07 GEOM=      8759.     TOTAL=     0.1068E+07
 function value    1067633.4    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.834     1.644
Bond angles  : others                          3242     1.511     1.582
Torsion angles, period  1. refined              184     6.833     5.000
Torsion angles, period  2. refined               90    35.496    22.778
Torsion angles, period  3. refined              268    12.934    15.000
Torsion angles, period  4. refined                9    11.380    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   298     0.272     0.200
VDW repulsions.others                          1347     0.207     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             779     0.084     0.200
HBOND: refined_atoms                            219     0.203     0.200
HBOND.others                                      1     0.020     0.200
VDW repulsions: symmetry: refined_atoms          10     0.188     0.200
VDW repulsions: symmetry: others                 25     0.185     0.200
HBOND: symmetry: refined_atoms                   21     0.279     0.200
M. chain bond B values: refined atoms           745     1.871     1.688
M. chain bond B values: others                  745     1.867     1.688
M. chain angle B values: refined atoms          926     2.829     2.520
M. chain angle B values: others                 927     2.828     2.519
S. chain bond B values: refined atoms           811     3.290     2.107
S. chain bond B values: others                  810     3.284     2.107
S. chain angle B values: refined atoms         1177     4.999     2.989
S. chain angle B values: others                1178     4.996     2.988
Long range B values: refined atoms             1841     7.933    23.089
Long range B values: others                    1744     7.724    21.497
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0005
Partial structure    1: scale =     0.3940, B  =   38.3752
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5068 100.00   381.1   389.8  0.18  0.18     261   385.2   391.8  0.21  0.21
 0.186    8695  99.98   206.7   182.5  0.19  0.17     448   206.1   183.5  0.23  0.20
 0.310   11019 100.00    92.3    89.1  0.23  0.20     628    91.2    89.3  0.27  0.23
 0.434   12814  98.63    38.9    48.4  0.47  0.46     681    38.1    47.7  0.50  0.50
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.909   1222   0.815   5068   0.886  0.947  0.9590  0.9684  0.8975  0.9340
  0.1863   7447   0.887   1248   0.784   8695   0.873  1.099  0.9495  0.9620  0.8883  0.9382
  0.3102   9772   0.820   1247   0.748  11019   0.812  0.953  0.9301  0.9421  0.8798  0.9157
  0.4340  11570   0.433   1244   0.388  12814   0.428  0.401  0.5984  0.6513  0.5725  0.6474
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37596
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0942
Overall R factor                     =     0.2188
Free R factor                        =     0.2560
Average Fourier shell correlation    =     0.8512
AverageFree Fourier shell correlation=     0.8262
Overall weighted R factor            =     0.1830
Free weighted R factor               =     0.2161
Overall weighted R2 factor           =     0.2110
Free weighted R2 factor              =     0.2451
Average correlation coefficient      =     0.8319
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9423
Cruickshanks DPI for coordinate error=     0.0780
DPI based on free R factor           =     0.0819
Overall figure of merit              =     0.7054
ML based su of positional parameters =     0.0662
ML based su of thermal parameters    =     1.9018
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    175062.69       8758.8848       1067869.6       1067570.9    

 fvalues    175062.69       8758.8848       1067873.4       1067860.3    
 fvalues    175062.69       8758.8848       1067873.4       1067860.3    

    ****                              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.= 0.878 id.= 3.000 dev= -2.12 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_R12_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     1.834     1.644
Bond angles  : others                          3242     1.510     1.582
Torsion angles, period  1. refined              184     6.833     5.000
Torsion angles, period  2. refined               90    35.492    22.778
Torsion angles, period  3. refined              268    12.934    15.000
Torsion angles, period  4. refined                9    11.384    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   298     0.272     0.200
VDW repulsions.others                          1349     0.207     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             778     0.084     0.200
HBOND: refined_atoms                            217     0.204     0.200
HBOND.others                                      1     0.019     0.200
VDW repulsions: symmetry: refined_atoms          10     0.188     0.200
VDW repulsions: symmetry: others                 25     0.185     0.200
HBOND: symmetry: refined_atoms                   21     0.280     0.200
M. chain bond B values: refined atoms           745     1.871     1.688
M. chain bond B values: others                  745     1.867     1.688
M. chain angle B values: refined atoms          926     2.829     2.520
M. chain angle B values: others                 927     2.828     2.519
S. chain bond B values: refined atoms           811     3.290     2.107
S. chain bond B values: others                  810     3.285     2.107
S. chain angle B values: refined atoms         1177     4.999     2.989
S. chain angle B values: others                1178     4.997     2.988
Long range B values: refined atoms             1839     7.913    23.047
Long range B values: others                    1743     7.715    21.472
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0020
Partial structure    1: scale =     0.3939, B  =   38.3521
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5068 100.00   381.1   389.8  0.18  0.18     261   385.2   391.8  0.21  0.21
 0.186    8695  99.98   206.6   182.5  0.19  0.17     448   206.1   183.5  0.23  0.20
 0.310   11019 100.00    92.3    89.1  0.23  0.20     628    91.2    89.3  0.27  0.23
 0.434   12814  98.63    38.9    48.4  0.47  0.46     681    38.1    47.7  0.50  0.50
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.909   1222   0.815   5068   0.886  0.947  0.9590  0.9684  0.8975  0.9340
  0.1863   7447   0.887   1248   0.784   8695   0.873  1.099  0.9495  0.9620  0.8884  0.9382
  0.3102   9772   0.821   1247   0.748  11019   0.812  0.953  0.9301  0.9422  0.8798  0.9157
  0.4340  11570   0.373   1244   0.337  12814   0.369  0.355  0.5724  0.6291  0.5724  0.6474
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37596
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0942
Overall R factor                     =     0.2188
Free R factor                        =     0.2561
Average Fourier shell correlation    =     0.8436
AverageFree Fourier shell correlation=     0.8174
Overall weighted R factor            =     0.1830
Free weighted R factor               =     0.2161
Overall weighted R2 factor           =     0.2110
Free weighted R2 factor              =     0.2450
Average correlation coefficient      =     0.8319
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9423
Cruickshanks DPI for coordinate error=     0.0780
DPI based on free R factor           =     0.0819
Overall figure of merit              =     0.6852
ML based su of positional parameters =     0.0662
ML based su of thermal parameters    =     1.9018
-----------------------------------------------------------------------------
  Time in seconds: CPU =        30.27
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2199   0.2569   0.679      176387.    9617.0   0.0123  0.918   1.767  1.030   0.086
       1   0.2199   0.2567   0.698      175284.    9590.3   0.0120  0.895   1.741  1.015   0.086
       2   0.2189   0.2560   0.700      175078.    9585.1   0.0132  0.983   1.800  1.050   0.088
       3   0.2188   0.2560   0.699      175040.    9584.5   0.0132  0.989   1.818  1.061   0.089
       4   0.2187   0.2559   0.703      175008.    9583.4   0.0133  0.991   1.827  1.066   0.089
       5   0.2188   0.2559   0.702      175030.    9584.8   0.0133  0.992   1.831  1.069   0.090
       6   0.2187   0.2559   0.701      175040.    9585.2   0.0133  0.992   1.832  1.069   0.090
       7   0.2188   0.2560   0.701      175040.    9585.3   0.0133  0.992   1.832  1.070   0.090
       8   0.2187   0.2560   0.700      175041.    9585.4   0.0133  0.992   1.833  1.070   0.090
       9   0.2188   0.2560   0.705      175025.    9584.6   0.0133  0.992   1.834  1.070   0.090
      10   0.2188   0.2561   0.685      175064.    9587.5   0.0133  0.992   1.834  1.071   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2199   0.2188
             R free    0.2569   0.2561
     Rms BondLength    0.0123   0.0133
      Rms BondAngle    1.7665   1.8340
     Rms ChirVolume    0.0859   0.0899
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      62.4s System:    0.2s Elapsed:     1:02