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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: 22:07:51 


 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 19
  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_R19_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R19_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_R19_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:    19
  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_R19_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=   2.056 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=   2.195 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=   1.837 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=   2.216 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=   2.402 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=   2.389 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=   2.079 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                           19
Number of "free" reflections       2041
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.= 0.905 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   0.25776395    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                39.0
Norm of Geom. positional gradient                79.6
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                 0.232E+05
Product of X_ray and Geom posit. gradients     -0.136E+08
 Cosine of angle between them                      -0.452
Product of X_ray and Geom B-fact gradients     -0.301E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1064E+07 GEOM=     0.2649E+05 TOTAL=     0.1091E+07
 function value    1090866.1    

-------------------------------------------------------------------------------
             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     1.769     1.644
Bond angles  : others                          3242     2.340     1.582
Torsion angles, period  1. refined              184     6.866     5.000
Torsion angles, period  2. refined               90    36.002    22.778
Torsion angles, period  3. refined              268    13.036    15.000
Torsion angles, period  4. refined                9    11.517    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                   315     0.263     0.200
VDW repulsions.others                          1341     0.229     0.200
VDW; torsion: refined_atoms                     727     0.172     0.200
VDW; torsion.others                             724     0.080     0.200
HBOND: refined_atoms                            226     0.186     0.200
HBOND.others                                      1     0.012     0.200
VDW repulsions: symmetry: refined_atoms           9     0.201     0.200
VDW repulsions: symmetry: others                 27     0.172     0.200
HBOND: symmetry: refined_atoms                   20     0.230     0.200
HBOND: symmetry: others                           1     0.038     0.200
M. chain bond B values: refined atoms           745     1.716     1.620
M. chain bond B values: others                  745     1.713     1.620
M. chain angle B values: refined atoms          926     2.673     2.417
M. chain angle B values: others                 927     2.672     2.416
S. chain bond B values: refined atoms           811     3.055     2.020
S. chain bond B values: others                  810     3.049     2.020
S. chain angle B values: refined atoms         1177     4.675     2.865
S. chain angle B values: others                1178     4.673     2.864
Long range B values: refined atoms             1868     7.494    22.748
Long range B values: others                    1778     7.259    21.274
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.7772
Partial structure    1: scale =     0.3949, B  =   46.0068
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5064 100.00   379.2   388.6  0.18  0.18     265   395.8   407.3  0.21  0.21
 0.186    8697  99.98   205.8   181.8  0.19  0.17     446   208.8   185.7  0.22  0.19
 0.310   11041 100.00    91.8    88.4  0.23  0.20     606    94.4    91.8  0.26  0.23
 0.434   12783  98.63    38.7    48.1  0.47  0.46     712    37.9    47.1  0.49  0.48
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3837   0.897   1227   0.786   5064   0.870  0.945  0.9604  0.9650  0.9115  0.9324
  0.1863   7453   0.871   1244   0.771   8697   0.857  1.098  0.9522  0.9593  0.9157  0.9383
  0.3102   9796   0.801   1245   0.722  11041   0.792  0.948  0.9214  0.9321  0.8748  0.9114
  0.4340  11539   0.370   1244   0.331  12783   0.367  0.358  0.5908  0.6191  0.5922  0.6435
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37585
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.1219
Overall R factor                     =     0.2198
Free R factor                        =     0.2521
Average Fourier shell correlation    =     0.8364
AverageFree Fourier shell correlation=     0.8173
Overall weighted R factor            =     0.1843
Free weighted R factor               =     0.2115
Overall weighted R2 factor           =     0.2132
Free weighted R2 factor              =     0.2318
Average correlation coefficient      =     0.8293
Overall correlation coefficient      =     0.9590
Free correlation coefficient         =     0.9486
Cruickshanks DPI for coordinate error=     0.0784
DPI based on free R factor           =     0.0807
Overall figure of merit              =     0.6729
ML based su of positional parameters =     0.0743
ML based su of thermal parameters    =     2.1444
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    175934.02       26493.322       1090866.1      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31333396    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068534.9    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0506
Partial structure    1: scale =     0.3951, B  =   45.4513
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                     =     0.2198
Free R factor                        =     0.2513
Average Fourier shell correlation    =     0.8467
AverageFree Fourier shell correlation=     0.8276
Average correlation coefficient      =     0.8297
Overall figure of merit              =     0.6911
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    174959.66       10056.851       1068534.9       1090866.1    


     CGMAT cycle number =      3

 Weight matrix   0.31693080    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066588.9    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0100
Partial structure    1: scale =     0.3953, B  =   41.8677
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                        =     0.2511
Average Fourier shell correlation    =     0.8487
AverageFree Fourier shell correlation=     0.8293
Average correlation coefficient      =     0.8307
Overall figure of merit              =     0.6932
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174781.45       9189.0537       1066588.9       1068534.9    


     CGMAT cycle number =      4

 Weight matrix   0.31772742    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066009.3    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0169
Partial structure    1: scale =     0.3956, B  =   38.7126
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2185
Free R factor                        =     0.2511
Average Fourier shell correlation    =     0.8490
AverageFree Fourier shell correlation=     0.8294
Average correlation coefficient      =     0.8312
Overall figure of merit              =     0.6935
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174742.89       8842.5918       1066009.3       1066588.9    


     CGMAT cycle number =      5

 Weight matrix   0.31834871    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065857.9    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0111
Partial structure    1: scale =     0.3956, B  =   38.6126
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                     =     0.2184
Free R factor                        =     0.2510
Average Fourier shell correlation    =     0.8491
AverageFree Fourier shell correlation=     0.8296
Average correlation coefficient      =     0.8314
Overall figure of merit              =     0.6937
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    174724.69       8801.3428       1065857.9       1066009.3    


     CGMAT cycle number =      6

 Weight matrix   0.31868553    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065827.3    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0126
Partial structure    1: scale =     0.3957, B  =   38.6282
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                     =     0.2184
Free R factor                        =     0.2511
Average Fourier shell correlation    =     0.8491
AverageFree Fourier shell correlation=     0.8296
Average correlation coefficient      =     0.8314
Overall figure of merit              =     0.6937
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    174716.53       8820.1777       1065827.3       1065857.9    


     CGMAT cycle number =      7

 Weight matrix   0.31888235    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065836.6    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0018
Partial structure    1: scale =     0.3958, B  =   38.6318
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                     =     0.2184
Free R factor                        =     0.2510
Average Fourier shell correlation    =     0.8492
AverageFree Fourier shell correlation=     0.8296
Average correlation coefficient      =     0.8315
Overall figure of merit              =     0.6938
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    174723.22       8830.2432       1065892.3       1065827.3    

 fvalues    174723.22       8830.2432       1065896.9       1065877.9    
 fvalues    174723.22       8830.2432       1065896.9       1065877.9    


     CGMAT cycle number =      8

 Weight matrix   0.31866384    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065888.3    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0026
Partial structure    1: scale =     0.3958, B  =   38.6221
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                     =     0.2184
Free R factor                        =     0.2511
Average Fourier shell correlation    =     0.8492
AverageFree Fourier shell correlation=     0.8296
Average correlation coefficient      =     0.8315
Overall figure of merit              =     0.6938
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    174726.92       8830.3633       1065885.1       1065877.9    
 fvalues    174726.92       8830.3633       1065885.1       1065900.4    


     CGMAT cycle number =      9

 Weight matrix   0.31891322    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065886.8    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0000
Partial structure    1: scale =     0.3958, B  =   38.6206
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                     =     0.2184
Free R factor                        =     0.2511
Average Fourier shell correlation    =     0.8492
AverageFree Fourier shell correlation=     0.8297
Average correlation coefficient      =     0.8314
Overall figure of merit              =     0.6938
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    174724.14       8833.6543       1065886.8       1065900.4    


     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.= 0.918 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.31886184    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                43.4
Norm of Geom. positional gradient                43.4
Norm of X_ray B-factor gradient                  104.
Norm of Geom. B-factor gradient                  103.
Product of X_ray and Geom posit. gradients     -0.182E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.344E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.1057E+07 GEOM=      8838.     TOTAL=     0.1066E+07
 function value    1065883.4    

-------------------------------------------------------------------------------
             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     1.846     1.644
Bond angles  : others                          3242     1.522     1.582
Torsion angles, period  1. refined              184     6.853     5.000
Torsion angles, period  2. refined               90    35.943    22.778
Torsion angles, period  3. refined              268    13.037    15.000
Torsion angles, period  4. refined                9    11.725    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   316     0.267     0.200
VDW repulsions.others                          1373     0.204     0.200
VDW; torsion: refined_atoms                     733     0.173     0.200
VDW; torsion.others                             788     0.084     0.200
HBOND: refined_atoms                            224     0.193     0.200
HBOND.others                                      2     0.131     0.200
VDW repulsions: symmetry: refined_atoms          10     0.194     0.200
VDW repulsions: symmetry: others                 28     0.157     0.200
HBOND: symmetry: refined_atoms                   22     0.247     0.200
HBOND: symmetry: others                           1     0.034     0.200
M. chain bond B values: refined atoms           745     1.842     1.690
M. chain bond B values: others                  745     1.838     1.690
M. chain angle B values: refined atoms          926     2.807     2.521
M. chain angle B values: others                 927     2.805     2.521
S. chain bond B values: refined atoms           811     3.323     2.112
S. chain bond B values: others                  810     3.317     2.111
S. chain angle B values: refined atoms         1177     5.028     2.993
S. chain angle B values: others                1178     5.026     2.993
Long range B values: refined atoms             1871     7.751    23.633
Long range B values: others                    1783     7.577    22.222
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0045
Partial structure    1: scale =     0.3960, B  =   38.6784
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5064 100.00   379.5   388.8  0.18  0.18     265   396.1   407.0  0.21  0.21
 0.186    8697  99.98   206.0   182.1  0.19  0.17     446   209.0   186.1  0.22  0.19
 0.310   11041 100.00    91.9    88.7  0.23  0.20     606    94.5    92.0  0.26  0.23
 0.434   12783  98.63    38.8    48.2  0.47  0.46     712    37.9    47.2  0.49  0.49
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3837   0.912   1227   0.814   5064   0.888  0.947  0.9645  0.9693  0.9117  0.9329
  0.1863   7453   0.893   1244   0.793   8697   0.879  1.102  0.9571  0.9648  0.9165  0.9398
  0.3102   9796   0.818   1245   0.739  11041   0.809  0.951  0.9282  0.9387  0.8783  0.9136
  0.4340  11539   0.395   1244   0.356  12783   0.391  0.371  0.6157  0.6457  0.5872  0.6466
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37585
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.1219
Overall R factor                     =     0.2184
Free R factor                        =     0.2511
Average Fourier shell correlation    =     0.8492
AverageFree Fourier shell correlation=     0.8296
Overall weighted R factor            =     0.1831
Free weighted R factor               =     0.2103
Overall weighted R2 factor           =     0.2117
Free weighted R2 factor              =     0.2302
Average correlation coefficient      =     0.8315
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9490
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0803
Overall figure of merit              =     0.6938
ML based su of positional parameters =     0.0667
ML based su of thermal parameters    =     1.9325
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    174722.91       8837.6143       1065883.4       1065886.8    

    ****                              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.= 0.919 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R19_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     1.847     1.644
Bond angles  : others                          3242     1.522     1.582
Torsion angles, period  1. refined              184     6.853     5.000
Torsion angles, period  2. refined               90    35.941    22.778
Torsion angles, period  3. refined              268    13.039    15.000
Torsion angles, period  4. refined                9    11.730    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   316     0.267     0.200
VDW repulsions.others                          1375     0.203     0.200
VDW; torsion: refined_atoms                     733     0.173     0.200
VDW; torsion.others                             793     0.084     0.200
HBOND: refined_atoms                            224     0.194     0.200
HBOND.others                                      2     0.150     0.200
VDW repulsions: symmetry: refined_atoms          10     0.194     0.200
VDW repulsions: symmetry: others                 28     0.157     0.200
HBOND: symmetry: refined_atoms                   22     0.251     0.200
HBOND: symmetry: others                           1     0.034     0.200
M. chain bond B values: refined atoms           745     1.842     1.690
M. chain bond B values: others                  745     1.837     1.690
M. chain angle B values: refined atoms          926     2.807     2.521
M. chain angle B values: others                 927     2.806     2.520
S. chain bond B values: refined atoms           811     3.325     2.112
S. chain bond B values: others                  810     3.318     2.111
S. chain angle B values: refined atoms         1177     5.030     2.993
S. chain angle B values: others                1178     5.028     2.993
Long range B values: refined atoms             1871     7.756    23.632
Long range B values: others                    1783     7.582    22.221
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0045
Partial structure    1: scale =     0.3960, B  =   38.6931
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5064 100.00   379.5   388.8  0.18  0.18     265   396.1   406.9  0.21  0.21
 0.186    8697  99.98   206.0   182.1  0.19  0.17     446   209.0   186.1  0.22  0.19
 0.310   11041 100.00    91.9    88.7  0.23  0.20     606    94.5    92.0  0.26  0.23
 0.434   12783  98.63    38.8    48.2  0.47  0.46     712    37.9    47.2  0.49  0.49
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3837   0.912   1227   0.814   5064   0.888  0.947  0.9644  0.9693  0.9115  0.9330
  0.1863   7453   0.893   1244   0.793   8697   0.879  1.102  0.9571  0.9647  0.9164  0.9398
  0.3102   9796   0.818   1245   0.739  11041   0.809  0.951  0.9283  0.9388  0.8784  0.9136
  0.4340  11539   0.395   1244   0.356  12783   0.391  0.371  0.6158  0.6458  0.5872  0.6466
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37585
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.1219
Overall R factor                     =     0.2184
Free R factor                        =     0.2511
Average Fourier shell correlation    =     0.8492
AverageFree Fourier shell correlation=     0.8297
Overall weighted R factor            =     0.1830
Free weighted R factor               =     0.2104
Overall weighted R2 factor           =     0.2116
Free weighted R2 factor              =     0.2302
Average correlation coefficient      =     0.8315
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9489
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0804
Overall figure of merit              =     0.6938
ML based su of positional parameters =     0.0667
ML based su of thermal parameters    =     1.9325
-----------------------------------------------------------------------------
  Time in seconds: CPU =        27.10
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2198   0.2521   0.673      175934.    9650.9   0.0121  0.912   1.769  1.026   0.088
       1   0.2198   0.2513   0.691      174960.    9620.9   0.0120  0.905   1.756  1.021   0.089
       2   0.2188   0.2511   0.693      174781.    9616.2   0.0131  0.987   1.809  1.051   0.091
       3   0.2185   0.2511   0.693      174743.    9615.1   0.0131  0.994   1.827  1.061   0.092
       4   0.2184   0.2510   0.694      174725.    9614.5   0.0132  0.997   1.836  1.066   0.092
       5   0.2184   0.2511   0.694      174717.    9614.5   0.0132  0.999   1.841  1.069   0.092
       6   0.2184   0.2510   0.694      174716.    9614.3   0.0132  1.000   1.845  1.071   0.092
       7   0.2184   0.2511   0.694      174725.    9614.7   0.0132  1.000   1.845  1.071   0.092
       8   0.2184   0.2511   0.694      174724.    9614.8   0.0132  1.000   1.846  1.071   0.092
       9   0.2184   0.2511   0.694      174723.    9614.6   0.0132  1.000   1.846  1.072   0.092
      10   0.2184   0.2511   0.694      174724.    9614.7   0.0132  1.000   1.847  1.072   0.092
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2198   0.2184
             R free    0.2521   0.2511
     Rms BondLength    0.0121   0.0132
      Rms BondAngle    1.7691   1.8471
     Rms ChirVolume    0.0881   0.0925
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      59.4s System:    0.2s Elapsed:     1:00