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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: 17:20:46 


 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 1.60     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 0
  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_R00_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R00_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R00_1-60A.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       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:     0
  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  1.6000

  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_R00_1-70A.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=   2.047 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=   2.208 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=   1.836 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=   2.230 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=   2.421 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=   2.394 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=   2.121 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                            0
Number of "free" reflections       1433
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.28425992    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                37.4
Norm of Geom. positional gradient                81.0
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                 0.221E+05
Product of X_ray and Geom posit. gradients     -0.132E+08
 Cosine of angle between them                      -0.449
Product of X_ray and Geom B-fact gradients     -0.379E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8737E+06 GEOM=     0.2682E+05 TOTAL=     0.9005E+06
 function value    900518.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.831     1.644
Bond angles  : others                          3242     2.356     1.582
Torsion angles, period  1. refined              184     6.856     5.000
Torsion angles, period  2. refined               90    36.102    22.778
Torsion angles, period  3. refined              268    13.835    15.000
Torsion angles, period  4. refined                9    11.911    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.019     0.020
VDW repulsions: refined_atoms                   303     0.266     0.200
VDW repulsions.others                          1341     0.227     0.200
VDW; torsion: refined_atoms                     718     0.174     0.200
VDW; torsion.others                             713     0.082     0.200
HBOND: refined_atoms                            206     0.195     0.200
HBOND.others                                      1     0.016     0.200
VDW repulsions: symmetry: refined_atoms           8     0.198     0.200
VDW repulsions: symmetry: others                 22     0.188     0.200
HBOND: symmetry: refined_atoms                   21     0.195     0.200
M. chain bond B values: refined atoms           745     1.697     1.384
M. chain bond B values: others                  745     1.694     1.384
M. chain angle B values: refined atoms          926     2.652     2.060
M. chain angle B values: others                 927     2.651     2.060
S. chain bond B values: refined atoms           811     3.005     1.785
S. chain bond B values: others                  810     2.997     1.784
S. chain angle B values: refined atoms         1177     4.639     2.509
S. chain angle B values: others                1178     4.637     2.508
Long range B values: refined atoms             1829     6.936    19.134
Long range B values: others                    1743     6.675    17.798
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    1.2789
Partial structure    1: scale =     0.3856, B  =   46.8876
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3613 100.00   432.4   442.2  0.17  0.17     169   436.3   441.9  0.20  0.21
 0.147    6097  99.97   258.7   243.6  0.17  0.15     347   262.2   239.9  0.22  0.20
 0.244    7806 100.00   167.2   151.3  0.19  0.16     412   171.9   157.0  0.22  0.19
 0.342    9086 100.00    71.5    85.8  0.33  0.26     504    69.5    84.8  0.38  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2636   0.905    977   0.800   3613   0.877  0.946  0.9602  0.9679  0.9041  0.9365
  0.1468   5122   0.868    975   0.771   6097   0.853  1.020  0.9423  0.9568  0.8805  0.9393
  0.2444   6820   0.863    986   0.755   7806   0.850  1.051  0.9486  0.9558  0.9011  0.9382
  0.3419   8114   0.670    976   0.589   9090   0.661  0.704  0.8499  0.8677  0.8069  0.8569
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26606
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.1074
Overall R factor                     =     0.1930
Free R factor                        =     0.2370
Average Fourier shell correlation    =     0.9276
AverageFree Fourier shell correlation=     0.9137
Overall weighted R factor            =     0.1678
Free weighted R factor               =     0.2071
Overall weighted R2 factor           =     0.1993
Free weighted R2 factor              =     0.2427
Average correlation coefficient      =     0.9105
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9344
Cruickshanks DPI for coordinate error=     0.0970
DPI based on free R factor           =     0.1014
Overall figure of merit              =     0.7896
ML based su of positional parameters =     0.0733
ML based su of thermal parameters    =     2.2000
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134421.78       26823.777       900518.63      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35918939    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    876236.75    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0610
Partial structure    1: scale =     0.3861, B  =   46.4404
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1933
Free R factor                        =     0.2363
Average Fourier shell correlation    =     0.9403
AverageFree Fourier shell correlation=     0.9276
Average correlation coefficient      =     0.9109
Overall figure of merit              =     0.8275
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133329.92       9638.6113       876236.75       900518.63    


     CGMAT cycle number =      3

 Weight matrix   0.37305000    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    873777.38    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0067
Partial structure    1: scale =     0.3881, B  =   42.7197
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2358
Average Fourier shell correlation    =     0.9429
AverageFree Fourier shell correlation=     0.9301
Average correlation coefficient      =     0.9132
Overall figure of merit              =     0.8349
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    133034.00       9102.6133       873777.38       876236.75    


     CGMAT cycle number =      4

 Weight matrix   0.37508678    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    873092.50    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0073
Partial structure    1: scale =     0.3884, B  =   42.4726
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1922
Free R factor                        =     0.2356
Average Fourier shell correlation    =     0.9434
AverageFree Fourier shell correlation=     0.9305
Average correlation coefficient      =     0.9141
Overall figure of merit              =     0.8360
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132948.75       8971.7813       873092.50       873777.38    


     CGMAT cycle number =      5

 Weight matrix   0.37610868    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872913.19    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0190
Partial structure    1: scale =     0.3884, B  =   42.4210
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1922
Free R factor                        =     0.2354
Average Fourier shell correlation    =     0.9436
AverageFree Fourier shell correlation=     0.9307
Average correlation coefficient      =     0.9145
Overall figure of merit              =     0.8362
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132916.50       9002.1035       872913.19       873092.50    


     CGMAT cycle number =      6

 Weight matrix   0.37605754    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872880.69    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0000
Partial structure    1: scale =     0.3885, B  =   42.4857
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1922
Free R factor                        =     0.2354
Average Fourier shell correlation    =     0.9436
AverageFree Fourier shell correlation=     0.9307
Average correlation coefficient      =     0.9147
Overall figure of merit              =     0.8361
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    132907.94       9025.3428       872880.69       872913.19    


     CGMAT cycle number =      7

 Weight matrix   0.37678081    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872881.06    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0027
Partial structure    1: scale =     0.3884, B  =   42.5395
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1923
Free R factor                        =     0.2355
Average Fourier shell correlation    =     0.9437
AverageFree Fourier shell correlation=     0.9307
Average correlation coefficient      =     0.9148
Overall figure of merit              =     0.8362
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05

 fvalues    132905.33       9041.4316       872879.88       872880.69    


     CGMAT cycle number =      8

 Weight matrix   0.37679490    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872960.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0163
Partial structure    1: scale =     0.3871, B  =   42.4643
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1923
Free R factor                        =     0.2356
Average Fourier shell correlation    =     0.9437
AverageFree Fourier shell correlation=     0.9307
Average correlation coefficient      =     0.9150
Overall figure of merit              =     0.8362
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    132919.61       9042.4785       872977.50       872879.88    

 fvalues    132919.61       9042.4785       872969.19       872973.75    
 fvalues    132919.61       9042.4785       872969.19       872973.75    


     CGMAT cycle number =      9

 Weight matrix   0.37663284    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872974.06    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0172
Partial structure    1: scale =     0.3869, B  =   42.4151
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1923
Free R factor                        =     0.2356
Average Fourier shell correlation    =     0.9437
AverageFree Fourier shell correlation=     0.9307
Average correlation coefficient      =     0.9150
Overall figure of merit              =     0.8361
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    132920.92       9039.4336       872994.75       872973.75    

 fvalues    132920.92       9039.4336       872981.50       872979.25    
 fvalues    132920.92       9039.4336       872981.50       872979.25    


     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.= 0.905 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.37684083    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                43.1
Norm of Geom. positional gradient                43.0
Norm of X_ray B-factor gradient                  116.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.179E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.437E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.8639E+06 GEOM=      9040.     TOTAL=     0.8729E+06
 function value    872948.81    

-------------------------------------------------------------------------------
             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     1.861     1.644
Bond angles  : others                          3242     1.520     1.582
Torsion angles, period  1. refined              184     6.793     5.000
Torsion angles, period  2. refined               90    35.539    22.778
Torsion angles, period  3. refined              268    13.290    15.000
Torsion angles, period  4. refined                9    12.013    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.267     0.200
VDW repulsions.others                          1365     0.202     0.200
VDW; torsion: refined_atoms                     721     0.174     0.200
VDW; torsion.others                             794     0.085     0.200
HBOND: refined_atoms                            208     0.196     0.200
HBOND.others                                      1     0.026     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 22     0.190     0.200
HBOND: symmetry: refined_atoms                   17     0.202     0.200
M. chain bond B values: refined atoms           745     1.747     1.508
M. chain bond B values: others                  745     1.743     1.508
M. chain angle B values: refined atoms          926     2.725     2.248
M. chain angle B values: others                 927     2.724     2.248
S. chain bond B values: refined atoms           811     3.142     1.913
S. chain bond B values: others                  810     3.137     1.912
S. chain angle B values: refined atoms         1177     4.782     2.700
S. chain angle B values: others                1178     4.780     2.700
Long range B values: refined atoms             1836     7.056    20.693
Long range B values: others                    1749     6.771    19.291
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0183
Partial structure    1: scale =     0.3868, B  =   42.4320
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3613 100.00   432.8   442.3  0.17  0.18     169   436.7   443.5  0.20  0.21
 0.147    6097  99.97   258.9   243.6  0.17  0.15     347   262.4   240.0  0.23  0.20
 0.244    7806 100.00   167.3   151.4  0.19  0.16     412   172.1   156.7  0.22  0.19
 0.342    9086 100.00    71.6    85.5  0.32  0.25     504    69.6    84.8  0.37  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2636   0.923    977   0.822   3613   0.896  0.949  0.9654  0.9717  0.9071  0.9363
  0.1468   5122   0.871    975   0.773   6097   0.856  1.020  0.9421  0.9570  0.8781  0.9388
  0.2444   6820   0.874    986   0.769   7806   0.861  1.053  0.9526  0.9593  0.9038  0.9384
  0.3419   8114   0.787    976   0.705   9090   0.778  0.760  0.8935  0.9103  0.8112  0.8705
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26606
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.1074
Overall R factor                     =     0.1923
Free R factor                        =     0.2356
Average Fourier shell correlation    =     0.9437
AverageFree Fourier shell correlation=     0.9307
Overall weighted R factor            =     0.1680
Free weighted R factor               =     0.2067
Overall weighted R2 factor           =     0.1998
Free weighted R2 factor              =     0.2425
Average correlation coefficient      =     0.9150
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9352
Cruickshanks DPI for coordinate error=     0.0967
DPI based on free R factor           =     0.1008
Overall figure of merit              =     0.8362
ML based su of positional parameters =     0.0636
ML based su of thermal parameters    =     1.8531
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    132916.14       9040.0986       872948.81       872979.25    

    ****                              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= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R00_1-60A.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     1.861     1.644
Bond angles  : others                          3242     1.520     1.582
Torsion angles, period  1. refined              184     6.793     5.000
Torsion angles, period  2. refined               90    35.529    22.778
Torsion angles, period  3. refined              268    13.283    15.000
Torsion angles, period  4. refined                9    12.018    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.267     0.200
VDW repulsions.others                          1364     0.202     0.200
VDW; torsion: refined_atoms                     722     0.174     0.200
VDW; torsion.others                             795     0.085     0.200
HBOND: refined_atoms                            208     0.196     0.200
HBOND.others                                      1     0.027     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 22     0.190     0.200
HBOND: symmetry: refined_atoms                   18     0.196     0.200
M. chain bond B values: refined atoms           745     1.747     1.508
M. chain bond B values: others                  745     1.743     1.508
M. chain angle B values: refined atoms          926     2.725     2.248
M. chain angle B values: others                 927     2.724     2.248
S. chain bond B values: refined atoms           811     3.143     1.912
S. chain bond B values: others                  810     3.138     1.912
S. chain angle B values: refined atoms         1177     4.783     2.700
S. chain angle B values: others                1178     4.781     2.699
Long range B values: refined atoms             1837     7.054    20.701
Long range B values: others                    1750     6.770    19.301
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0169
Partial structure    1: scale =     0.3868, B  =   42.4017
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3613 100.00   432.9   442.3  0.17  0.18     169   436.8   443.5  0.20  0.21
 0.147    6097  99.97   258.9   243.6  0.17  0.15     347   262.4   240.0  0.23  0.20
 0.244    7806 100.00   167.3   151.4  0.19  0.16     412   172.1   156.7  0.22  0.19
 0.342    9086 100.00    71.6    85.5  0.32  0.25     504    69.6    84.8  0.37  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2636   0.923    977   0.822   3613   0.896  0.949  0.9654  0.9717  0.9072  0.9363
  0.1468   5122   0.871    975   0.773   6097   0.856  1.020  0.9421  0.9570  0.8781  0.9388
  0.2444   6820   0.874    986   0.769   7806   0.861  1.053  0.9525  0.9593  0.9038  0.9384
  0.3419   8114   0.787    976   0.705   9090   0.778  0.760  0.8935  0.9103  0.8112  0.8706
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26606
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.1074
Overall R factor                     =     0.1923
Free R factor                        =     0.2355
Average Fourier shell correlation    =     0.9437
AverageFree Fourier shell correlation=     0.9307
Overall weighted R factor            =     0.1680
Free weighted R factor               =     0.2066
Overall weighted R2 factor           =     0.1998
Free weighted R2 factor              =     0.2424
Average correlation coefficient      =     0.9151
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9352
Cruickshanks DPI for coordinate error=     0.0967
DPI based on free R factor           =     0.1007
Overall figure of merit              =     0.8362
ML based su of positional parameters =     0.0636
ML based su of thermal parameters    =     1.8531
-----------------------------------------------------------------------------
  Time in seconds: CPU =        22.13
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1930   0.2370   0.790      134422.    7399.7   0.0128  0.965   1.831  1.060   0.091
       1   0.1933   0.2363   0.828      133330.    7359.7   0.0119  0.893   1.774  1.027   0.088
       2   0.1924   0.2358   0.835      133034.    7349.3   0.0128  0.964   1.811  1.051   0.090
       3   0.1922   0.2356   0.836      132949.    7346.6   0.0130  0.976   1.832  1.063   0.090
       4   0.1922   0.2354   0.836      132917.    7346.0   0.0131  0.980   1.844  1.070   0.090
       5   0.1922   0.2354   0.836      132908.    7346.4   0.0131  0.982   1.851  1.074   0.090
       6   0.1923   0.2355   0.836      132906.    7347.0   0.0131  0.982   1.856  1.077   0.091
       7   0.1923   0.2356   0.836      132918.    7348.3   0.0131  0.983   1.860  1.078   0.091
       8   0.1923   0.2356   0.836      132920.    7348.5   0.0131  0.983   1.860  1.079   0.091
       9   0.1923   0.2356   0.836      132916.    7348.4   0.0131  0.984   1.861  1.079   0.091
      10   0.1923   0.2355   0.836      132919.    7348.4   0.0131  0.984   1.861  1.079   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1930   0.1923
             R free    0.2370   0.2355
     Rms BondLength    0.0128   0.0131
      Rms BondAngle    1.8307   1.8610
     Rms ChirVolume    0.0913   0.0908
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      54.2s System:    0.2s Elapsed:     0:54