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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 19:14:24 


 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 1.50     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 6
  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_R06_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R06_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R06_1-50A.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       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:     6
  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  1.5000

  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_R06_1-60A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.048 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.188 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=   1.821 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.195 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.373 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=   2.400 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=   2.122 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                            6
Number of "free" reflections       1722
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 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.= 0.888 id.= 3.000 dev= -2.11 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  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.28084546    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                38.2
Norm of Geom. positional gradient                80.0
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                 0.219E+05
Product of X_ray and Geom posit. gradients     -0.136E+08
 Cosine of angle between them                      -0.459
Product of X_ray and Geom B-fact gradients     -0.359E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.9773E+06 GEOM=     0.2602E+05 TOTAL=     0.1003E+07
 function value    1003360.0    

-------------------------------------------------------------------------------
             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     1.791     1.644
Bond angles  : others                          3242     2.349     1.582
Torsion angles, period  1. refined              184     6.865     5.000
Torsion angles, period  2. refined               90    35.196    22.778
Torsion angles, period  3. refined              268    12.719    15.000
Torsion angles, period  4. refined                9    11.412    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   304     0.264     0.200
VDW repulsions.others                          1332     0.233     0.200
VDW; torsion: refined_atoms                     719     0.174     0.200
VDW; torsion.others                             709     0.082     0.200
HBOND: refined_atoms                            229     0.186     0.200
HBOND.others                                      2     0.040     0.200
VDW repulsions: symmetry: refined_atoms           9     0.182     0.200
VDW repulsions: symmetry: others                 26     0.174     0.200
HBOND: symmetry: refined_atoms                   20     0.171     0.200
M. chain bond B values: refined atoms           745     1.676     1.496
M. chain bond B values: others                  745     1.673     1.496
M. chain angle B values: refined atoms          926     2.597     2.232
M. chain angle B values: others                 927     2.597     2.231
S. chain bond B values: refined atoms           811     2.909     1.878
S. chain bond B values: others                  810     2.904     1.877
S. chain angle B values: refined atoms         1177     4.444     2.660
S. chain angle B values: others                1178     4.442     2.660
Long range B values: refined atoms             1855     7.032    20.861
Long range B values: others                    1761     6.711    19.335
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    1.2137
Partial structure    1: scale =     0.3909, B  =   45.9122
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4301 100.00   405.7   415.3  0.18  0.18     246   410.4   431.7  0.22  0.23
 0.167    7430  99.97   228.0   208.3  0.18  0.16     368   230.7   206.7  0.21  0.19
 0.278    9383 100.00   123.8   114.2  0.21  0.18     527   125.8   115.1  0.24  0.21
 0.389   11062 100.00    50.3    62.5  0.41  0.36     579    48.4    62.1  0.44  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3198   0.882   1103   0.773   4301   0.854  0.936  0.9547  0.9605  0.9011  0.9305
  0.1670   6316   0.877   1114   0.773   7430   0.861  1.060  0.9504  0.9594  0.9037  0.9370
  0.2780   8262   0.835   1121   0.752   9383   0.825  1.018  0.9389  0.9460  0.9059  0.9299
  0.3890   9950   0.535   1122   0.463  11072   0.528  0.536  0.7293  0.7728  0.6970  0.7796
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32186
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0784
Overall R factor                     =     0.2088
Free R factor                        =     0.2437
Average Fourier shell correlation    =     0.8914
AverageFree Fourier shell correlation=     0.8729
Overall weighted R factor            =     0.1786
Free weighted R factor               =     0.2195
Overall weighted R2 factor           =     0.2106
Free weighted R2 factor              =     0.2662
Average correlation coefficient      =     0.8799
Overall correlation coefficient      =     0.9578
Free correlation coefficient         =     0.9415
Cruickshanks DPI for coordinate error=     0.0866
DPI based on free R factor           =     0.0888
Overall figure of merit              =     0.7351
ML based su of positional parameters =     0.0723
ML based su of thermal parameters    =     2.1013
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156382.39       26021.793       1003360.0      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36962664    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978732.81    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0591
Partial structure    1: scale =     0.3905, B  =   44.9460
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2085
Free R factor                        =     0.2437
Average Fourier shell correlation    =     0.9101
AverageFree Fourier shell correlation=     0.8953
Average correlation coefficient      =     0.8797
Overall figure of merit              =     0.7767
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155078.66       9542.5293       978732.81       1003360.0    


     CGMAT cycle number =      3

 Weight matrix   0.38334510    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976317.88    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0224
Partial structure    1: scale =     0.3919, B  =   41.0912
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2075
Free R factor                        =     0.2431
Average Fourier shell correlation    =     0.9144
AverageFree Fourier shell correlation=     0.9004
Average correlation coefficient      =     0.8821
Overall figure of merit              =     0.7864
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    154773.64       9033.7988       976317.88       978732.81    


     CGMAT cycle number =      4

 Weight matrix   0.38662556    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    975558.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0103
Partial structure    1: scale =     0.3921, B  =   39.6901
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2072
Free R factor                        =     0.2430
Average Fourier shell correlation    =     0.9156
AverageFree Fourier shell correlation=     0.9017
Average correlation coefficient      =     0.8830
Overall figure of merit              =     0.7893
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154678.66       8867.7900       975558.25       976317.88    


     CGMAT cycle number =      5

 Weight matrix   0.38360465    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    975891.19    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0187
Partial structure    1: scale =     0.3922, B  =   39.6868
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2071
Free R factor                        =     0.2430
Average Fourier shell correlation    =     0.9140
AverageFree Fourier shell correlation=     0.8992
Average correlation coefficient      =     0.8834
Overall figure of merit              =     0.7833
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03

 fvalues    154669.97       8896.0137       975532.13       975558.25    


     CGMAT cycle number =      6

 Weight matrix   0.35223362    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    887552.44    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0200
Partial structure    1: scale =     0.3921, B  =   39.5754
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2070
Free R factor                        =     0.2430
Average Fourier shell correlation    =     0.9157
AverageFree Fourier shell correlation=     0.9018
Average correlation coefficient      =     0.8836
Overall figure of merit              =     0.7894
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    154646.38       8926.4590       887552.44       975532.13    


     CGMAT cycle number =      7

 Weight matrix   0.31716347    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808059.50    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0184
Partial structure    1: scale =     0.3919, B  =   39.3760
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2074
Free R factor                        =     0.2430
Average Fourier shell correlation    =     0.9139
AverageFree Fourier shell correlation=     0.8992
Average correlation coefficient      =     0.8833
Overall figure of merit              =     0.7834
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    154771.81       8660.7539       808059.50       887552.44    


     CGMAT cycle number =      8

 Weight matrix   0.31887215    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    807847.75    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0083
Partial structure    1: scale =     0.3918, B  =   39.3104
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2079
Free R factor                        =     0.2430
Average Fourier shell correlation    =     0.9149
AverageFree Fourier shell correlation=     0.9010
Average correlation coefficient      =     0.8827
Overall figure of merit              =     0.7877
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    154794.86       8329.9199       807847.75       808059.50    


     CGMAT cycle number =      9

 Weight matrix   0.31960115    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    807739.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0109
Partial structure    1: scale =     0.3917, B  =   39.2985
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2080
Free R factor                        =     0.2430
Average Fourier shell correlation    =     0.9155
AverageFree Fourier shell correlation=     0.9017
Average correlation coefficient      =     0.8826
Overall figure of merit              =     0.7896
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    154788.94       8252.5723       807739.75       807847.75    


     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= -2.10 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  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.31629133    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                38.4
Norm of Geom. positional gradient                38.6
Norm of X_ray B-factor gradient                  102.
Norm of Geom. B-factor gradient                  102.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.337E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.7999E+06 GEOM=      8220.     TOTAL=     0.8082E+06
 function value    808163.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.768     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.872     5.000
Torsion angles, period  2. refined               90    35.087    22.778
Torsion angles, period  3. refined              268    12.736    15.000
Torsion angles, period  4. refined                9    11.318    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.264     0.200
VDW repulsions.others                          1360     0.204     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             786     0.083     0.200
HBOND: refined_atoms                            232     0.182     0.200
HBOND.others                                      1     0.052     0.200
VDW repulsions: symmetry: refined_atoms           8     0.192     0.200
VDW repulsions: symmetry: others                 28     0.163     0.200
HBOND: symmetry: refined_atoms                   19     0.172     0.200
M. chain bond B values: refined atoms           745     1.716     1.613
M. chain bond B values: others                  745     1.713     1.613
M. chain angle B values: refined atoms          926     2.643     2.407
M. chain angle B values: others                 927     2.642     2.407
S. chain bond B values: refined atoms           811     2.956     2.001
S. chain bond B values: others                  810     2.951     2.001
S. chain angle B values: refined atoms         1177     4.525     2.844
S. chain angle B values: others                1178     4.523     2.844
Long range B values: refined atoms             1858     7.034    22.308
Long range B values: others                    1762     6.717    20.731
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0137
Partial structure    1: scale =     0.3916, B  =   39.3643
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4301 100.00   406.1   415.7  0.18  0.18     246   410.8   432.6  0.22  0.23
 0.167    7430  99.97   228.2   208.5  0.18  0.16     368   230.9   207.1  0.21  0.19
 0.278    9383 100.00   123.9   114.5  0.21  0.18     527   125.9   115.4  0.24  0.21
 0.389   11062 100.00    50.3    62.5  0.40  0.35     579    48.5    62.1  0.44  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3198   0.904   1103   0.807   4301   0.879  0.942  0.9601  0.9665  0.8999  0.9302
  0.1670   6316   0.894   1114   0.791   7430   0.878  1.063  0.9549  0.9636  0.9052  0.9379
  0.2780   8262   0.852   1121   0.770   9383   0.842  1.019  0.9459  0.9523  0.9072  0.9301
  0.3890   9950   0.639   1122   0.572  11072   0.633  0.598  0.7956  0.8270  0.6973  0.7867
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32186
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0784
Overall R factor                     =     0.2080
Free R factor                        =     0.2431
Average Fourier shell correlation    =     0.9137
AverageFree Fourier shell correlation=     0.8991
Overall weighted R factor            =     0.1783
Free weighted R factor               =     0.2193
Overall weighted R2 factor           =     0.2104
Free weighted R2 factor              =     0.2671
Average correlation coefficient      =     0.8826
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9415
Cruickshanks DPI for coordinate error=     0.0863
DPI based on free R factor           =     0.0886
Overall figure of merit              =     0.7834
ML based su of positional parameters =     0.0619
ML based su of thermal parameters    =     1.7711
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    154825.30       8220.1064       807796.81       807739.75    
 fvalues    154825.30       8220.1064       807796.81       807895.13    

    ****                              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_R06_1-50A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.765     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.871     5.000
Torsion angles, period  2. refined               90    35.073    22.778
Torsion angles, period  3. refined              268    12.731    15.000
Torsion angles, period  4. refined                9    11.303    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   301     0.264     0.200
VDW repulsions.others                          1358     0.204     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             785     0.083     0.200
HBOND: refined_atoms                            233     0.181     0.200
HBOND.others                                      1     0.051     0.200
VDW repulsions: symmetry: refined_atoms           8     0.192     0.200
VDW repulsions: symmetry: others                 28     0.163     0.200
HBOND: symmetry: refined_atoms                   19     0.172     0.200
M. chain bond B values: refined atoms           745     1.714     1.613
M. chain bond B values: others                  745     1.711     1.613
M. chain angle B values: refined atoms          926     2.640     2.407
M. chain angle B values: others                 927     2.639     2.407
S. chain bond B values: refined atoms           811     2.950     2.001
S. chain bond B values: others                  810     2.945     2.000
S. chain angle B values: refined atoms         1177     4.517     2.844
S. chain angle B values: others                1178     4.515     2.843
Long range B values: refined atoms             1858     7.031    22.318
Long range B values: others                    1761     6.715    20.716
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0149
Partial structure    1: scale =     0.3916, B  =   39.3218
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4301 100.00   406.2   415.7  0.18  0.18     246   410.9   432.5  0.22  0.23
 0.167    7430  99.97   228.2   208.5  0.18  0.16     368   231.0   207.1  0.21  0.19
 0.278    9383 100.00   124.0   114.5  0.21  0.18     527   125.9   115.4  0.24  0.21
 0.389   11062 100.00    50.3    62.5  0.40  0.35     579    48.5    62.1  0.44  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3198   0.904   1103   0.806   4301   0.879  0.942  0.9600  0.9664  0.8997  0.9302
  0.1670   6316   0.894   1114   0.791   7430   0.878  1.063  0.9549  0.9636  0.9052  0.9379
  0.2780   8262   0.852   1121   0.770   9383   0.842  1.019  0.9458  0.9523  0.9071  0.9300
  0.3890   9950   0.658   1122   0.588  11072   0.650  0.610  0.8032  0.8320  0.6973  0.7866
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32186
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0784
Overall R factor                     =     0.2081
Free R factor                        =     0.2431
Average Fourier shell correlation    =     0.9154
AverageFree Fourier shell correlation=     0.9017
Overall weighted R factor            =     0.1783
Free weighted R factor               =     0.2195
Overall weighted R2 factor           =     0.2105
Free weighted R2 factor              =     0.2675
Average correlation coefficient      =     0.8825
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9414
Cruickshanks DPI for coordinate error=     0.0863
DPI based on free R factor           =     0.0886
Overall figure of merit              =     0.7894
ML based su of positional parameters =     0.0619
ML based su of thermal parameters    =     1.7711
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.38
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2088   0.2437   0.735      156382.    8533.7   0.0121  0.916   1.791  1.043   0.087
       1   0.2085   0.2437   0.777      155079.    8486.1   0.0119  0.898   1.756  1.021   0.087
       2   0.2075   0.2431   0.786      154774.    8474.9   0.0130  0.985   1.808  1.053   0.090
       3   0.2072   0.2430   0.789      154679.    8471.2   0.0131  0.996   1.830  1.066   0.091
       4   0.2071   0.2430   0.783      154727.    8474.2   0.0131  1.000   1.841  1.072   0.091
       5   0.2070   0.2430   0.789      154646.    8470.2   0.0132  1.001   1.848  1.076   0.091
       6   0.2074   0.2430   0.783      154772.    8474.4   0.0126  0.958   1.820  1.059   0.090
       7   0.2079   0.2430   0.788      154795.    8472.6   0.0120  0.912   1.782  1.037   0.087
       8   0.2080   0.2430   0.790      154789.    8471.9   0.0119  0.908   1.772  1.032   0.087
       9   0.2080   0.2431   0.783      154877.    8476.0   0.0119  0.906   1.768  1.029   0.087
      10   0.2081   0.2431   0.789      154816.    8473.0   0.0119  0.905   1.765  1.028   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2088   0.2081
             R free    0.2437   0.2431
     Rms BondLength    0.0121   0.0119
      Rms BondAngle    1.7913   1.7649
     Rms ChirVolume    0.0872   0.0871
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      55.5s System:    0.2s Elapsed:     0:56