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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: 16:44:38 


 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 1.70     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 10
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R10_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R10_1-70A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R10_1-70A.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       0.0865
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7000
  Estimated number of reflections :      29131
  Free R exclusion - flag equals:    10
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.7000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R10_1-80A.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=   2.038 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=   2.213 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.837 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.164 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=   2.434 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=   2.397 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=   2.105 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                           10
Number of "free" reflections       1200
Number of   all  reflections      23491
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23491

   Current auto weighting coefficient =    6.7496872    

 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.= 0.899 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        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.31402630    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                40.8
Norm of Geom. positional gradient                80.7
Norm of X_ray B-factor gradient                  130.
Norm of Geom. B-factor gradient                 0.217E+05
Product of X_ray and Geom posit. gradients     -0.139E+08
 Cosine of angle between them                      -0.435
Product of X_ray and Geom B-fact gradients     -0.471E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7813E+06 GEOM=     0.2679E+05 TOTAL=     0.8081E+06
 function value    808126.44    

-------------------------------------------------------------------------------
             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     1.837     1.644
Bond angles  : others                          3242     2.350     1.582
Torsion angles, period  1. refined              184     6.872     5.000
Torsion angles, period  2. refined               90    36.213    22.778
Torsion angles, period  3. refined              268    13.666    15.000
Torsion angles, period  4. refined                9    11.067    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   312     0.264     0.200
VDW repulsions.others                          1312     0.234     0.200
VDW; torsion: refined_atoms                     723     0.171     0.200
VDW; torsion.others                             709     0.082     0.200
HBOND: refined_atoms                            238     0.194     0.200
HBOND.others                                      2     0.021     0.200
VDW repulsions: symmetry: refined_atoms          10     0.215     0.200
VDW repulsions: symmetry: others                 26     0.189     0.200
HBOND: symmetry: refined_atoms                   24     0.203     0.200
HBOND: symmetry: others                           1     0.020     0.200
M. chain bond B values: refined atoms           745     1.656     1.285
M. chain bond B values: others                  745     1.655     1.285
M. chain angle B values: refined atoms          926     2.579     1.908
M. chain angle B values: others                 927     2.578     1.908
S. chain bond B values: refined atoms           811     2.886     1.661
S. chain bond B values: others                  810     2.882     1.661
S. chain angle B values: refined atoms         1177     4.460     2.333
S. chain angle B values: others                1178     4.458     2.332
Long range B values: refined atoms             1874     7.008    18.258
Long range B values: others                    1774     6.688    16.733
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.1018
Partial structure    1: scale =     0.3881, B  =   48.8053
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3011 100.00   455.0   464.3  0.17  0.18     160   435.6   440.7  0.21  0.22
 0.130    5114 100.00   298.5   285.4  0.16  0.14     286   310.6   292.4  0.19  0.18
 0.216    6538  99.97   203.0   187.1  0.17  0.14     334   192.6   178.3  0.22  0.20
 0.303    7623 100.00   104.1   117.0  0.26  0.20     420   106.6   117.9  0.29  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2159   0.909    852   0.806   3011   0.880  0.949  0.9558  0.9682  0.8867  0.9364
  0.1301   4242   0.900    872   0.794   5114   0.882  1.008  0.9591  0.9658  0.9225  0.9464
  0.2165   5656   0.879    882   0.771   6538   0.864  1.042  0.9419  0.9602  0.8708  0.9411
  0.3028   6770   0.755    856   0.695   7626   0.748  0.807  0.9107  0.9188  0.8563  0.8952
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22289
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1088
Overall R factor                     =     0.1788
Free R factor                        =     0.2203
Average Fourier shell correlation    =     0.9484
AverageFree Fourier shell correlation=     0.9369
Overall weighted R factor            =     0.1589
Free weighted R factor               =     0.1972
Overall weighted R2 factor           =     0.1919
Free weighted R2 factor              =     0.2388
Average correlation coefficient      =     0.9260
Overall correlation coefficient      =     0.9572
Free correlation coefficient         =     0.9319
Cruickshanks DPI for coordinate error=     0.1084
DPI based on free R factor           =     0.1094
Overall figure of merit              =     0.8305
ML based su of positional parameters =     0.0711
ML based su of thermal parameters    =     2.2182
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    115759.18       26788.191       808126.44      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35936236    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    787036.63    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0504
Partial structure    1: scale =     0.3881, B  =   48.1608
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1785
Free R factor                        =     0.2192
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9425
Average correlation coefficient      =     0.9272
Overall figure of merit              =     0.8513
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115091.40       10205.689       787036.63       808126.44    


     CGMAT cycle number =      3

 Weight matrix   0.36879256    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784792.00    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0085
Partial structure    1: scale =     0.3880, B  =   45.1331
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1776
Free R factor                        =     0.2186
Average Fourier shell correlation    =     0.9553
AverageFree Fourier shell correlation=     0.9435
Average correlation coefficient      =     0.9289
Overall figure of merit              =     0.8549
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    114860.80       9517.5742       784792.00       787036.63    


     CGMAT cycle number =      4

 Weight matrix   0.37117323    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784098.25    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0085
Partial structure    1: scale =     0.3881, B  =   44.7586
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1772
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9557
AverageFree Fourier shell correlation=     0.9439
Average correlation coefficient      =     0.9296
Overall figure of merit              =     0.8556
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    114785.75       9330.3379       784098.25       784792.00    


     CGMAT cycle number =      5

 Weight matrix   0.37267470    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    783861.75    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0000
Partial structure    1: scale =     0.3884, B  =   44.9761
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1771
Free R factor                        =     0.2185
Average Fourier shell correlation    =     0.9559
AverageFree Fourier shell correlation=     0.9440
Average correlation coefficient      =     0.9299
Overall figure of merit              =     0.8559
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114748.23       9347.1055       783861.75       784098.25    


     CGMAT cycle number =      6

 Weight matrix   0.37403035    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    783702.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0052
Partial structure    1: scale =     0.3886, B  =   44.9187
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1771
Free R factor                        =     0.2183
Average Fourier shell correlation    =     0.9560
AverageFree Fourier shell correlation=     0.9442
Average correlation coefficient      =     0.9301
Overall figure of merit              =     0.8562
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114719.60       9381.3965       783702.81       783861.75    


     CGMAT cycle number =      7

 Weight matrix   0.37494618    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    783597.00    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0075
Partial structure    1: scale =     0.3887, B  =   44.8016
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1770
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9443
Average correlation coefficient      =     0.9302
Overall figure of merit              =     0.8564
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    114700.91       9401.7656       783597.00       783702.81    


     CGMAT cycle number =      8

 Weight matrix   0.37606660    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    783536.88    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0035
Partial structure    1: scale =     0.3888, B  =   44.8122
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1771
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9443
Average correlation coefficient      =     0.9303
Overall figure of merit              =     0.8565
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    114689.88       9416.0449       783536.88       783597.00    


     CGMAT cycle number =      9

 Weight matrix   0.37592435    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    783503.38    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0122
Partial structure    1: scale =     0.3888, B  =   44.8332
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1771
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9443
Average correlation coefficient      =     0.9304
Overall figure of merit              =     0.8566
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    114684.17       9421.0781       783503.38       783536.88    


     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.= 0.911 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        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.37641856    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                43.2
Norm of Geom. positional gradient                43.2
Norm of X_ray B-factor gradient                  129.
Norm of Geom. B-factor gradient                  128.
Product of X_ray and Geom posit. gradients     -0.181E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.536E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7741E+06 GEOM=      9427.     TOTAL=     0.7835E+06
 function value    783485.44    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.839     1.644
Bond angles  : others                          3242     1.509     1.582
Torsion angles, period  1. refined              184     6.804     5.000
Torsion angles, period  2. refined               90    35.711    22.778
Torsion angles, period  3. refined              268    13.164    15.000
Torsion angles, period  4. refined                9    11.311    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                   312     0.266     0.200
VDW repulsions.others                          1354     0.206     0.200
VDW; torsion: refined_atoms                     724     0.172     0.200
VDW; torsion.others                             786     0.085     0.200
HBOND: refined_atoms                            235     0.190     0.200
HBOND.others                                      2     0.018     0.200
VDW repulsions: symmetry: refined_atoms          11     0.189     0.200
VDW repulsions: symmetry: others                 25     0.178     0.200
HBOND: symmetry: refined_atoms                   23     0.203     0.200
M. chain bond B values: refined atoms           745     1.710     1.382
M. chain bond B values: others                  745     1.708     1.382
M. chain angle B values: refined atoms          926     2.649     2.057
M. chain angle B values: others                 927     2.647     2.057
S. chain bond B values: refined atoms           811     3.052     1.779
S. chain bond B values: others                  810     3.044     1.778
S. chain angle B values: refined atoms         1177     4.671     2.502
S. chain angle B values: others                1178     4.669     2.501
Long range B values: refined atoms             1869     6.986    19.668
Long range B values: others                    1769     6.683    18.123
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0075
Partial structure    1: scale =     0.3888, B  =   44.9077
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3011 100.00   454.8   464.9  0.17  0.18     160   435.4   442.8  0.21  0.22
 0.130    5114 100.00   298.4   284.9  0.16  0.14     286   310.5   291.8  0.19  0.17
 0.216    6538  99.97   202.9   187.1  0.17  0.15     334   192.5   178.2  0.22  0.19
 0.303    7623 100.00   104.1   116.5  0.25  0.19     420   106.6   118.2  0.28  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2159   0.917    852   0.817   3011   0.888  0.949  0.9579  0.9697  0.8851  0.9350
  0.1301   4242   0.902    872   0.796   5114   0.884  1.008  0.9602  0.9667  0.9242  0.9471
  0.2165   5656   0.890    882   0.786   6538   0.876  1.042  0.9472  0.9628  0.8792  0.9411
  0.3028   6770   0.817    856   0.747   7626   0.809  0.831  0.9263  0.9382  0.8611  0.9083
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22289
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1088
Overall R factor                     =     0.1771
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9444
Overall weighted R factor            =     0.1592
Free weighted R factor               =     0.1966
Overall weighted R2 factor           =     0.1937
Free weighted R2 factor              =     0.2408
Average correlation coefficient      =     0.9304
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9328
Cruickshanks DPI for coordinate error=     0.1074
DPI based on free R factor           =     0.1084
Overall figure of merit              =     0.8567
ML based su of positional parameters =     0.0649
ML based su of thermal parameters    =     1.9871
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    114680.64       9426.9883       783485.44       783503.38    

    ****                              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.= 0.911 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_R10_1-70A.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     1.840     1.644
Bond angles  : others                          3242     1.509     1.582
Torsion angles, period  1. refined              184     6.803     5.000
Torsion angles, period  2. refined               90    35.672    22.778
Torsion angles, period  3. refined              268    13.120    15.000
Torsion angles, period  4. refined                9    11.323    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   311     0.266     0.200
VDW repulsions.others                          1354     0.206     0.200
VDW; torsion: refined_atoms                     723     0.172     0.200
VDW; torsion.others                             790     0.084     0.200
HBOND: refined_atoms                            236     0.190     0.200
HBOND.others                                      2     0.017     0.200
VDW repulsions: symmetry: refined_atoms          11     0.188     0.200
VDW repulsions: symmetry: others                 25     0.178     0.200
HBOND: symmetry: refined_atoms                   23     0.202     0.200
M. chain bond B values: refined atoms           745     1.710     1.382
M. chain bond B values: others                  745     1.708     1.382
M. chain angle B values: refined atoms          926     2.647     2.056
M. chain angle B values: others                 927     2.646     2.056
S. chain bond B values: refined atoms           811     3.051     1.778
S. chain bond B values: others                  810     3.043     1.778
S. chain angle B values: refined atoms         1177     4.670     2.501
S. chain angle B values: others                1178     4.668     2.501
Long range B values: refined atoms             1868     6.994    19.674
Long range B values: others                    1768     6.693    18.128
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0118
Partial structure    1: scale =     0.3887, B  =   45.0412
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3011 100.00   454.8   464.9  0.17  0.18     160   435.4   442.7  0.21  0.22
 0.130    5114 100.00   298.4   284.9  0.16  0.14     286   310.5   291.8  0.19  0.17
 0.216    6538  99.97   202.9   187.1  0.17  0.15     334   192.5   178.2  0.22  0.19
 0.303    7623 100.00   104.1   116.5  0.25  0.19     420   106.6   118.2  0.28  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2159   0.916    852   0.817   3011   0.888  0.949  0.9576  0.9696  0.8843  0.9350
  0.1301   4242   0.902    872   0.796   5114   0.884  1.008  0.9601  0.9667  0.9240  0.9471
  0.2165   5656   0.890    882   0.786   6538   0.876  1.042  0.9472  0.9628  0.8792  0.9411
  0.3028   6770   0.817    856   0.747   7626   0.809  0.831  0.9263  0.9382  0.8613  0.9084
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22289
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1088
Overall R factor                     =     0.1771
Free R factor                        =     0.2186
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9444
Overall weighted R factor            =     0.1592
Free weighted R factor               =     0.1969
Overall weighted R2 factor           =     0.1937
Free weighted R2 factor              =     0.2415
Average correlation coefficient      =     0.9305
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9326
Cruickshanks DPI for coordinate error=     0.1074
DPI based on free R factor           =     0.1085
Overall figure of merit              =     0.8566
ML based su of positional parameters =     0.0649
ML based su of thermal parameters    =     1.9871
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.37
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1788   0.2203   0.831      115759.    6391.3   0.0129  0.957   1.837  1.060   0.087
       1   0.1785   0.2192   0.851      115091.    6371.6   0.0125  0.928   1.800  1.041   0.087
       2   0.1776   0.2186   0.855      114861.    6365.0   0.0130  0.972   1.818  1.055   0.089
       3   0.1772   0.2184   0.856      114786.    6362.6   0.0131  0.979   1.825  1.060   0.090
       4   0.1771   0.2185   0.856      114748.    6361.4   0.0131  0.982   1.828  1.064   0.090
       5   0.1771   0.2183   0.856      114720.    6359.8   0.0131  0.983   1.831  1.066   0.090
       6   0.1770   0.2184   0.856      114701.    6359.3   0.0131  0.984   1.833  1.068   0.090
       7   0.1771   0.2184   0.857      114690.    6358.6   0.0131  0.985   1.835  1.069   0.091
       8   0.1771   0.2184   0.857      114684.    6358.3   0.0131  0.986   1.837  1.071   0.091
       9   0.1771   0.2184   0.857      114681.    6358.2   0.0131  0.986   1.839  1.071   0.091
      10   0.1771   0.2186   0.857      114683.    6358.6   0.0131  0.986   1.840  1.072   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1788   0.1771
             R free    0.2203   0.2186
     Rms BondLength    0.0129   0.0131
      Rms BondAngle    1.8368   1.8397
     Rms ChirVolume    0.0871   0.0909
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.6s System:    0.1s Elapsed:     0:47