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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: 16:26:33 


 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 5
  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_R05_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R05_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_R05_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:     5
  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_R05_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=   2.061 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=   2.202 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=   1.848 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=   2.192 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=   2.389 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=   2.403 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=   2.085 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                            5
Number of "free" reflections       1163
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.= 0.909 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   0.27662593    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                38.0
Norm of Geom. positional gradient                80.1
Norm of X_ray B-factor gradient                  122.
Norm of Geom. B-factor gradient                 0.206E+05
Product of X_ray and Geom posit. gradients     -0.124E+08
 Cosine of angle between them                      -0.419
Product of X_ray and Geom B-fact gradients     -0.419E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7850E+06 GEOM=     0.2592E+05 TOTAL=     0.8109E+06
 function value    810882.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.829     1.644
Bond angles  : others                          3242     2.352     1.582
Torsion angles, period  1. refined              184     7.094     5.000
Torsion angles, period  2. refined               90    36.709    22.778
Torsion angles, period  3. refined              268    14.244    15.000
Torsion angles, period  4. refined                9    13.482    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.013     0.020
VDW repulsions: refined_atoms                   308     0.266     0.200
VDW repulsions.others                          1358     0.229     0.200
VDW; torsion: refined_atoms                     719     0.173     0.200
VDW; torsion.others                             711     0.082     0.200
HBOND: refined_atoms                            229     0.202     0.200
HBOND.others                                      2     0.038     0.200
VDW repulsions: symmetry: refined_atoms           9     0.206     0.200
VDW repulsions: symmetry: others                 28     0.161     0.200
HBOND: symmetry: refined_atoms                   24     0.206     0.200
M. chain bond B values: refined atoms           745     1.640     1.292
M. chain bond B values: others                  745     1.638     1.292
M. chain angle B values: refined atoms          926     2.602     1.918
M. chain angle B values: others                 927     2.601     1.918
S. chain bond B values: refined atoms           811     2.926     1.682
S. chain bond B values: others                  810     2.923     1.681
S. chain angle B values: refined atoms         1177     4.614     2.358
S. chain angle B values: others                1178     4.612     2.357
Long range B values: refined atoms             1860     7.072    18.250
Long range B values: others                    1766     6.768    16.851
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =    1.0800
Partial structure    1: scale =     0.3872, B  =   49.0395
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    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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3001 100.00   456.6   465.5  0.16  0.17     170   399.3   413.0  0.21  0.21
 0.130    5147 100.00   299.0   285.5  0.16  0.15     253   294.9   287.5  0.21  0.19
 0.216    6537  99.97   202.5   186.1  0.17  0.15     335   197.6   180.5  0.22  0.19
 0.303    7639 100.00   104.3   116.7  0.26  0.20     404   100.9   116.8  0.31  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2156   0.925    845   0.838   3001   0.901  0.949  0.9624  0.9742  0.9243  0.9417
  0.1301   4273   0.881    874   0.775   5147   0.863  1.000  0.9513  0.9625  0.9068  0.9448
  0.2165   5652   0.871    885   0.755   6537   0.856  1.042  0.9431  0.9569  0.8881  0.9377
  0.3028   6775   0.754    867   0.689   7642   0.747  0.810  0.9063  0.9157  0.8674  0.8944
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22327
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9470
Overall R factor                     =     0.1787
Free R factor                        =     0.2291
Average Fourier shell correlation    =     0.9464
AverageFree Fourier shell correlation=     0.9349
Overall weighted R factor            =     0.1572
Free weighted R factor               =     0.1997
Overall weighted R2 factor           =     0.1864
Free weighted R2 factor              =     0.2283
Average correlation coefficient      =     0.9251
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9342
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.1136
Overall figure of merit              =     0.8262
ML based su of positional parameters =     0.0757
ML based su of thermal parameters    =     2.3779
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    116295.71       25922.926       810882.63      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35191977    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    789138.50    

-------------------------------------------------------------------------------
             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  =   -0.0675
Partial structure    1: scale =     0.3869, B  =   48.2641
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1785
Free R factor                        =     0.2285
Average Fourier shell correlation    =     0.9546
AverageFree Fourier shell correlation=     0.9437
Average correlation coefficient      =     0.9261
Overall figure of merit              =     0.8570
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115438.83       9962.4844       789138.50       810882.63    


     CGMAT cycle number =      3

 Weight matrix   0.36243799    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786834.56    

-------------------------------------------------------------------------------
             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  =   -0.0054
Partial structure    1: scale =     0.3877, B  =   44.7756
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1775
Free R factor                        =     0.2262
Average Fourier shell correlation    =     0.9559
AverageFree Fourier shell correlation=     0.9448
Average correlation coefficient      =     0.9285
Overall figure of merit              =     0.8602
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    115157.41       9558.0645       786834.56       789138.50    


     CGMAT cycle number =      4

 Weight matrix   0.36376292    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786045.25    

-------------------------------------------------------------------------------
             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  =    0.0084
Partial structure    1: scale =     0.3886, B  =   44.6812
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1772
Free R factor                        =     0.2256
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9450
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8606
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    115055.07       9459.4785       786045.25       786834.56    


     CGMAT cycle number =      5

 Weight matrix   0.33118367    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    715225.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0125
Partial structure    1: scale =     0.3887, B  =   44.6654
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1771
Free R factor                        =     0.2252
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9450
Average correlation coefficient      =     0.9295
Overall figure of merit              =     0.8607
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    115013.84       9491.0156       715225.06       786045.25    


     CGMAT cycle number =      6

 Weight matrix   0.30119249    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651008.19    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0081
Partial structure    1: scale =     0.3889, B  =   44.5984
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1776
Free R factor                        =     0.2251
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9449
Average correlation coefficient      =     0.9291
Overall figure of merit              =     0.8608
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    115052.92       9213.8311       651008.19       715225.06    


     CGMAT cycle number =      7

 Weight matrix   0.30017102    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651065.63    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0144
Partial structure    1: scale =     0.3879, B  =   44.2930
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1781
Free R factor                        =     0.2251
Average Fourier shell correlation    =     0.9559
AverageFree Fourier shell correlation=     0.9448
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8605
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    115129.41       8854.0313       651117.56       651008.19    

 fvalues    115129.41       8854.0313       651101.31       651075.13    
 fvalues    115129.41       8854.0313       651101.31       651075.13    


     CGMAT cycle number =      8

 Weight matrix   0.29962829    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651097.69    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0055
Partial structure    1: scale =     0.3878, B  =   44.2922
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1782
Free R factor                        =     0.2251
Average Fourier shell correlation    =     0.9558
AverageFree Fourier shell correlation=     0.9447
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8604
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    115138.97       8829.5420       651108.31       651075.13    

 fvalues    115138.97       8829.5420       651111.31       651103.94    
 fvalues    115138.97       8829.5420       651111.31       651103.94    


     CGMAT cycle number =      9

 Weight matrix   0.29948249    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651112.25    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0044
Partial structure    1: scale =     0.3877, B  =   44.2892
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1782
Free R factor                        =     0.2251
Average Fourier shell correlation    =     0.9558
AverageFree Fourier shell correlation=     0.9447
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8604
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    115141.12       8822.0234       651115.31       651103.94    

 fvalues    115141.12       8822.0234       651116.19       651108.38    
 fvalues    115141.12       8822.0234       651116.19       651108.38    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.918 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.29945955    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                37.0
Norm of Geom. positional gradient                37.4
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.134E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.432E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.6423E+06 GEOM=      8819.     TOTAL=     0.6511E+06
 function value    651117.69    

-------------------------------------------------------------------------------
             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     1.770     1.644
Bond angles  : others                          3242     1.497     1.582
Torsion angles, period  1. refined              184     6.996     5.000
Torsion angles, period  2. refined               90    36.502    22.778
Torsion angles, period  3. refined              268    14.006    15.000
Torsion angles, period  4. refined                9    13.217    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                   308     0.266     0.200
VDW repulsions.others                          1370     0.204     0.200
VDW; torsion: refined_atoms                     723     0.173     0.200
VDW; torsion.others                             768     0.084     0.200
HBOND: refined_atoms                            217     0.199     0.200
HBOND.others                                      2     0.075     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 26     0.163     0.200
HBOND: symmetry: refined_atoms                   22     0.205     0.200
M. chain bond B values: refined atoms           745     1.626     1.390
M. chain bond B values: others                  745     1.623     1.391
M. chain angle B values: refined atoms          926     2.608     2.070
M. chain angle B values: others                 927     2.607     2.070
S. chain bond B values: refined atoms           811     2.936     1.786
S. chain bond B values: others                  810     2.931     1.785
S. chain angle B values: refined atoms         1177     4.601     2.513
S. chain angle B values: others                1178     4.599     2.513
Long range B values: refined atoms             1850     7.022    19.591
Long range B values: others                    1761     6.748    18.219
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0042
Partial structure    1: scale =     0.3877, B  =   44.2813
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3001 100.00   457.2   466.7  0.16  0.17     170   399.9   413.8  0.20  0.20
 0.130    5147 100.00   299.4   285.1  0.16  0.15     253   295.3   286.1  0.21  0.19
 0.216    6537  99.97   202.8   186.3  0.17  0.15     335   197.8   180.6  0.22  0.19
 0.303    7639 100.00   104.5   116.1  0.25  0.19     404   101.0   115.7  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2156   0.937    845   0.858   3001   0.915  0.950  0.9666  0.9764  0.9292  0.9402
  0.1301   4273   0.883    874   0.778   5147   0.865  1.000  0.9517  0.9626  0.9068  0.9430
  0.2165   5652   0.883    885   0.770   6537   0.867  1.042  0.9472  0.9597  0.8921  0.9367
  0.3028   6775   0.838    867   0.764   7642   0.830  0.845  0.9289  0.9399  0.8703  0.9074
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22327
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9470
Overall R factor                     =     0.1782
Free R factor                        =     0.2252
Average Fourier shell correlation    =     0.9558
AverageFree Fourier shell correlation=     0.9447
Overall weighted R factor            =     0.1587
Free weighted R factor               =     0.1968
Overall weighted R2 factor           =     0.1889
Free weighted R2 factor              =     0.2252
Average correlation coefficient      =     0.9286
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9363
Cruickshanks DPI for coordinate error=     0.1079
DPI based on free R factor           =     0.1116
Overall figure of merit              =     0.8604
ML based su of positional parameters =     0.0661
ML based su of thermal parameters    =     2.0065
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    115142.27       8819.0059       651118.06       651108.38    

 fvalues    115142.27       8819.0059       651113.25       651111.81    
 fvalues    115142.27       8819.0059       651113.25       651111.81    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.918 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 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_R05_1-70A.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     1.770     1.644
Bond angles  : others                          3242     1.497     1.582
Torsion angles, period  1. refined              184     6.996     5.000
Torsion angles, period  2. refined               90    36.502    22.778
Torsion angles, period  3. refined              268    14.005    15.000
Torsion angles, period  4. refined                9    13.216    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                   308     0.266     0.200
VDW repulsions.others                          1370     0.204     0.200
VDW; torsion: refined_atoms                     723     0.173     0.200
VDW; torsion.others                             768     0.084     0.200
HBOND: refined_atoms                            217     0.199     0.200
HBOND.others                                      2     0.075     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 26     0.163     0.200
HBOND: symmetry: refined_atoms                   22     0.205     0.200
M. chain bond B values: refined atoms           745     1.626     1.390
M. chain bond B values: others                  745     1.622     1.391
M. chain angle B values: refined atoms          926     2.608     2.070
M. chain angle B values: others                 927     2.607     2.070
S. chain bond B values: refined atoms           811     2.936     1.786
S. chain bond B values: others                  810     2.930     1.785
S. chain angle B values: refined atoms         1177     4.600     2.513
S. chain angle B values: others                1178     4.598     2.513
Long range B values: refined atoms             1850     7.022    19.590
Long range B values: others                    1761     6.748    18.219
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0044
Partial structure    1: scale =     0.3877, B  =   44.2848
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3001 100.00   457.2   466.7  0.16  0.17     170   399.9   413.9  0.20  0.20
 0.130    5147 100.00   299.4   285.1  0.16  0.15     253   295.3   286.2  0.21  0.19
 0.216    6537  99.97   202.8   186.3  0.17  0.15     335   197.9   180.6  0.22  0.19
 0.303    7639 100.00   104.5   116.1  0.25  0.19     404   101.0   115.7  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2156   0.937    845   0.858   3001   0.915  0.950  0.9666  0.9764  0.9292  0.9402
  0.1301   4273   0.883    874   0.778   5147   0.865  1.000  0.9517  0.9626  0.9068  0.9430
  0.2165   5652   0.883    885   0.770   6537   0.867  1.042  0.9472  0.9597  0.8921  0.9367
  0.3028   6775   0.838    867   0.764   7642   0.830  0.845  0.9289  0.9399  0.8703  0.9074
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22327
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9470
Overall R factor                     =     0.1782
Free R factor                        =     0.2252
Average Fourier shell correlation    =     0.9558
AverageFree Fourier shell correlation=     0.9447
Overall weighted R factor            =     0.1587
Free weighted R factor               =     0.1968
Overall weighted R2 factor           =     0.1889
Free weighted R2 factor              =     0.2252
Average correlation coefficient      =     0.9286
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9363
Cruickshanks DPI for coordinate error=     0.1079
DPI based on free R factor           =     0.1116
Overall figure of merit              =     0.8604
ML based su of positional parameters =     0.0661
ML based su of thermal parameters    =     2.0065
-----------------------------------------------------------------------------
  Time in seconds: CPU =        21.58
             Elapsed =         128.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1787   0.2291   0.826      116296.    6194.4   0.0129  0.956   1.829  1.052   0.087
       1   0.1785   0.2285   0.857      115439.    6162.5   0.0121  0.907   1.777  1.024   0.086
       2   0.1775   0.2262   0.860      115157.    6153.1   0.0133  0.993   1.814  1.049   0.089
       3   0.1772   0.2256   0.861      115055.    6150.7   0.0134  1.006   1.829  1.060   0.091
       4   0.1771   0.2252   0.861      115014.    6149.9   0.0134  1.008   1.836  1.065   0.091
       5   0.1776   0.2251   0.861      115053.    6150.6   0.0128  0.964   1.810  1.050   0.089
       6   0.1781   0.2251   0.861      115128.    6152.5   0.0122  0.918   1.775  1.030   0.087
       7   0.1782   0.2251   0.860      115138.    6152.9   0.0122  0.916   1.771  1.028   0.087
       8   0.1782   0.2251   0.860      115142.    6153.1   0.0122  0.916   1.771  1.028   0.087
       9   0.1782   0.2252   0.860      115143.    6153.2   0.0122  0.916   1.770  1.028   0.087
      10   0.1782   0.2252   0.860      115144.    6153.2   0.0122  0.916   1.770  1.027   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1787   0.1782
             R free    0.2291   0.2252
     Rms BondLength    0.0129   0.0122
      Rms BondAngle    1.8286   1.7700
     Rms ChirVolume    0.0868   0.0870
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      53.7s System:    0.1s Elapsed:     0:54