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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 17:09:56 


 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 17
  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_R17_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R17_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_R17_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:    17
  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_R17_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=   2.037 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=   2.222 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=   1.838 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=   2.190 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=   2.382 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=   2.148 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                           17
Number of "free" reflections       1168
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.= 0.906 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   0.27565870    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                39.7
Norm of Geom. positional gradient                79.1
Norm of X_ray B-factor gradient                  131.
Norm of Geom. B-factor gradient                 0.214E+05
Product of X_ray and Geom posit. gradients     -0.113E+08
 Cosine of angle between them                      -0.373
Product of X_ray and Geom B-fact gradients     -0.383E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.7856E+06 GEOM=     0.2598E+05 TOTAL=     0.8116E+06
 function value    811558.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.799     1.644
Bond angles  : others                          3242     2.346     1.582
Torsion angles, period  1. refined              184     6.950     5.000
Torsion angles, period  2. refined               90    37.010    22.778
Torsion angles, period  3. refined              268    14.110    15.000
Torsion angles, period  4. refined                9    11.128    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   304     0.262     0.200
VDW repulsions.others                          1330     0.231     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             715     0.081     0.200
HBOND: refined_atoms                            227     0.199     0.200
HBOND.others                                      1     0.037     0.200
VDW repulsions: symmetry: refined_atoms           8     0.220     0.200
VDW repulsions: symmetry: others                 23     0.168     0.200
HBOND: symmetry: refined_atoms                   20     0.224     0.200
M. chain bond B values: refined atoms           745     1.596     1.291
M. chain bond B values: others                  745     1.595     1.291
M. chain angle B values: refined atoms          926     2.516     1.919
M. chain angle B values: others                 927     2.515     1.918
S. chain bond B values: refined atoms           811     2.790     1.662
S. chain bond B values: others                  810     2.787     1.661
S. chain angle B values: refined atoms         1177     4.378     2.336
S. chain angle B values: others                1178     4.376     2.335
Long range B values: refined atoms             1855     7.070    18.221
Long range B values: others                    1758     6.753    16.733
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.0997
Partial structure    1: scale =     0.3884, B  =   49.4267
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3018 100.00   453.3   462.6  0.16  0.17     153   470.8   466.3  0.19  0.20
 0.130    5132 100.00   298.4   285.2  0.16  0.14     268   315.9   299.5  0.19  0.18
 0.216    6536  99.97   202.8   186.6  0.17  0.15     336   198.1   180.7  0.23  0.19
 0.303    7632 100.00   104.2   116.9  0.27  0.20     411   107.1   118.6  0.30  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2166   0.910    852   0.829   3018   0.887  0.947  0.9638  0.9694  0.9133  0.9380
  0.1301   4265   0.884    867   0.779   5132   0.866  1.004  0.9573  0.9644  0.9140  0.9489
  0.2165   5668   0.871    868   0.760   6536   0.856  1.041  0.9440  0.9577  0.8919  0.9394
  0.3028   6777   0.759    858   0.691   7635   0.751  0.808  0.9019  0.9133  0.8533  0.8865
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22321
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9725
Overall R factor                     =     0.1799
Free R factor                        =     0.2171
Average Fourier shell correlation    =     0.9456
AverageFree Fourier shell correlation=     0.9348
Overall weighted R factor            =     0.1579
Free weighted R factor               =     0.1900
Overall weighted R2 factor           =     0.1877
Free weighted R2 factor              =     0.2204
Average correlation coefficient      =     0.9233
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9388
Cruickshanks DPI for coordinate error=     0.1089
DPI based on free R factor           =     0.1077
Overall figure of merit              =     0.8267
ML based su of positional parameters =     0.0759
ML based su of thermal parameters    =     2.3705
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    116388.05       25975.355       811558.31      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30755267    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    791569.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0756
Partial structure    1: scale =     0.3879, B  =   48.5393
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1796
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9501
AverageFree Fourier shell correlation=     0.9393
Average correlation coefficient      =     0.9254
Overall figure of merit              =     0.8416
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115828.91       9760.8848       791569.75       811558.31    


     CGMAT cycle number =      3

 Weight matrix   0.31600451    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    789423.00    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0346
Partial structure    1: scale =     0.3878, B  =   45.1247
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1787
Free R factor                        =     0.2153
Average Fourier shell correlation    =     0.9514
AverageFree Fourier shell correlation=     0.9404
Average correlation coefficient      =     0.9272
Overall figure of merit              =     0.8451
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    115605.84       9119.7295       789423.00       791569.75    


     CGMAT cycle number =      4

 Weight matrix   0.31799030    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788728.94    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0139
Partial structure    1: scale =     0.3878, B  =   45.0686
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1785
Free R factor                        =     0.2148
Average Fourier shell correlation    =     0.9518
AverageFree Fourier shell correlation=     0.9408
Average correlation coefficient      =     0.9279
Overall figure of merit              =     0.8460
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    115526.64       8960.2197       788728.94       789423.00    


     CGMAT cycle number =      5

 Weight matrix   0.31904382    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788594.63    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0106
Partial structure    1: scale =     0.3875, B  =   45.0579
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1784
Free R factor                        =     0.2147
Average Fourier shell correlation    =     0.9519
AverageFree Fourier shell correlation=     0.9410
Average correlation coefficient      =     0.9282
Overall figure of merit              =     0.8463
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    115504.01       8978.6680       788594.63       788728.94    


     CGMAT cycle number =      6

 Weight matrix   0.32002321    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788542.00    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0000
Partial structure    1: scale =     0.3875, B  =   45.0585
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1784
Free R factor                        =     0.2144
Average Fourier shell correlation    =     0.9520
AverageFree Fourier shell correlation=     0.9411
Average correlation coefficient      =     0.9283
Overall figure of merit              =     0.8465
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    115491.52       9010.3564       788542.00       788594.63    


     CGMAT cycle number =      7

 Weight matrix   0.32032892    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788533.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0162
Partial structure    1: scale =     0.3875, B  =   45.2628
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1784
Free R factor                        =     0.2144
Average Fourier shell correlation    =     0.9521
AverageFree Fourier shell correlation=     0.9411
Average correlation coefficient      =     0.9285
Overall figure of merit              =     0.8466
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    115489.63       9014.9014       788533.69       788542.00    


     CGMAT cycle number =      8

 Weight matrix   0.32065046    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788518.69    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0101
Partial structure    1: scale =     0.3875, B  =   45.2180
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1784
Free R factor                        =     0.2141
Average Fourier shell correlation    =     0.9521
AverageFree Fourier shell correlation=     0.9412
Average correlation coefficient      =     0.9285
Overall figure of merit              =     0.8466
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    115485.27       9029.2344       788518.69       788533.69    


     CGMAT cycle number =      9

 Weight matrix   0.32055503    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788492.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0018
Partial structure    1: scale =     0.3875, B  =   45.2257
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1784
Free R factor                        =     0.2140
Average Fourier shell correlation    =     0.9521
AverageFree Fourier shell correlation=     0.9412
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8467
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    115481.24       9030.1924       788492.44       788518.69    


     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.= 0.912 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   0.32132396    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                39.6
Norm of Geom. positional gradient                39.5
Norm of X_ray B-factor gradient                  121.
Norm of Geom. B-factor gradient                  121.
Product of X_ray and Geom posit. gradients     -0.151E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.470E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7794E+06 GEOM=      9038.     TOTAL=     0.7885E+06
 function value    788465.25    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.810     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.857     5.000
Torsion angles, period  2. refined               90    36.632    22.778
Torsion angles, period  3. refined              268    13.899    15.000
Torsion angles, period  4. refined                9    11.362    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.267     0.200
VDW repulsions.others                          1363     0.204     0.200
VDW; torsion: refined_atoms                     727     0.172     0.200
VDW; torsion.others                             793     0.084     0.200
HBOND: refined_atoms                            220     0.194     0.200
HBOND.others                                      1     0.062     0.200
VDW repulsions: symmetry: refined_atoms           8     0.208     0.200
VDW repulsions: symmetry: others                 23     0.160     0.200
HBOND: symmetry: refined_atoms                   22     0.208     0.200
M. chain bond B values: refined atoms           745     1.669     1.386
M. chain bond B values: others                  745     1.667     1.386
M. chain angle B values: refined atoms          926     2.623     2.064
M. chain angle B values: others                 927     2.621     2.064
S. chain bond B values: refined atoms           811     2.987     1.778
S. chain bond B values: others                  810     2.980     1.778
S. chain angle B values: refined atoms         1177     4.618     2.504
S. chain angle B values: others                1178     4.616     2.503
Long range B values: refined atoms             1849     7.498    19.568
Long range B values: others                    1757     7.186    18.098
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0160
Partial structure    1: scale =     0.3877, B  =   45.4140
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3018 100.00   454.4   463.8  0.17  0.17     153   471.8   468.9  0.19  0.20
 0.130    5132 100.00   299.1   284.8  0.16  0.14     268   316.6   299.4  0.19  0.18
 0.216    6536  99.97   203.2   187.0  0.17  0.15     336   198.5   181.7  0.22  0.18
 0.303    7632 100.00   104.4   116.5  0.25  0.19     411   107.4   118.8  0.29  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2166   0.920    852   0.844   3018   0.898  0.947  0.9662  0.9712  0.9121  0.9373
  0.1301   4265   0.888    867   0.784   5132   0.870  1.005  0.9589  0.9652  0.9154  0.9475
  0.2165   5668   0.880    868   0.772   6536   0.866  1.041  0.9482  0.9603  0.8973  0.9398
  0.3028   6777   0.803    858   0.730   7635   0.795  0.828  0.9147  0.9289  0.8581  0.9029
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22321
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9725
Overall R factor                     =     0.1784
Free R factor                        =     0.2139
Average Fourier shell correlation    =     0.9522
AverageFree Fourier shell correlation=     0.9412
Overall weighted R factor            =     0.1586
Free weighted R factor               =     0.1884
Overall weighted R2 factor           =     0.1897
Free weighted R2 factor              =     0.2190
Average correlation coefficient      =     0.9286
Overall correlation coefficient      =     0.9578
Free correlation coefficient         =     0.9397
Cruickshanks DPI for coordinate error=     0.1080
DPI based on free R factor           =     0.1061
Overall figure of merit              =     0.8469
ML based su of positional parameters =     0.0702
ML based su of thermal parameters    =     2.1603
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    115476.11       9037.6270       788465.25       788492.44    

    ****                              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.= 0.912 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_R17_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     1.811     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.854     5.000
Torsion angles, period  2. refined               90    36.605    22.778
Torsion angles, period  3. refined              268    13.902    15.000
Torsion angles, period  4. refined                9    11.359    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.267     0.200
VDW repulsions.others                          1367     0.203     0.200
VDW; torsion: refined_atoms                     727     0.172     0.200
VDW; torsion.others                             797     0.084     0.200
HBOND: refined_atoms                            219     0.195     0.200
HBOND.others                                      1     0.061     0.200
VDW repulsions: symmetry: refined_atoms           8     0.209     0.200
VDW repulsions: symmetry: others                 23     0.160     0.200
HBOND: symmetry: refined_atoms                   22     0.209     0.200
M. chain bond B values: refined atoms           745     1.671     1.385
M. chain bond B values: others                  745     1.669     1.385
M. chain angle B values: refined atoms          926     2.624     2.063
M. chain angle B values: others                 927     2.623     2.063
S. chain bond B values: refined atoms           811     2.992     1.778
S. chain bond B values: others                  810     2.986     1.777
S. chain angle B values: refined atoms         1177     4.624     2.503
S. chain angle B values: others                1178     4.622     2.502
Long range B values: refined atoms             1848     7.503    19.529
Long range B values: others                    1757     7.190    18.103
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0123
Partial structure    1: scale =     0.3878, B  =   45.4929
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3018 100.00   454.4   463.9  0.17  0.17     153   471.9   469.0  0.19  0.20
 0.130    5132 100.00   299.1   284.8  0.16  0.14     268   316.7   299.4  0.19  0.18
 0.216    6536  99.97   203.2   187.0  0.17  0.15     336   198.6   181.7  0.22  0.18
 0.303    7632 100.00   104.4   116.5  0.25  0.19     411   107.4   118.9  0.29  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2166   0.920    852   0.844   3018   0.898  0.947  0.9662  0.9712  0.9119  0.9372
  0.1301   4265   0.888    867   0.784   5132   0.870  1.005  0.9589  0.9653  0.9155  0.9475
  0.2165   5668   0.880    868   0.772   6536   0.866  1.041  0.9483  0.9603  0.8973  0.9399
  0.3028   6777   0.803    858   0.730   7635   0.795  0.828  0.9148  0.9290  0.8582  0.9030
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22321
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9725
Overall R factor                     =     0.1784
Free R factor                        =     0.2139
Average Fourier shell correlation    =     0.9522
AverageFree Fourier shell correlation=     0.9413
Overall weighted R factor            =     0.1587
Free weighted R factor               =     0.1885
Overall weighted R2 factor           =     0.1897
Free weighted R2 factor              =     0.2190
Average correlation coefficient      =     0.9287
Overall correlation coefficient      =     0.9578
Free correlation coefficient         =     0.9397
Cruickshanks DPI for coordinate error=     0.1080
DPI based on free R factor           =     0.1061
Overall figure of merit              =     0.8470
ML based su of positional parameters =     0.0702
ML based su of thermal parameters    =     2.1603
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.50
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1799   0.2171   0.827      116388.    6263.4   0.0124  0.919   1.799  1.030   0.083
       1   0.1796   0.2161   0.842      115829.    6247.6   0.0122  0.905   1.770  1.015   0.084
       2   0.1787   0.2153   0.845      115606.    6241.1   0.0127  0.948   1.789  1.029   0.086
       3   0.1785   0.2148   0.846      115527.    6238.5   0.0128  0.956   1.798  1.036   0.087
       4   0.1784   0.2147   0.846      115504.    6237.1   0.0128  0.958   1.803  1.040   0.087
       5   0.1784   0.2144   0.846      115492.    6236.3   0.0128  0.959   1.806  1.042   0.087
       6   0.1784   0.2144   0.847      115490.    6236.5   0.0129  0.960   1.807  1.043   0.088
       7   0.1784   0.2141   0.847      115485.    6236.0   0.0129  0.960   1.808  1.043   0.088
       8   0.1784   0.2140   0.847      115481.    6235.8   0.0129  0.960   1.809  1.044   0.088
       9   0.1784   0.2139   0.847      115476.    6235.7   0.0129  0.960   1.810  1.044   0.088
      10   0.1784   0.2139   0.847      115468.    6235.4   0.0129  0.961   1.811  1.045   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1799   0.1784
             R free    0.2171   0.2139
     Rms BondLength    0.0124   0.0129
      Rms BondAngle    1.7992   1.8108
     Rms ChirVolume    0.0831   0.0879
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.7s System:    0.1s Elapsed:     0:47