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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: 21:56:49 


 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 1.42     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_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R17_1-42A.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_1-42A.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       0.1240
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4200
  Estimated number of reflections :      51186
  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  1.4200

  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_1-50A.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=   2.053 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=   2.211 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=   1.820 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=   2.218 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=   2.376 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=   2.375 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=   2.116 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       2008
Number of   all  reflections      39817
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          39817

   Current auto weighting coefficient =    6.0498405    

 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.= 0.887 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.22939475    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                36.2
Norm of Geom. positional gradient                81.6
Norm of X_ray B-factor gradient                  99.0
Norm of Geom. B-factor gradient                 0.237E+05
Product of X_ray and Geom posit. gradients     -0.136E+08
 Cosine of angle between them                      -0.476
Product of X_ray and Geom B-fact gradients     -0.290E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1068E+07 GEOM=     0.2732E+05 TOTAL=     0.1095E+07
 function value    1095446.6    

-------------------------------------------------------------------------------
             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     1.814     1.644
Bond angles  : others                          3242     2.353     1.582
Torsion angles, period  1. refined              184     6.817     5.000
Torsion angles, period  2. refined               90    35.943    22.778
Torsion angles, period  3. refined              268    13.370    15.000
Torsion angles, period  4. refined                9    11.762    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   306     0.266     0.200
VDW repulsions.others                          1365     0.230     0.200
VDW; torsion: refined_atoms                     727     0.172     0.200
VDW; torsion.others                             725     0.081     0.200
HBOND: refined_atoms                            209     0.199     0.200
HBOND.others                                      2     0.051     0.200
VDW repulsions: symmetry: refined_atoms           8     0.213     0.200
VDW repulsions: symmetry: others                 25     0.163     0.200
HBOND: symmetry: refined_atoms                   18     0.254     0.200
M. chain bond B values: refined atoms           745     1.796     1.622
M. chain bond B values: others                  745     1.792     1.622
M. chain angle B values: refined atoms          926     2.766     2.421
M. chain angle B values: others                 927     2.765     2.421
S. chain bond B values: refined atoms           811     3.220     2.034
S. chain bond B values: others                  810     3.215     2.033
S. chain angle B values: refined atoms         1177     4.911     2.881
S. chain angle B values: others                1178     4.909     2.881
Long range B values: refined atoms             1842     7.747    22.446
Long range B values: others                    1754     7.412    20.958
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.7969
Partial structure    1: scale =     0.3939, B  =   46.2971
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5065 100.00   378.9   388.8  0.17  0.18     264   398.1   399.7  0.19  0.20
 0.186    8713  99.98   205.7   181.5  0.19  0.17     430   208.7   183.6  0.22  0.20
 0.310   11038 100.00    91.8    88.4  0.23  0.20     609    92.8    90.2  0.27  0.23
 0.434   12800  98.63    38.7    48.0  0.47  0.46     695    39.1    49.3  0.47  0.45
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3823   0.901   1242   0.796   5065   0.875  0.948  0.9619  0.9670  0.9086  0.9356
  0.1863   7476   0.861   1237   0.762   8713   0.847  1.094  0.9468  0.9566  0.8988  0.9382
  0.3102   9800   0.782   1238   0.705  11038   0.773  0.941  0.9137  0.9277  0.8703  0.9114
  0.4340  11544   0.339   1256   0.301  12800   0.335  0.340  0.5948  0.5893  0.6418  0.6463
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37616
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0437
Overall R factor                     =     0.2192
Free R factor                        =     0.2459
Average Fourier shell correlation    =     0.8245
AverageFree Fourier shell correlation=     0.8162
Overall weighted R factor            =     0.1827
Free weighted R factor               =     0.2045
Overall weighted R2 factor           =     0.2103
Free weighted R2 factor              =     0.2331
Average correlation coefficient      =     0.8306
Overall correlation coefficient      =     0.9598
Free correlation coefficient         =     0.9475
Cruickshanks DPI for coordinate error=     0.0781
DPI based on free R factor           =     0.0786
Overall figure of merit              =     0.6549
ML based su of positional parameters =     0.0787
ML based su of thermal parameters    =     2.2954
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176554.50       27320.105       1095446.6      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.28012797    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1071967.3    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0881
Partial structure    1: scale =     0.3935, B  =   45.7095
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2199
Free R factor                        =     0.2461
Average Fourier shell correlation    =     0.8417
AverageFree Fourier shell correlation=     0.8344
Average correlation coefficient      =     0.8290
Overall figure of merit              =     0.6861
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175547.92       9930.4287       1071967.3       1095446.6    


     CGMAT cycle number =      3

 Weight matrix   0.28538004    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1069672.6    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0132
Partial structure    1: scale =     0.3946, B  =   42.1601
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2189
Free R factor                        =     0.2459
Average Fourier shell correlation    =     0.8457
AverageFree Fourier shell correlation=     0.8381
Average correlation coefficient      =     0.8301
Overall figure of merit              =     0.6905
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    175334.61       8926.2285       1069672.6       1071967.3    


     CGMAT cycle number =      4

 Weight matrix   0.28646353    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068996.5    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0099
Partial structure    1: scale =     0.3940, B  =   39.2212
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2188
Free R factor                        =     0.2458
Average Fourier shell correlation    =     0.8467
AverageFree Fourier shell correlation=     0.8390
Average correlation coefficient      =     0.8306
Overall figure of merit              =     0.6914
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    175288.83       8526.9580       1068996.5       1069672.6    


     CGMAT cycle number =      5

 Weight matrix   0.28663301    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068861.1    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0000
Partial structure    1: scale =     0.3940, B  =   39.2212
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2187
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8467
AverageFree Fourier shell correlation=     0.8391
Average correlation coefficient      =     0.8308
Overall figure of merit              =     0.6915
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    175278.08       8456.7539       1068861.1       1068996.5    


     CGMAT cycle number =      6

 Weight matrix   0.28683978    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068825.0    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0002
Partial structure    1: scale =     0.3940, B  =   39.2249
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2187
Free R factor                        =     0.2458
Average Fourier shell correlation    =     0.8468
AverageFree Fourier shell correlation=     0.8391
Average correlation coefficient      =     0.8308
Overall figure of merit              =     0.6915
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    175272.72       8453.0000       1068825.0       1068861.1    


     CGMAT cycle number =      7

 Weight matrix   0.28699413    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068821.1    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0013
Partial structure    1: scale =     0.3940, B  =   39.3115
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2187
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8468
AverageFree Fourier shell correlation=     0.8392
Average correlation coefficient      =     0.8308
Overall figure of merit              =     0.6916
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    175272.64       8449.6846       1068821.1       1068825.0    


     CGMAT cycle number =      8

 Weight matrix   0.28744167    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068824.9    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0002
Partial structure    1: scale =     0.3940, B  =   39.3275
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2187
Free R factor                        =     0.2456
Average Fourier shell correlation    =     0.8469
AverageFree Fourier shell correlation=     0.8392
Average correlation coefficient      =     0.8308
Overall figure of merit              =     0.6916
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    175273.83       8447.6768       1068820.6       1068821.1    
 fvalues    175273.83       8447.6768       1068820.6       1068826.4    


     CGMAT cycle number =      9

 Weight matrix   0.28739521    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068829.5    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0002
Partial structure    1: scale =     0.3940, B  =   39.3181
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2187
Free R factor                        =     0.2455
Average Fourier shell correlation    =     0.8469
AverageFree Fourier shell correlation=     0.8392
Average correlation coefficient      =     0.8308
Overall figure of merit              =     0.6916
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    175275.41       8441.2910       1068836.4       1068826.4    

 fvalues    175275.41       8441.2910       1068835.6       1068829.5    
 fvalues    175275.41       8441.2910       1068835.6       1068829.5    


     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.= 0.906 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        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.28734922    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                40.6
Norm of Geom. positional gradient                40.6
Norm of X_ray B-factor gradient                  98.7
Norm of Geom. B-factor gradient                  98.5
Product of X_ray and Geom posit. gradients     -0.160E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.314E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.1060E+07 GEOM=      8441.     TOTAL=     0.1069E+07
 function value    1068856.8    

-------------------------------------------------------------------------------
             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     1.799     1.644
Bond angles  : others                          3242     1.493     1.582
Torsion angles, period  1. refined              184     6.814     5.000
Torsion angles, period  2. refined               90    35.688    22.778
Torsion angles, period  3. refined              268    13.022    15.000
Torsion angles, period  4. refined                9    11.663    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   306     0.265     0.200
VDW repulsions.others                          1364     0.203     0.200
VDW; torsion: refined_atoms                     730     0.172     0.200
VDW; torsion.others                             793     0.083     0.200
HBOND: refined_atoms                            208     0.198     0.200
HBOND.others                                      1     0.046     0.200
VDW repulsions: symmetry: refined_atoms           8     0.210     0.200
VDW repulsions: symmetry: others                 24     0.159     0.200
HBOND: symmetry: refined_atoms                   17     0.286     0.200
M. chain bond B values: refined atoms           745     1.821     1.698
M. chain bond B values: others                  745     1.818     1.698
M. chain angle B values: refined atoms          926     2.793     2.535
M. chain angle B values: others                 927     2.792     2.535
S. chain bond B values: refined atoms           811     3.238     2.111
S. chain bond B values: others                  810     3.233     2.111
S. chain angle B values: refined atoms         1177     4.935     2.997
S. chain angle B values: others                1178     4.933     2.997
Long range B values: refined atoms             1843     7.795    23.312
Long range B values: others                    1756     7.455    21.846
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0006
Partial structure    1: scale =     0.3939, B  =   39.3010
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5065 100.00   379.4   389.3  0.18  0.18     264   398.6   400.4  0.19  0.20
 0.186    8713  99.98   206.0   182.0  0.19  0.17     430   209.0   183.8  0.22  0.20
 0.310   11038 100.00    92.0    88.6  0.23  0.20     609    92.9    90.3  0.27  0.23
 0.434   12800  98.63    38.7    48.0  0.47  0.46     695    39.1    49.3  0.47  0.45
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3823   0.916   1242   0.821   5065   0.893  0.951  0.9657  0.9705  0.9086  0.9351
  0.1863   7476   0.882   1237   0.782   8713   0.868  1.096  0.9522  0.9620  0.9007  0.9389
  0.3102   9800   0.802   1238   0.725  11038   0.793  0.948  0.9184  0.9328  0.8692  0.9118
  0.4340  11544   0.408   1256   0.368  12800   0.404  0.383  0.6519  0.6455  0.6410  0.6460
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37616
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0437
Overall R factor                     =     0.2187
Free R factor                        =     0.2455
Average Fourier shell correlation    =     0.8469
AverageFree Fourier shell correlation=     0.8392
Overall weighted R factor            =     0.1824
Free weighted R factor               =     0.2043
Overall weighted R2 factor           =     0.2105
Free weighted R2 factor              =     0.2326
Average correlation coefficient      =     0.8308
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9476
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0785
Overall figure of merit              =     0.6916
ML based su of positional parameters =     0.0703
ML based su of thermal parameters    =     2.0412
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    175280.17       8441.3359       1068859.4       1068829.5    

 fvalues    175280.17       8441.3359       1068861.3       1068858.5    
 fvalues    175280.17       8441.3359       1068861.3       1068858.5    

    ****                              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

 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
          28          24          36  0.70425701      2.37302221E-02  0.70425248    
          36           8          36  0.70425701      2.37302221E-02  0.70425248    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R17_1-42A.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     1.799     1.644
Bond angles  : others                          3242     1.493     1.582
Torsion angles, period  1. refined              184     6.814     5.000
Torsion angles, period  2. refined               90    35.686    22.778
Torsion angles, period  3. refined              268    13.021    15.000
Torsion angles, period  4. refined                9    11.662    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   306     0.265     0.200
VDW repulsions.others                          1364     0.203     0.200
VDW; torsion: refined_atoms                     730     0.172     0.200
VDW; torsion.others                             794     0.083     0.200
HBOND: refined_atoms                            208     0.198     0.200
HBOND.others                                      1     0.046     0.200
VDW repulsions: symmetry: refined_atoms           8     0.210     0.200
VDW repulsions: symmetry: others                 24     0.159     0.200
HBOND: symmetry: refined_atoms                   17     0.287     0.200
M. chain bond B values: refined atoms           745     1.821     1.698
M. chain bond B values: others                  745     1.818     1.698
M. chain angle B values: refined atoms          926     2.793     2.535
M. chain angle B values: others                 927     2.792     2.535
S. chain bond B values: refined atoms           811     3.238     2.111
S. chain bond B values: others                  810     3.232     2.111
S. chain angle B values: refined atoms         1177     4.935     2.997
S. chain angle B values: others                1178     4.933     2.997
Long range B values: refined atoms             1843     7.794    23.312
Long range B values: others                    1756     7.454    21.846
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0003
Partial structure    1: scale =     0.3939, B  =   39.3007
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5065 100.00   379.4   389.3  0.18  0.18     264   398.6   400.4  0.19  0.20
 0.186    8713  99.98   206.0   182.0  0.19  0.17     430   209.0   183.8  0.22  0.20
 0.310   11038 100.00    92.0    88.6  0.23  0.20     609    92.9    90.3  0.27  0.23
 0.434   12800  98.63    38.7    48.0  0.47  0.46     695    39.1    49.3  0.47  0.45
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3823   0.916   1242   0.821   5065   0.893  0.951  0.9657  0.9705  0.9087  0.9351
  0.1863   7476   0.882   1237   0.782   8713   0.868  1.096  0.9522  0.9620  0.9007  0.9389
  0.3102   9800   0.802   1238   0.725  11038   0.793  0.948  0.9184  0.9328  0.8691  0.9118
  0.4340  11544   0.408   1256   0.368  12800   0.404  0.383  0.6519  0.6455  0.6410  0.6460
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37616
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0437
Overall R factor                     =     0.2187
Free R factor                        =     0.2454
Average Fourier shell correlation    =     0.8469
AverageFree Fourier shell correlation=     0.8392
Overall weighted R factor            =     0.1824
Free weighted R factor               =     0.2043
Overall weighted R2 factor           =     0.2105
Free weighted R2 factor              =     0.2326
Average correlation coefficient      =     0.8308
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9476
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0785
Overall figure of merit              =     0.6916
ML based su of positional parameters =     0.0703
ML based su of thermal parameters    =     2.0412
-----------------------------------------------------------------------------
  Time in seconds: CPU =        27.35
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2192   0.2459   0.655      176555.    9549.6   0.0129  0.967   1.814  1.052   0.089
       1   0.2199   0.2461   0.686      175548.    9520.1   0.0118  0.889   1.744  1.013   0.087
       2   0.2189   0.2459   0.690      175335.    9514.4   0.0127  0.952   1.778  1.032   0.088
       3   0.2188   0.2458   0.691      175289.    9513.1   0.0127  0.956   1.789  1.038   0.089
       4   0.2187   0.2457   0.691      175278.    9512.7   0.0127  0.958   1.794  1.041   0.089
       5   0.2187   0.2458   0.692      175273.    9512.7   0.0128  0.959   1.796  1.042   0.089
       6   0.2187   0.2457   0.692      175273.    9512.8   0.0128  0.959   1.797  1.043   0.089
       7   0.2187   0.2456   0.692      175274.    9512.7   0.0128  0.959   1.798  1.044   0.089
       8   0.2187   0.2455   0.692      175275.    9512.9   0.0128  0.960   1.799  1.044   0.089
       9   0.2187   0.2455   0.692      175280.    9513.1   0.0128  0.960   1.799  1.044   0.089
      10   0.2187   0.2454   0.692      175280.    9513.1   0.0128  0.960   1.799  1.044   0.089
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2192   0.2187
             R free    0.2459   0.2454
     Rms BondLength    0.0129   0.0128
      Rms BondAngle    1.8136   1.7991
     Rms ChirVolume    0.0888   0.0894
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      59.6s System:    0.2s Elapsed:     1:00