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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: 18:45:11 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.50     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  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_R00_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R00_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R00_1-50A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.5000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R00_1-60A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.052 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=   2.193 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=   1.823 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=   2.220 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=   2.417 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=   2.398 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=   2.121 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                            0
Number of "free" reflections       1689
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.888 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.26730892    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                36.0
Norm of Geom. positional gradient                82.3
Norm of X_ray B-factor gradient                  99.0
Norm of Geom. B-factor gradient                 0.224E+05
Product of X_ray and Geom posit. gradients     -0.142E+08
 Cosine of angle between them                      -0.494
Product of X_ray and Geom B-fact gradients     -0.338E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.9795E+06 GEOM=     0.2691E+05 TOTAL=     0.1006E+07
 function value    1006398.5    

-------------------------------------------------------------------------------
             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     1.861     1.644
Bond angles  : others                          3242     2.363     1.582
Torsion angles, period  1. refined              184     6.792     5.000
Torsion angles, period  2. refined               90    35.528    22.778
Torsion angles, period  3. refined              268    13.284    15.000
Torsion angles, period  4. refined                9    12.008    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.018     0.020
VDW repulsions: refined_atoms                   303     0.267     0.200
VDW repulsions.others                          1354     0.228     0.200
VDW; torsion: refined_atoms                     719     0.175     0.200
VDW; torsion.others                             719     0.083     0.200
HBOND: refined_atoms                            208     0.196     0.200
HBOND.others                                      1     0.010     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 22     0.203     0.200
HBOND: symmetry: refined_atoms                   18     0.196     0.200
M. chain bond B values: refined atoms           745     1.747     1.508
M. chain bond B values: others                  745     1.743     1.508
M. chain angle B values: refined atoms          926     2.725     2.248
M. chain angle B values: others                 927     2.724     2.248
S. chain bond B values: refined atoms           811     3.143     1.912
S. chain bond B values: others                  810     3.138     1.912
S. chain angle B values: refined atoms         1177     4.783     2.700
S. chain angle B values: others                1178     4.781     2.699
Long range B values: refined atoms             1833     7.060    20.689
Long range B values: others                    1746     6.777    19.287
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    1.1422
Partial structure    1: scale =     0.3914, B  =   45.1932
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4341 100.00   406.7   416.4  0.17  0.18     206   398.9   403.8  0.21  0.21
 0.167    7383  99.97   227.7   207.7  0.18  0.16     415   239.6   215.7  0.22  0.20
 0.278    9395 100.00   124.1   114.2  0.21  0.18     515   123.3   114.7  0.25  0.22
 0.389   11089 100.00    50.2    62.5  0.41  0.36     552    50.5    63.8  0.43  0.39
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3228   0.899   1113   0.789   4341   0.871  0.945  0.9572  0.9665  0.9033  0.9350
  0.1670   6271   0.865   1112   0.763   7383   0.849  1.058  0.9455  0.9548  0.8904  0.9346
  0.2780   8277   0.830   1118   0.745   9395   0.820  1.017  0.9345  0.9454  0.8912  0.9302
  0.3890   9980   0.547   1120   0.477  11100   0.540  0.558  0.7593  0.7675  0.7390  0.7764
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32219
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9811
Overall R factor                     =     0.2078
Free R factor                        =     0.2460
Average Fourier shell correlation    =     0.8891
AverageFree Fourier shell correlation=     0.8826
Overall weighted R factor            =     0.1767
Free weighted R factor               =     0.2125
Overall weighted R2 factor           =     0.2068
Free weighted R2 factor              =     0.2485
Average correlation coefficient      =     0.8789
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9378
Cruickshanks DPI for coordinate error=     0.0861
DPI based on free R factor           =     0.0896
Overall figure of merit              =     0.7371
ML based su of positional parameters =     0.0741
ML based su of thermal parameters    =     2.1580
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156725.73       26914.512       1006398.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.34266064    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    981938.00    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0647
Partial structure    1: scale =     0.3907, B  =   43.9710
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2083
Free R factor                        =     0.2449
Average Fourier shell correlation    =     0.9053
AverageFree Fourier shell correlation=     0.8997
Average correlation coefficient      =     0.8783
Overall figure of merit              =     0.7691
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155571.27       9669.0352       981938.00       1006398.5    


     CGMAT cycle number =      3

 Weight matrix   0.35396659    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979594.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0007
Partial structure    1: scale =     0.3904, B  =   40.0329
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2073
Free R factor                        =     0.2449
Average Fourier shell correlation    =     0.9096
AverageFree Fourier shell correlation=     0.9035
Average correlation coefficient      =     0.8804
Overall figure of merit              =     0.7768
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155297.11       9039.2324       979594.81       981938.00    


     CGMAT cycle number =      4

 Weight matrix   0.35780847    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978938.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0010
Partial structure    1: scale =     0.3914, B  =   38.4343
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2071
Free R factor                        =     0.2451
Average Fourier shell correlation    =     0.9110
AverageFree Fourier shell correlation=     0.9047
Average correlation coefficient      =     0.8813
Overall figure of merit              =     0.7795
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    155228.86       8809.8613       978938.88       979594.81    


     CGMAT cycle number =      5

 Weight matrix   0.35906026    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978699.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0124
Partial structure    1: scale =     0.3915, B  =   38.4076
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2070
Free R factor                        =     0.2450
Average Fourier shell correlation    =     0.9114
AverageFree Fourier shell correlation=     0.9050
Average correlation coefficient      =     0.8817
Overall figure of merit              =     0.7804
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    155190.58       8809.4932       978699.25       978938.88    


     CGMAT cycle number =      6

 Weight matrix   0.35913053    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978669.94    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0176
Partial structure    1: scale =     0.3916, B  =   38.3679
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2069
Free R factor                        =     0.2451
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9050
Average correlation coefficient      =     0.8819
Overall figure of merit              =     0.7805
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    155181.97       8833.9717       978669.94       978699.25    


     CGMAT cycle number =      7

 Weight matrix   0.35901260    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978670.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0203
Partial structure    1: scale =     0.3917, B  =   38.3441
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2070
Free R factor                        =     0.2450
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9049
Average correlation coefficient      =     0.8820
Overall figure of merit              =     0.7804
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05

 fvalues    155174.23       8840.5088       978628.13       978669.94    


     CGMAT cycle number =      8

 Weight matrix   0.35864878    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978719.00    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0217
Partial structure    1: scale =     0.3920, B  =   38.4382
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2070
Free R factor                        =     0.2449
Average Fourier shell correlation    =     0.9114
AverageFree Fourier shell correlation=     0.9049
Average correlation coefficient      =     0.8820
Overall figure of merit              =     0.7804
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    155183.20       8844.6777       978673.06       978628.13    
 fvalues    155183.20       8844.6777       978673.06       978688.38    


     CGMAT cycle number =      9

 Weight matrix   0.35886428    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978716.31    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0182
Partial structure    1: scale =     0.3918, B  =   38.4003
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2070
Free R factor                        =     0.2447
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9049
Average correlation coefficient      =     0.8820
Overall figure of merit              =     0.7805
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    155191.91       8835.9170       978729.38       978688.38    
 fvalues    155191.91       8835.9170       978729.38       978734.00    


     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.= 0.907 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  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.35876414    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                43.4
Norm of Geom. positional gradient                43.4
Norm of X_ray B-factor gradient                  110.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.182E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.383E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.9699E+06 GEOM=      8841.     TOTAL=     0.9787E+06
 function value    978747.63    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.861     1.644
Bond angles  : others                          3242     1.515     1.582
Torsion angles, period  1. refined              184     6.797     5.000
Torsion angles, period  2. refined               90    35.364    22.778
Torsion angles, period  3. refined              268    13.168    15.000
Torsion angles, period  4. refined                9    12.262    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   301     0.268     0.200
VDW repulsions.others                          1370     0.201     0.200
VDW; torsion: refined_atoms                     722     0.174     0.200
VDW; torsion.others                             792     0.085     0.200
HBOND: refined_atoms                            202     0.196     0.200
HBOND.others                                      1     0.024     0.200
VDW repulsions: symmetry: refined_atoms           8     0.199     0.200
VDW repulsions: symmetry: others                 22     0.190     0.200
HBOND: symmetry: refined_atoms                   21     0.169     0.200
M. chain bond B values: refined atoms           745     1.804     1.614
M. chain bond B values: others                  745     1.799     1.614
M. chain angle B values: refined atoms          926     2.784     2.408
M. chain angle B values: others                 927     2.783     2.408
S. chain bond B values: refined atoms           811     3.227     2.029
S. chain bond B values: others                  810     3.223     2.029
S. chain angle B values: refined atoms         1177     4.905     2.873
S. chain angle B values: others                1178     4.903     2.872
Long range B values: refined atoms             1830     7.018    21.964
Long range B values: others                    1745     6.793    20.553
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0173
Partial structure    1: scale =     0.3909, B  =   38.4736
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4341 100.00   407.4   417.0  0.17  0.18     206   399.7   404.9  0.21  0.21
 0.167    7383  99.97   228.1   208.1  0.18  0.16     415   240.0   216.0  0.22  0.20
 0.278    9395 100.00   124.3   114.6  0.21  0.18     515   123.5   114.8  0.25  0.22
 0.389   11089 100.00    50.3    62.5  0.40  0.35     552    50.5    63.9  0.43  0.39
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3228   0.918   1113   0.816   4341   0.892  0.948  0.9629  0.9712  0.9053  0.9354
  0.1670   6271   0.877   1112   0.776   7383   0.862  1.058  0.9486  0.9575  0.8917  0.9341
  0.2780   8277   0.849   1118   0.766   9395   0.839  1.019  0.9413  0.9518  0.8934  0.9313
  0.3890   9980   0.639   1120   0.573  11100   0.633  0.606  0.8166  0.8233  0.7410  0.7848
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32219
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9811
Overall R factor                     =     0.2070
Free R factor                        =     0.2444
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9049
Overall weighted R factor            =     0.1764
Free weighted R factor               =     0.2107
Overall weighted R2 factor           =     0.2064
Free weighted R2 factor              =     0.2452
Average correlation coefficient      =     0.8821
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9388
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0890
Overall figure of merit              =     0.7805
ML based su of positional parameters =     0.0639
ML based su of thermal parameters    =     1.8300
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    155190.56       8840.6602       978730.38       978734.00    

    ****                              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.= 0.907 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_R00_1-50A.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     1.861     1.644
Bond angles  : others                          3242     1.515     1.582
Torsion angles, period  1. refined              184     6.796     5.000
Torsion angles, period  2. refined               90    35.341    22.778
Torsion angles, period  3. refined              268    13.168    15.000
Torsion angles, period  4. refined                9    12.258    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.269     0.200
VDW repulsions.others                          1367     0.201     0.200
VDW; torsion: refined_atoms                     723     0.174     0.200
VDW; torsion.others                             795     0.085     0.200
HBOND: refined_atoms                            202     0.196     0.200
HBOND.others                                      1     0.023     0.200
VDW repulsions: symmetry: refined_atoms           8     0.199     0.200
VDW repulsions: symmetry: others                 22     0.191     0.200
HBOND: symmetry: refined_atoms                   21     0.169     0.200
M. chain bond B values: refined atoms           745     1.804     1.614
M. chain bond B values: others                  745     1.799     1.614
M. chain angle B values: refined atoms          926     2.783     2.408
M. chain angle B values: others                 927     2.782     2.408
S. chain bond B values: refined atoms           811     3.227     2.029
S. chain bond B values: others                  810     3.222     2.029
S. chain angle B values: refined atoms         1177     4.904     2.872
S. chain angle B values: others                1178     4.902     2.872
Long range B values: refined atoms             1829     7.019    21.937
Long range B values: others                    1744     6.793    20.523
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0204
Partial structure    1: scale =     0.3905, B  =   38.4943
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4341 100.00   407.4   417.1  0.17  0.18     206   399.7   404.8  0.21  0.21
 0.167    7383  99.97   228.1   208.1  0.18  0.16     415   240.0   216.0  0.22  0.20
 0.278    9395 100.00   124.3   114.6  0.21  0.18     515   123.5   114.8  0.25  0.22
 0.389   11089 100.00    50.3    62.5  0.40  0.35     552    50.5    63.9  0.43  0.39
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3228   0.919   1113   0.816   4341   0.892  0.948  0.9629  0.9712  0.9054  0.9355
  0.1670   6271   0.877   1112   0.776   7383   0.862  1.058  0.9485  0.9575  0.8916  0.9341
  0.2780   8277   0.849   1118   0.766   9395   0.839  1.019  0.9414  0.9519  0.8935  0.9313
  0.3890   9980   0.639   1120   0.573  11100   0.633  0.606  0.8166  0.8233  0.7410  0.7849
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32219
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9811
Overall R factor                     =     0.2071
Free R factor                        =     0.2444
Average Fourier shell correlation    =     0.9115
AverageFree Fourier shell correlation=     0.9049
Overall weighted R factor            =     0.1764
Free weighted R factor               =     0.2107
Overall weighted R2 factor           =     0.2064
Free weighted R2 factor              =     0.2452
Average correlation coefficient      =     0.8821
Overall correlation coefficient      =     0.9592
Free correlation coefficient         =     0.9388
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0890
Overall figure of merit              =     0.7805
ML based su of positional parameters =     0.0639
ML based su of thermal parameters    =     1.8300
-----------------------------------------------------------------------------
  Time in seconds: CPU =        24.85
             Elapsed =         128.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2078   0.2460   0.737      156726.    8410.9   0.0131  0.985   1.861  1.079   0.091
       1   0.2083   0.2449   0.769      155571.    8373.1   0.0118  0.892   1.782  1.033   0.088
       2   0.2073   0.2449   0.777      155297.    8364.9   0.0129  0.972   1.824  1.058   0.090
       3   0.2071   0.2451   0.780      155229.    8362.2   0.0130  0.979   1.840  1.067   0.091
       4   0.2070   0.2450   0.780      155191.    8360.6   0.0130  0.983   1.849  1.073   0.091
       5   0.2069   0.2451   0.780      155182.    8360.5   0.0131  0.985   1.854  1.076   0.092
       6   0.2070   0.2450   0.780      155181.    8360.4   0.0131  0.985   1.857  1.077   0.092
       7   0.2070   0.2449   0.780      155188.    8361.0   0.0131  0.986   1.859  1.078   0.092
       8   0.2070   0.2447   0.781      155189.    8360.8   0.0131  0.985   1.860  1.079   0.092
       9   0.2070   0.2444   0.780      155193.    8361.2   0.0131  0.986   1.861  1.079   0.092
      10   0.2071   0.2444   0.781      155192.    8361.1   0.0131  0.986   1.861  1.079   0.092
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2078   0.2071
             R free    0.2460   0.2444
     Rms BondLength    0.0131   0.0131
      Rms BondAngle    1.8611   1.8609
     Rms ChirVolume    0.0908   0.0921
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      56.9s System:    0.3s Elapsed:     0:57