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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 19:38:47 


 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 11
  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_R11_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R11_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_R11_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:    11
  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_R11_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=   2.042 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=   2.178 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=   1.831 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=   2.203 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=   2.390 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.403 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.086 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                           11
Number of "free" reflections       1682
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.= 0.902 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.27698264    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                38.9
Norm of Geom. positional gradient                79.7
Norm of X_ray B-factor gradient                  108.
Norm of Geom. B-factor gradient                 0.221E+05
Product of X_ray and Geom posit. gradients     -0.137E+08
 Cosine of angle between them                      -0.456
Product of X_ray and Geom B-fact gradients     -0.342E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.9792E+06 GEOM=     0.2621E+05 TOTAL=     0.1005E+07
 function value    1005432.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.775     1.644
Bond angles  : others                          3242     2.344     1.582
Torsion angles, period  1. refined              184     6.876     5.000
Torsion angles, period  2. refined               90    35.786    22.778
Torsion angles, period  3. refined              268    13.397    15.000
Torsion angles, period  4. refined                9    10.681    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   307     0.264     0.200
VDW repulsions.others                          1335     0.233     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             731     0.080     0.200
HBOND: refined_atoms                            222     0.199     0.200
HBOND.others                                      2     0.096     0.200
VDW repulsions: symmetry: refined_atoms           9     0.215     0.200
VDW repulsions: symmetry: others                 24     0.182     0.200
HBOND: symmetry: refined_atoms                   21     0.268     0.200
M. chain bond B values: refined atoms           745     1.715     1.509
M. chain bond B values: others                  745     1.712     1.509
M. chain angle B values: refined atoms          926     2.679     2.251
M. chain angle B values: others                 927     2.678     2.251
S. chain bond B values: refined atoms           811     3.053     1.906
S. chain bond B values: others                  810     3.048     1.906
S. chain angle B values: refined atoms         1177     4.703     2.694
S. chain angle B values: others                1178     4.701     2.693
Long range B values: refined atoms             1855     7.736    21.232
Long range B values: others                    1762     7.468    19.756
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    1.1650
Partial structure    1: scale =     0.3914, B  =   47.4607
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4331 100.00   405.6   415.2  0.17  0.18     216   410.6   434.1  0.21  0.21
 0.167    7422  99.97   228.4   208.3  0.18  0.16     376   220.7   199.8  0.21  0.19
 0.278    9426 100.00   124.1   114.3  0.21  0.19     484   120.5   112.2  0.26  0.23
 0.389   11037 100.00    50.2    62.5  0.41  0.36     604    50.0    63.1  0.44  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3231   0.904   1100   0.800   4331   0.878  0.945  0.9633  0.9672  0.9129  0.9345
  0.1670   6314   0.883   1108   0.785   7422   0.869  1.066  0.9528  0.9621  0.9043  0.9385
  0.2780   8306   0.825   1120   0.745   9426   0.816  1.013  0.9257  0.9412  0.8762  0.9260
  0.3890   9919   0.540   1128   0.473  11047   0.533  0.552  0.7559  0.7589  0.7436  0.7733
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32226
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9605
Overall R factor                     =     0.2071
Free R factor                        =     0.2471
Average Fourier shell correlation    =     0.8870
AverageFree Fourier shell correlation=     0.8754
Overall weighted R factor            =     0.1752
Free weighted R factor               =     0.2085
Overall weighted R2 factor           =     0.2048
Free weighted R2 factor              =     0.2383
Average correlation coefficient      =     0.8777
Overall correlation coefficient      =     0.9590
Free correlation coefficient         =     0.9437
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0900
Overall figure of merit              =     0.7393
ML based su of positional parameters =     0.0728
ML based su of thermal parameters    =     2.1577
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156683.36       26213.238       1005432.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36292997    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    980108.88    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0602
Partial structure    1: scale =     0.3917, B  =   46.5947
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                        =     0.2477
Average Fourier shell correlation    =     0.9071
AverageFree Fourier shell correlation=     0.8961
Average correlation coefficient      =     0.8778
Overall figure of merit              =     0.7794
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155269.36       9726.7773       980108.88       1005432.4    


     CGMAT cycle number =      3

 Weight matrix   0.37695351    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    977616.50    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0115
Partial structure    1: scale =     0.3917, B  =   42.6630
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                     =     0.2057
Free R factor                        =     0.2471
Average Fourier shell correlation    =     0.9116
AverageFree Fourier shell correlation=     0.9002
Average correlation coefficient      =     0.8800
Overall figure of merit              =     0.7880
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    154949.80       9231.5645       977616.50       980108.88    


     CGMAT cycle number =      4

 Weight matrix   0.34506270    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    888954.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0078
Partial structure    1: scale =     0.3924, B  =   41.2292
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                     =     0.2054
Free R factor                        =     0.2465
Average Fourier shell correlation    =     0.9125
AverageFree Fourier shell correlation=     0.9009
Average correlation coefficient      =     0.8809
Overall figure of merit              =     0.7897
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154863.81       9092.7627       888954.13       977616.50    


     CGMAT cycle number =      5

 Weight matrix   0.31401345    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808915.31    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0141
Partial structure    1: scale =     0.3924, B  =   41.2167
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                     =     0.2057
Free R factor                        =     0.2465
Average Fourier shell correlation    =     0.9125
AverageFree Fourier shell correlation=     0.9009
Average correlation coefficient      =     0.8808
Overall figure of merit              =     0.7898
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    154901.83       8845.0225       808915.31       888954.13    


     CGMAT cycle number =      6

 Weight matrix   0.31373531    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808934.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0138
Partial structure    1: scale =     0.3924, B  =   41.1045
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                     =     0.2061
Free R factor                        =     0.2463
Average Fourier shell correlation    =     0.9123
AverageFree Fourier shell correlation=     0.9009
Average correlation coefficient      =     0.8805
Overall figure of merit              =     0.7898
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    154971.91       8541.8955       808962.19       808915.31    
 fvalues    154971.91       8541.8955       808962.19       808974.13    


     CGMAT cycle number =      7

 Weight matrix   0.31331611    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808985.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0185
Partial structure    1: scale =     0.3925, B  =   41.1154
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                     =     0.2062
Free R factor                        =     0.2462
Average Fourier shell correlation    =     0.9123
AverageFree Fourier shell correlation=     0.9008
Average correlation coefficient      =     0.8804
Overall figure of merit              =     0.7897
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05

 fvalues    154982.80       8471.5723       808960.06       808974.13    


     CGMAT cycle number =      8

 Weight matrix   0.31328464    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809004.00    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0220
Partial structure    1: scale =     0.3925, B  =   40.9648
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                     =     0.2062
Free R factor                        =     0.2462
Average Fourier shell correlation    =     0.9122
AverageFree Fourier shell correlation=     0.9008
Average correlation coefficient      =     0.8803
Overall figure of merit              =     0.7897
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    154997.30       8441.7432       809028.50       808960.06    

 fvalues    154997.30       8441.7432       809001.38       809005.13    
 fvalues    154997.30       8441.7432       809001.38       809005.13    


     CGMAT cycle number =      9

 Weight matrix   0.31317881    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809024.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0205
Partial structure    1: scale =     0.3925, B  =   40.9520
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                     =     0.2062
Free R factor                        =     0.2462
Average Fourier shell correlation    =     0.9122
AverageFree Fourier shell correlation=     0.9008
Average correlation coefficient      =     0.8803
Overall figure of merit              =     0.7897
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    155002.61       8428.1768       809035.75       809005.13    

 fvalues    155002.61       8428.1768       809013.56       809019.00    
 fvalues    155002.61       8428.1768       809013.56       809019.00    


     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.= 0.919 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.31289414    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                38.5
Norm of Geom. positional gradient                38.6
Norm of X_ray B-factor gradient                  101.
Norm of Geom. B-factor gradient                  99.9
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.326E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.8006E+06 GEOM=      8424.     TOTAL=     0.8090E+06
 function value    809022.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.769     1.644
Bond angles  : others                          3242     1.495     1.582
Torsion angles, period  1. refined              184     6.865     5.000
Torsion angles, period  2. refined               90    35.649    22.778
Torsion angles, period  3. refined              268    13.369    15.000
Torsion angles, period  4. refined                9    10.582    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.264     0.200
VDW repulsions.others                          1363     0.204     0.200
VDW; torsion: refined_atoms                     717     0.173     0.200
VDW; torsion.others                             790     0.083     0.200
HBOND: refined_atoms                            216     0.199     0.200
HBOND.others                                      1     0.117     0.200
VDW repulsions: symmetry: refined_atoms           9     0.213     0.200
VDW repulsions: symmetry: others                 30     0.159     0.200
HBOND: symmetry: refined_atoms                   20     0.290     0.200
HBOND: symmetry: others                           1     0.007     0.200
M. chain bond B values: refined atoms           745     1.776     1.619
M. chain bond B values: others                  745     1.772     1.619
M. chain angle B values: refined atoms          926     2.754     2.417
M. chain angle B values: others                 927     2.753     2.416
S. chain bond B values: refined atoms           811     3.135     2.029
S. chain bond B values: others                  810     3.129     2.029
S. chain angle B values: refined atoms         1177     4.822     2.874
S. chain angle B values: others                1178     4.820     2.874
Long range B values: refined atoms             1843     7.640    22.341
Long range B values: others                    1753     7.343    20.866
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0235
Partial structure    1: scale =     0.3926, B  =   40.9471
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4331 100.00   406.3   415.6  0.17  0.18     216   411.3   434.4  0.21  0.21
 0.167    7422  99.97   228.8   208.6  0.18  0.16     376   221.0   200.0  0.21  0.18
 0.278    9426 100.00   124.3   114.6  0.21  0.19     484   120.7   112.7  0.26  0.22
 0.389   11037 100.00    50.3    62.6  0.41  0.36     604    50.1    63.2  0.44  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3231   0.926   1100   0.837   4331   0.903  0.949  0.9682  0.9726  0.9130  0.9348
  0.1670   6314   0.901   1108   0.806   7422   0.886  1.068  0.9571  0.9661  0.9053  0.9392
  0.2780   8306   0.844   1120   0.765   9426   0.835  1.016  0.9328  0.9477  0.8780  0.9266
  0.3890   9919   0.648   1128   0.581  11047   0.641  0.606  0.8160  0.8221  0.7446  0.7798
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32226
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9605
Overall R factor                     =     0.2062
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.9122
AverageFree Fourier shell correlation=     0.9007
Overall weighted R factor            =     0.1745
Free weighted R factor               =     0.2082
Overall weighted R2 factor           =     0.2039
Free weighted R2 factor              =     0.2369
Average correlation coefficient      =     0.8803
Overall correlation coefficient      =     0.9593
Free correlation coefficient         =     0.9439
Cruickshanks DPI for coordinate error=     0.0855
DPI based on free R factor           =     0.0897
Overall figure of merit              =     0.7896
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.8138
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    155002.92       8423.7539       809016.19       809019.00    

    ****                              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.= 0.919 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R11_1-50A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.769     1.644
Bond angles  : others                          3242     1.494     1.582
Torsion angles, period  1. refined              184     6.864     5.000
Torsion angles, period  2. refined               90    35.644    22.778
Torsion angles, period  3. refined              268    13.369    15.000
Torsion angles, period  4. refined                9    10.571    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.264     0.200
VDW repulsions.others                          1362     0.204     0.200
VDW; torsion: refined_atoms                     718     0.173     0.200
VDW; torsion.others                             790     0.083     0.200
HBOND: refined_atoms                            216     0.199     0.200
HBOND.others                                      1     0.116     0.200
VDW repulsions: symmetry: refined_atoms           9     0.212     0.200
VDW repulsions: symmetry: others                 30     0.159     0.200
HBOND: symmetry: refined_atoms                   20     0.290     0.200
HBOND: symmetry: others                           1     0.007     0.200
M. chain bond B values: refined atoms           745     1.775     1.619
M. chain bond B values: others                  745     1.772     1.619
M. chain angle B values: refined atoms          926     2.754     2.417
M. chain angle B values: others                 927     2.752     2.417
S. chain bond B values: refined atoms           811     3.133     2.029
S. chain bond B values: others                  810     3.127     2.029
S. chain angle B values: refined atoms         1177     4.818     2.874
S. chain angle B values: others                1178     4.816     2.874
Long range B values: refined atoms             1844     7.634    22.341
Long range B values: others                    1754     7.336    20.866
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0233
Partial structure    1: scale =     0.3927, B  =   40.9381
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4331 100.00   406.3   415.6  0.17  0.18     216   411.2   434.4  0.21  0.21
 0.167    7422  99.97   228.8   208.6  0.18  0.16     376   221.0   200.0  0.21  0.18
 0.278    9426 100.00   124.3   114.6  0.21  0.19     484   120.7   112.7  0.26  0.22
 0.389   11037 100.00    50.3    62.6  0.41  0.36     604    50.1    63.2  0.44  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3231   0.926   1100   0.837   4331   0.903  0.949  0.9682  0.9726  0.9129  0.9348
  0.1670   6314   0.901   1108   0.806   7422   0.886  1.068  0.9572  0.9661  0.9053  0.9392
  0.2780   8306   0.844   1120   0.765   9426   0.835  1.016  0.9328  0.9477  0.8780  0.9265
  0.3890   9919   0.648   1128   0.581  11047   0.641  0.606  0.8160  0.8221  0.7446  0.7798
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32226
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9605
Overall R factor                     =     0.2062
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.9122
AverageFree Fourier shell correlation=     0.9007
Overall weighted R factor            =     0.1745
Free weighted R factor               =     0.2082
Overall weighted R2 factor           =     0.2039
Free weighted R2 factor              =     0.2370
Average correlation coefficient      =     0.8803
Overall correlation coefficient      =     0.9593
Free correlation coefficient         =     0.9438
Cruickshanks DPI for coordinate error=     0.0855
DPI based on free R factor           =     0.0897
Overall figure of merit              =     0.7896
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.8138
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.72
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2071   0.2471   0.739      156683.    8277.2   0.0124  0.931   1.775  1.033   0.086
       1   0.2070   0.2477   0.779      155269.    8230.8   0.0122  0.912   1.748  1.017   0.087
       2   0.2057   0.2471   0.788      154950.    8220.9   0.0134  1.007   1.805  1.050   0.090
       3   0.2054   0.2465   0.790      154864.    8216.8   0.0136  1.019   1.831  1.065   0.092
       4   0.2057   0.2465   0.790      154902.    8216.9   0.0130  0.979   1.815  1.055   0.090
       5   0.2061   0.2463   0.790      154964.    8217.3   0.0124  0.934   1.783  1.036   0.088
       6   0.2062   0.2462   0.790      154988.    8217.9   0.0124  0.931   1.775  1.031   0.088
       7   0.2062   0.2462   0.790      154997.    8218.2   0.0124  0.929   1.771  1.028   0.087
       8   0.2062   0.2462   0.790      155004.    8218.5   0.0124  0.929   1.770  1.028   0.087
       9   0.2062   0.2464   0.790      155004.    8219.2   0.0124  0.928   1.769  1.028   0.088
      10   0.2062   0.2464   0.790      155005.    8219.3   0.0124  0.928   1.769  1.027   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2071   0.2062
             R free    0.2471   0.2464
     Rms BondLength    0.0124   0.0124
      Rms BondAngle    1.7753   1.7687
     Rms ChirVolume    0.0862   0.0875
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      61.7s System:    0.2s Elapsed:     1:02