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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: 19:58:27 


 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 15
  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_R15_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R15_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_R15_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:    15
  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_R15_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=   2.058 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=   2.189 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=   1.828 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=   2.212 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=   2.392 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=   2.390 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=   2.060 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                           15
Number of "free" reflections       1708
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.= 0.896 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   0.29311419    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                39.7
Norm of Geom. positional gradient                80.1
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                 0.227E+05
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.466
Product of X_ray and Geom B-fact gradients     -0.374E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.9774E+06 GEOM=     0.2656E+05 TOTAL=     0.1004E+07
 function value    1003913.2    

-------------------------------------------------------------------------------
             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     1.777     1.644
Bond angles  : others                          3242     2.343     1.582
Torsion angles, period  1. refined              184     6.938     5.000
Torsion angles, period  2. refined               90    35.503    22.778
Torsion angles, period  3. refined              268    13.030    15.000
Torsion angles, period  4. refined                9    12.050    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   304     0.267     0.200
VDW repulsions.others                          1341     0.230     0.200
VDW; torsion: refined_atoms                     732     0.172     0.200
VDW; torsion.others                             716     0.081     0.200
HBOND: refined_atoms                            230     0.191     0.200
HBOND.others                                      1     0.101     0.200
VDW repulsions: symmetry: refined_atoms           7     0.241     0.200
VDW repulsions: symmetry: others                 23     0.199     0.200
HBOND: symmetry: refined_atoms                   26     0.198     0.200
M. chain bond B values: refined atoms           745     1.701     1.507
M. chain bond B values: others                  745     1.697     1.507
M. chain angle B values: refined atoms          926     2.688     2.248
M. chain angle B values: others                 927     2.687     2.247
S. chain bond B values: refined atoms           811     2.996     1.896
S. chain bond B values: others                  810     2.990     1.896
S. chain angle B values: refined atoms         1177     4.620     2.681
S. chain angle B values: others                1178     4.618     2.681
Long range B values: refined atoms             1869     7.391    21.311
Long range B values: others                    1772     6.970    19.773
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    1.1774
Partial structure    1: scale =     0.3907, B  =   45.5116
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4327 100.00   405.2   414.3  0.17  0.18     220   440.9   449.7  0.19  0.20
 0.167    7393  99.97   228.8   208.5  0.18  0.16     405   224.8   206.0  0.21  0.18
 0.278    9393 100.00   124.2   114.5  0.21  0.18     517   123.8   114.4  0.24  0.21
 0.389   11075 100.00    50.4    62.8  0.41  0.36     566    48.7    61.3  0.45  0.39
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3211   0.902   1116   0.789   4327   0.873  0.944  0.9666  0.9667  0.9212  0.9339
  0.1670   6270   0.879   1123   0.785   7393   0.864  1.062  0.9477  0.9597  0.9016  0.9349
  0.2780   8268   0.842   1125   0.762   9393   0.832  1.022  0.9391  0.9483  0.9059  0.9307
  0.3890   9963   0.559   1124   0.491  11087   0.552  0.564  0.7450  0.7650  0.7247  0.7732
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32200
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0372
Overall R factor                     =     0.2087
Free R factor                        =     0.2328
Average Fourier shell correlation    =     0.8903
AverageFree Fourier shell correlation=     0.8803
Overall weighted R factor            =     0.1771
Free weighted R factor               =     0.1998
Overall weighted R2 factor           =     0.2055
Free weighted R2 factor              =     0.2337
Average correlation coefficient      =     0.8779
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9499
Cruickshanks DPI for coordinate error=     0.0866
DPI based on free R factor           =     0.0848
Overall figure of merit              =     0.7486
ML based su of positional parameters =     0.0708
ML based su of thermal parameters    =     2.0725
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156384.88       26559.512       1003913.2      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36534446    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979550.38    

-------------------------------------------------------------------------------
             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  =   -0.0355
Partial structure    1: scale =     0.3909, B  =   44.4247
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                     =     0.2084
Free R factor                        =     0.2322
Average Fourier shell correlation    =     0.9073
AverageFree Fourier shell correlation=     0.8976
Average correlation coefficient      =     0.8782
Overall figure of merit              =     0.7785
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155166.11       9813.5781       979550.38       1003913.2    


     CGMAT cycle number =      3

 Weight matrix   0.37648675    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    977232.75    

-------------------------------------------------------------------------------
             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 =     0.3907, B  =   40.4053
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                        =     0.2314
Average Fourier shell correlation    =     0.9111
AverageFree Fourier shell correlation=     0.9012
Average correlation coefficient      =     0.8803
Overall figure of merit              =     0.7842
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    154891.59       9211.5527       977232.75       979550.38    


     CGMAT cycle number =      4

 Weight matrix   0.34492442    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    888667.25    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0059
Partial structure    1: scale =     0.3908, B  =   39.0607
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                        =     0.2315
Average Fourier shell correlation    =     0.9121
AverageFree Fourier shell correlation=     0.9020
Average correlation coefficient      =     0.8813
Overall figure of merit              =     0.7855
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154820.25       9053.3984       888667.25       977232.75    


     CGMAT cycle number =      5

 Weight matrix   0.31358218    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808602.88    

-------------------------------------------------------------------------------
             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  =    0.0038
Partial structure    1: scale =     0.3908, B  =   38.9482
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                     =     0.2072
Free R factor                        =     0.2317
Average Fourier shell correlation    =     0.9121
AverageFree Fourier shell correlation=     0.9020
Average correlation coefficient      =     0.8813
Overall figure of merit              =     0.7856
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    154852.17       8789.0625       808602.88       888667.25    


     CGMAT cycle number =      6

 Weight matrix   0.31328493    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808621.81    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0040
Partial structure    1: scale =     0.3910, B  =   38.9656
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                     =     0.2076
Free R factor                        =     0.2318
Average Fourier shell correlation    =     0.9119
AverageFree Fourier shell correlation=     0.9020
Average correlation coefficient      =     0.8810
Overall figure of merit              =     0.7856
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    154919.14       8485.7051       808634.81       808602.88    
 fvalues    154919.14       8485.7051       808634.81       808645.44    


     CGMAT cycle number =      7

 Weight matrix   0.31356135    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808650.19    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0015
Partial structure    1: scale =     0.3911, B  =   38.9841
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                     =     0.2076
Free R factor                        =     0.2319
Average Fourier shell correlation    =     0.9120
AverageFree Fourier shell correlation=     0.9020
Average correlation coefficient      =     0.8809
Overall figure of merit              =     0.7857
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    154934.84       8413.7900       808666.63       808645.44    

 fvalues    154934.84       8413.7900       808673.44       808654.63    
 fvalues    154934.84       8413.7900       808673.44       808654.63    


     CGMAT cycle number =      8

 Weight matrix   0.31324121    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808697.31    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0058
Partial structure    1: scale =     0.3911, B  =   39.0273
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                     =     0.2076
Free R factor                        =     0.2319
Average Fourier shell correlation    =     0.9119
AverageFree Fourier shell correlation=     0.9020
Average correlation coefficient      =     0.8809
Overall figure of merit              =     0.7856
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    154945.39       8403.8906       808701.13       808654.63    

 fvalues    154945.39       8403.8906       808709.81       808699.19    
 fvalues    154945.39       8403.8906       808709.81       808699.19    


     CGMAT cycle number =      9

 Weight matrix   0.31333306    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808697.94    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =    0.0044
Partial structure    1: scale =     0.3911, B  =   39.0278
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                     =     0.2077
Free R factor                        =     0.2319
Average Fourier shell correlation    =     0.9119
AverageFree Fourier shell correlation=     0.9020
Average correlation coefficient      =     0.8809
Overall figure of merit              =     0.7856
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    154945.59       8401.5537       808697.94       808699.19    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.31328115    
 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                  102.
Norm of Geom. B-factor gradient                  101.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.333E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.8003E+06 GEOM=      8398.     TOTAL=     0.8087E+06
 function value    808712.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.770     1.644
Bond angles  : others                          3242     1.494     1.582
Torsion angles, period  1. refined              184     6.944     5.000
Torsion angles, period  2. refined               90    35.450    22.778
Torsion angles, period  3. refined              268    12.946    15.000
Torsion angles, period  4. refined                9    12.318    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                   307     0.265     0.200
VDW repulsions.others                          1351     0.204     0.200
VDW; torsion: refined_atoms                     729     0.171     0.200
VDW; torsion.others                             766     0.084     0.200
HBOND: refined_atoms                            221     0.189     0.200
HBOND.others                                      1     0.124     0.200
VDW repulsions: symmetry: refined_atoms           7     0.246     0.200
VDW repulsions: symmetry: others                 20     0.203     0.200
HBOND: symmetry: refined_atoms                   24     0.217     0.200
M. chain bond B values: refined atoms           745     1.758     1.621
M. chain bond B values: others                  745     1.755     1.621
M. chain angle B values: refined atoms          926     2.757     2.419
M. chain angle B values: others                 927     2.756     2.419
S. chain bond B values: refined atoms           811     3.105     2.025
S. chain bond B values: others                  810     3.100     2.024
S. chain angle B values: refined atoms         1177     4.785     2.869
S. chain angle B values: others                1178     4.783     2.868
Long range B values: refined atoms             1858     7.529    22.571
Long range B values: others                    1765     7.148    21.054
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0062
Partial structure    1: scale =     0.3911, B  =   39.0334
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4327 100.00   405.5   414.6  0.17  0.18     220   441.3   450.1  0.19  0.20
 0.167    7393  99.97   229.0   208.8  0.18  0.16     405   225.0   206.0  0.21  0.18
 0.278    9393 100.00   124.3   114.7  0.21  0.18     517   123.9   114.8  0.24  0.20
 0.389   11075 100.00    50.4    62.8  0.41  0.36     566    48.7    61.3  0.45  0.39
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3211   0.922   1116   0.825   4327   0.897  0.947  0.9709  0.9718  0.9215  0.9345
  0.1670   6270   0.887   1123   0.794   7393   0.873  1.062  0.9501  0.9619  0.9031  0.9358
  0.2780   8268   0.857   1125   0.780   9393   0.848  1.024  0.9463  0.9543  0.9081  0.9308
  0.3890   9963   0.637   1124   0.573  11087   0.631  0.601  0.8003  0.8194  0.7263  0.7810
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32200
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0372
Overall R factor                     =     0.2077
Free R factor                        =     0.2319
Average Fourier shell correlation    =     0.9119
AverageFree Fourier shell correlation=     0.9020
Overall weighted R factor            =     0.1761
Free weighted R factor               =     0.1991
Overall weighted R2 factor           =     0.2040
Free weighted R2 factor              =     0.2335
Average correlation coefficient      =     0.8809
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9503
Cruickshanks DPI for coordinate error=     0.0861
DPI based on free R factor           =     0.0845
Overall figure of merit              =     0.7856
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.7965
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    154948.33       8397.8828       808705.88       808697.94    
 fvalues    154948.33       8397.8828       808705.88       808708.38    

    ****                              VDW outliers                              ****

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

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

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R15_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     1.770     1.644
Bond angles  : others                          3242     1.494     1.582
Torsion angles, period  1. refined              184     6.944     5.000
Torsion angles, period  2. refined               90    35.448    22.778
Torsion angles, period  3. refined              268    12.945    15.000
Torsion angles, period  4. refined                9    12.318    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                   307     0.265     0.200
VDW repulsions.others                          1355     0.204     0.200
VDW; torsion: refined_atoms                     729     0.171     0.200
VDW; torsion.others                             766     0.084     0.200
HBOND: refined_atoms                            221     0.189     0.200
HBOND.others                                      1     0.124     0.200
VDW repulsions: symmetry: refined_atoms           7     0.246     0.200
VDW repulsions: symmetry: others                 20     0.203     0.200
HBOND: symmetry: refined_atoms                   24     0.218     0.200
M. chain bond B values: refined atoms           745     1.758     1.621
M. chain bond B values: others                  745     1.755     1.621
M. chain angle B values: refined atoms          926     2.757     2.419
M. chain angle B values: others                 927     2.756     2.419
S. chain bond B values: refined atoms           811     3.104     2.024
S. chain bond B values: others                  810     3.099     2.024
S. chain angle B values: refined atoms         1177     4.784     2.869
S. chain angle B values: others                1178     4.782     2.868
Long range B values: refined atoms             1858     7.529    22.570
Long range B values: others                    1765     7.147    21.053
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    0.0003
Partial structure    1: scale =     0.3911, B  =   39.0342
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4327 100.00   405.5   414.6  0.17  0.18     220   441.3   450.1  0.19  0.20
 0.167    7393  99.97   229.0   208.8  0.18  0.16     405   225.0   206.1  0.21  0.18
 0.278    9393 100.00   124.3   114.7  0.21  0.18     517   123.9   114.8  0.24  0.20
 0.389   11075 100.00    50.4    62.8  0.41  0.36     566    48.7    61.3  0.45  0.39
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3211   0.922   1116   0.825   4327   0.897  0.947  0.9708  0.9718  0.9214  0.9345
  0.1670   6270   0.887   1123   0.794   7393   0.873  1.062  0.9501  0.9619  0.9031  0.9358
  0.2780   8268   0.857   1125   0.780   9393   0.848  1.024  0.9463  0.9543  0.9081  0.9308
  0.3890   9963   0.638   1124   0.574  11087   0.631  0.601  0.8004  0.8195  0.7263  0.7810
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32200
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0372
Overall R factor                     =     0.2077
Free R factor                        =     0.2319
Average Fourier shell correlation    =     0.9120
AverageFree Fourier shell correlation=     0.9020
Overall weighted R factor            =     0.1761
Free weighted R factor               =     0.1991
Overall weighted R2 factor           =     0.2040
Free weighted R2 factor              =     0.2335
Average correlation coefficient      =     0.8809
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9503
Cruickshanks DPI for coordinate error=     0.0861
DPI based on free R factor           =     0.0845
Overall figure of merit              =     0.7857
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.7965
-----------------------------------------------------------------------------
  Time in seconds: CPU =        27.88
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2087   0.2328   0.749      156385.    8437.1   0.0124  0.927   1.777  1.038   0.088
       1   0.2084   0.2322   0.778      155166.    8394.4   0.0123  0.921   1.755  1.024   0.088
       2   0.2073   0.2314   0.784      154892.    8386.1   0.0134  1.001   1.807  1.055   0.091
       3   0.2070   0.2315   0.786      154820.    8384.0   0.0135  1.014   1.830  1.069   0.092
       4   0.2072   0.2317   0.786      154852.    8384.2   0.0129  0.973   1.812  1.058   0.091
       5   0.2076   0.2318   0.786      154915.    8384.6   0.0123  0.929   1.781  1.040   0.089
       6   0.2076   0.2319   0.786      154934.    8384.6   0.0123  0.924   1.772  1.034   0.088
       7   0.2076   0.2319   0.786      154945.    8384.8   0.0123  0.924   1.771  1.034   0.088
       8   0.2077   0.2319   0.786      154946.    8384.8   0.0123  0.924   1.771  1.034   0.088
       9   0.2077   0.2319   0.786      154949.    8384.8   0.0123  0.924   1.770  1.034   0.088
      10   0.2077   0.2319   0.786      154948.    8384.9   0.0123  0.923   1.770  1.033   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2087   0.2077
             R free    0.2328   0.2319
     Rms BondLength    0.0124   0.0123
      Rms BondAngle    1.7767   1.7698
     Rms ChirVolume    0.0877   0.0882
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      60.0s System:    0.2s Elapsed:     1:01