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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: 18:50:01 


 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 1
  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_R01_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R01_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_R01_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:     1
  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_R01_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=   2.059 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=   2.196 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=   1.832 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=   2.201 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=   2.414 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=   2.394 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=   2.094 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                            1
Number of "free" reflections       1694
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.= 0.900 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   0.28911999    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                38.2
Norm of Geom. positional gradient                82.5
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                 0.231E+05
Product of X_ray and Geom posit. gradients     -0.150E+08
 Cosine of angle between them                      -0.493
Product of X_ray and Geom B-fact gradients     -0.350E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.9765E+06 GEOM=     0.2735E+05 TOTAL=     0.1004E+07
 function value    1003880.9    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.838     1.644
Bond angles  : others                          3242     2.354     1.582
Torsion angles, period  1. refined              184     6.802     5.000
Torsion angles, period  2. refined               90    35.592    22.778
Torsion angles, period  3. refined              268    12.848    15.000
Torsion angles, period  4. refined                9    11.889    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   298     0.272     0.200
VDW repulsions.others                          1337     0.232     0.200
VDW; torsion: refined_atoms                     720     0.173     0.200
VDW; torsion.others                             718     0.081     0.200
HBOND: refined_atoms                            215     0.203     0.200
HBOND.others                                      2     0.083     0.200
VDW repulsions: symmetry: refined_atoms           9     0.188     0.200
VDW repulsions: symmetry: others                 27     0.175     0.200
HBOND: symmetry: refined_atoms                   22     0.188     0.200
HBOND: symmetry: others                           1     0.002     0.200
M. chain bond B values: refined atoms           745     1.770     1.509
M. chain bond B values: others                  745     1.764     1.509
M. chain angle B values: refined atoms          926     2.740     2.250
M. chain angle B values: others                 927     2.739     2.250
S. chain bond B values: refined atoms           811     3.168     1.914
S. chain bond B values: others                  810     3.162     1.913
S. chain angle B values: refined atoms         1177     4.843     2.701
S. chain angle B values: others                1178     4.841     2.701
Long range B values: refined atoms             1837     7.114    20.888
Long range B values: others                    1748     6.888    19.461
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =    1.1713
Partial structure    1: scale =     0.3928, B  =   46.2170
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4313 100.00   405.7   415.5  0.17  0.18     234   403.3   415.3  0.20  0.20
 0.167    7383  99.97   227.6   207.6  0.18  0.16     415   233.7   215.1  0.22  0.19
 0.278    9445 100.00   123.8   113.9  0.21  0.19     465   124.9   117.8  0.24  0.20
 0.389   11061 100.00    50.2    62.6  0.41  0.36     580    48.8    60.1  0.42  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3216   0.906   1097   0.784   4313   0.875  0.946  0.9590  0.9674  0.8936  0.9356
  0.1670   6273   0.874   1110   0.771   7383   0.859  1.060  0.9502  0.9593  0.8947  0.9376
  0.2780   8310   0.830   1135   0.745   9445   0.820  1.017  0.9393  0.9450  0.9102  0.9291
  0.3890   9951   0.590   1122   0.520  11073   0.583  0.584  0.7623  0.7822  0.7631  0.7747
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32214
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9959
Overall R factor                     =     0.2070
Free R factor                        =     0.2381
Average Fourier shell correlation    =     0.8953
AverageFree Fourier shell correlation=     0.8841
Overall weighted R factor            =     0.1758
Free weighted R factor               =     0.2025
Overall weighted R2 factor           =     0.2074
Free weighted R2 factor              =     0.2295
Average correlation coefficient      =     0.8789
Overall correlation coefficient      =     0.9593
Free correlation coefficient         =     0.9403
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0867
Overall figure of merit              =     0.7546
ML based su of positional parameters =     0.0713
ML based su of thermal parameters    =     2.0926
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156253.08       27350.889       1003880.9      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35313234    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979465.88    

-------------------------------------------------------------------------------
             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  =   -0.0563
Partial structure    1: scale =     0.3923, B  =   45.0975
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                     =     0.2075
Free R factor                        =     0.2379
Average Fourier shell correlation    =     0.9107
AverageFree Fourier shell correlation=     0.9006
Average correlation coefficient      =     0.8787
Overall figure of merit              =     0.7840
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155149.91       9830.3125       979465.88       1003880.9    


     CGMAT cycle number =      3

 Weight matrix   0.36477730    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    977184.75    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0072
Partial structure    1: scale =     0.3925, B  =   40.9697
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                     =     0.2065
Free R factor                        =     0.2371
Average Fourier shell correlation    =     0.9141
AverageFree Fourier shell correlation=     0.9039
Average correlation coefficient      =     0.8807
Overall figure of merit              =     0.7901
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    154908.69       9056.6680       977184.75       979465.88    


     CGMAT cycle number =      4

 Weight matrix   0.36797002    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976497.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0115
Partial structure    1: scale =     0.3927, B  =   39.2967
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                     =     0.2063
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9149
AverageFree Fourier shell correlation=     0.9047
Average correlation coefficient      =     0.8815
Overall figure of merit              =     0.7916
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154835.80       8824.9238       976497.44       977184.75    


     CGMAT cycle number =      5

 Weight matrix   0.36917174    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976305.38    

-------------------------------------------------------------------------------
             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  =    0.0066
Partial structure    1: scale =     0.3928, B  =   39.2490
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                        =     0.2366
Average Fourier shell correlation    =     0.9152
AverageFree Fourier shell correlation=     0.9049
Average correlation coefficient      =     0.8819
Overall figure of merit              =     0.7921
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    154806.73       8814.5293       976305.38       976497.44    


     CGMAT cycle number =      6

 Weight matrix   0.36998200    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976245.56    

-------------------------------------------------------------------------------
             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  =    0.0043
Partial structure    1: scale =     0.3928, B  =   39.2513
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                        =     0.2367
Average Fourier shell correlation    =     0.9153
AverageFree Fourier shell correlation=     0.9050
Average correlation coefficient      =     0.8821
Overall figure of merit              =     0.7923
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    154792.92       8841.0098       976245.56       976305.38    


     CGMAT cycle number =      7

 Weight matrix   0.36973712    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976233.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0116
Partial structure    1: scale =     0.3928, B  =   39.2594
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                     =     0.2060
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9153
AverageFree Fourier shell correlation=     0.9050
Average correlation coefficient      =     0.8822
Overall figure of merit              =     0.7922
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    154789.38       8851.5635       976233.94       976245.56    


     CGMAT cycle number =      8

 Weight matrix   0.36981323    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976269.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0116
Partial structure    1: scale =     0.3929, B  =   39.4026
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                     =     0.2060
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9152
AverageFree Fourier shell correlation=     0.9050
Average correlation coefficient      =     0.8822
Overall figure of merit              =     0.7921
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    154790.95       8858.0615       976243.94       976233.94    
 fvalues    154790.95       8858.0615       976243.94       976250.31    


     CGMAT cycle number =      9

 Weight matrix   0.36980766    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976265.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0110
Partial structure    1: scale =     0.3930, B  =   39.5065
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                     =     0.2060
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9153
AverageFree Fourier shell correlation=     0.9050
Average correlation coefficient      =     0.8822
Overall figure of merit              =     0.7922
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    154793.91       8853.0801       976261.00       976250.31    
 fvalues    154793.91       8853.0801       976261.00       976263.75    


     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.= 0.916 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   0.36989826    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                43.6
Norm of Geom. positional gradient                43.6
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  106.
Product of X_ray and Geom posit. gradients     -0.184E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.369E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.9674E+06 GEOM=      8855.     TOTAL=     0.9763E+06
 function value    976259.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.844     1.644
Bond angles  : others                          3242     1.500     1.582
Torsion angles, period  1. refined              184     6.805     5.000
Torsion angles, period  2. refined               90    35.583    22.778
Torsion angles, period  3. refined              268    12.675    15.000
Torsion angles, period  4. refined                9    11.853    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   295     0.274     0.200
VDW repulsions.others                          1356     0.204     0.200
VDW; torsion: refined_atoms                     720     0.173     0.200
VDW; torsion.others                             789     0.084     0.200
HBOND: refined_atoms                            218     0.198     0.200
HBOND.others                                      1     0.101     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 25     0.168     0.200
HBOND: symmetry: refined_atoms                   22     0.179     0.200
HBOND: symmetry: others                           1     0.004     0.200
M. chain bond B values: refined atoms           745     1.829     1.620
M. chain bond B values: others                  745     1.823     1.620
M. chain angle B values: refined atoms          926     2.807     2.418
M. chain angle B values: others                 927     2.805     2.418
S. chain bond B values: refined atoms           811     3.274     2.038
S. chain bond B values: others                  810     3.269     2.037
S. chain angle B values: refined atoms         1177     4.997     2.884
S. chain angle B values: others                1178     4.994     2.883
Long range B values: refined atoms             1837     7.171    22.237
Long range B values: others                    1747     6.939    20.739
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0103
Partial structure    1: scale =     0.3931, B  =   39.5871
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4313 100.00   406.0   415.9  0.17  0.18     234   403.6   416.5  0.20  0.20
 0.167    7383  99.97   227.8   207.9  0.18  0.16     415   233.9   215.6  0.22  0.19
 0.278    9445 100.00   123.9   114.1  0.21  0.19     465   125.0   118.0  0.24  0.20
 0.389   11061 100.00    50.3    62.5  0.40  0.36     580    48.8    60.2  0.42  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3216   0.927   1097   0.820   4313   0.899  0.950  0.9638  0.9730  0.8932  0.9362
  0.1670   6273   0.888   1110   0.787   7383   0.873  1.060  0.9545  0.9629  0.8986  0.9379
  0.2780   8310   0.842   1135   0.758   9445   0.832  1.017  0.9439  0.9497  0.9111  0.9289
  0.3890   9951   0.669   1122   0.601  11073   0.662  0.624  0.8146  0.8317  0.7625  0.7842
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32214
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9959
Overall R factor                     =     0.2060
Free R factor                        =     0.2369
Average Fourier shell correlation    =     0.9153
AverageFree Fourier shell correlation=     0.9050
Overall weighted R factor            =     0.1750
Free weighted R factor               =     0.2009
Overall weighted R2 factor           =     0.2064
Free weighted R2 factor              =     0.2277
Average correlation coefficient      =     0.8823
Overall correlation coefficient      =     0.9597
Free correlation coefficient         =     0.9408
Cruickshanks DPI for coordinate error=     0.0854
DPI based on free R factor           =     0.0863
Overall figure of merit              =     0.7922
ML based su of positional parameters =     0.0629
ML based su of thermal parameters    =     1.8230
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    154792.77       8855.4844       976259.06       976263.75    

    ****                              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.= 0.916 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_R01_1-50A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.844     1.644
Bond angles  : others                          3242     1.500     1.582
Torsion angles, period  1. refined              184     6.804     5.000
Torsion angles, period  2. refined               90    35.573    22.778
Torsion angles, period  3. refined              268    12.669    15.000
Torsion angles, period  4. refined                9    11.841    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   294     0.274     0.200
VDW repulsions.others                          1360     0.203     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             791     0.084     0.200
HBOND: refined_atoms                            218     0.197     0.200
HBOND.others                                      1     0.101     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 25     0.169     0.200
HBOND: symmetry: refined_atoms                   22     0.179     0.200
HBOND: symmetry: others                           1     0.003     0.200
M. chain bond B values: refined atoms           745     1.829     1.620
M. chain bond B values: others                  745     1.824     1.620
M. chain angle B values: refined atoms          926     2.807     2.418
M. chain angle B values: others                 927     2.806     2.418
S. chain bond B values: refined atoms           811     3.274     2.038
S. chain bond B values: others                  810     3.269     2.037
S. chain angle B values: refined atoms         1177     4.997     2.884
S. chain angle B values: others                1178     4.995     2.883
Long range B values: refined atoms             1837     7.177    22.252
Long range B values: others                    1747     6.945    20.754
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0096
Partial structure    1: scale =     0.3931, B  =   39.6349
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4313 100.00   406.0   415.9  0.17  0.18     234   403.6   416.5  0.20  0.20
 0.167    7383  99.97   227.8   207.9  0.18  0.16     415   233.9   215.6  0.22  0.19
 0.278    9445 100.00   123.9   114.1  0.21  0.19     465   125.0   118.0  0.24  0.20
 0.389   11061 100.00    50.3    62.5  0.40  0.36     580    48.8    60.2  0.42  0.38
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3216   0.927   1097   0.820   4313   0.899  0.950  0.9638  0.9731  0.8932  0.9362
  0.1670   6273   0.888   1110   0.787   7383   0.873  1.060  0.9545  0.9629  0.8985  0.9379
  0.2780   8310   0.842   1135   0.758   9445   0.832  1.017  0.9439  0.9496  0.9111  0.9289
  0.3890   9951   0.669   1122   0.601  11073   0.662  0.624  0.8146  0.8317  0.7625  0.7842
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32214
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.9959
Overall R factor                     =     0.2060
Free R factor                        =     0.2370
Average Fourier shell correlation    =     0.9153
AverageFree Fourier shell correlation=     0.9050
Overall weighted R factor            =     0.1750
Free weighted R factor               =     0.2010
Overall weighted R2 factor           =     0.2064
Free weighted R2 factor              =     0.2277
Average correlation coefficient      =     0.8823
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9408
Cruickshanks DPI for coordinate error=     0.0854
DPI based on free R factor           =     0.0863
Overall figure of merit              =     0.7922
ML based su of positional parameters =     0.0629
ML based su of thermal parameters    =     1.8230
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.98
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2070   0.2381   0.755      156253.    8400.0   0.0132  0.992   1.838  1.070   0.089
       1   0.2075   0.2379   0.784      155150.    8366.9   0.0122  0.915   1.772  1.029   0.087
       2   0.2065   0.2371   0.790      154909.    8358.7   0.0130  0.977   1.805  1.048   0.088
       3   0.2063   0.2368   0.792      154836.    8355.4   0.0131  0.986   1.821  1.058   0.089
       4   0.2061   0.2366   0.792      154807.    8354.3   0.0131  0.990   1.830  1.063   0.090
       5   0.2061   0.2367   0.792      154793.    8354.0   0.0132  0.991   1.835  1.066   0.090
       6   0.2060   0.2368   0.792      154789.    8353.8   0.0132  0.992   1.839  1.068   0.090
       7   0.2060   0.2368   0.792      154794.    8353.9   0.0132  0.992   1.841  1.069   0.090
       8   0.2060   0.2368   0.792      154794.    8354.1   0.0132  0.992   1.843  1.070   0.090
       9   0.2060   0.2369   0.792      154793.    8354.1   0.0132  0.992   1.844  1.071   0.090
      10   0.2060   0.2370   0.792      154793.    8354.2   0.0132  0.992   1.844  1.071   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2070   0.2060
             R free    0.2381   0.2370
     Rms BondLength    0.0132   0.0132
      Rms BondAngle    1.8381   1.8445
     Rms ChirVolume    0.0892   0.0904
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      56.0s System:    0.2s Elapsed:     0:56