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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 18:11:18 


 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 1.60     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 12
  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_R12_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R12_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R12_1-60A.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       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:    12
  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  1.6000

  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_R12_1-70A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.042 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.211 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.804 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=   2.182 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=   2.360 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=   2.402 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                           12
Number of "free" reflections       1421
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 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.= 0.869 id.= 3.000 dev= -2.13 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.29101336    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                39.1
Norm of Geom. positional gradient                78.8
Norm of X_ray B-factor gradient                  119.
Norm of Geom. B-factor gradient                 0.213E+05
Product of X_ray and Geom posit. gradients     -0.129E+08
 Cosine of angle between them                      -0.431
Product of X_ray and Geom B-fact gradients     -0.388E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8749E+06 GEOM=     0.2574E+05 TOTAL=     0.9006E+06
 function value    900612.56    

-------------------------------------------------------------------------------
             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     1.763     1.644
Bond angles  : others                          3242     2.337     1.582
Torsion angles, period  1. refined              184     6.822     5.000
Torsion angles, period  2. refined               90    36.444    22.778
Torsion angles, period  3. refined              268    13.462    15.000
Torsion angles, period  4. refined                9    10.837    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   302     0.266     0.200
VDW repulsions.others                          1332     0.231     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             699     0.081     0.200
HBOND: refined_atoms                            232     0.192     0.200
VDW repulsions: symmetry: refined_atoms          10     0.192     0.200
VDW repulsions: symmetry: others                 26     0.170     0.200
HBOND: symmetry: refined_atoms                   24     0.209     0.200
M. chain bond B values: refined atoms           745     1.652     1.385
M. chain bond B values: others                  745     1.650     1.386
M. chain angle B values: refined atoms          926     2.591     2.063
M. chain angle B values: others                 927     2.590     2.063
S. chain bond B values: refined atoms           811     2.849     1.770
S. chain bond B values: others                  810     2.842     1.769
S. chain angle B values: refined atoms         1177     4.441     2.494
S. chain angle B values: others                1178     4.439     2.494
Long range B values: refined atoms             1856     7.991    19.552
Long range B values: others                    1755     7.458    17.914
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0440, B  =    1.2326
Partial structure    1: scale =     0.3858, B  =   48.9154
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3588 100.00   434.3   442.9  0.17  0.18     194   428.5   437.9  0.21  0.22
 0.147    6132  99.97   259.7   243.9  0.17  0.15     312   258.6   244.0  0.20  0.18
 0.244    7807 100.00   168.0   152.2  0.19  0.17     411   166.2   150.1  0.24  0.21
 0.342    9086 100.00    71.6    86.1  0.33  0.26     504    72.2    89.1  0.38  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2625   0.902    963   0.813   3588   0.878  0.944  0.9551  0.9665  0.8918  0.9338
  0.1468   5160   0.887    972   0.789   6132   0.872  1.027  0.9535  0.9624  0.9094  0.9423
  0.2444   6817   0.864    990   0.752   7807   0.849  1.052  0.9399  0.9533  0.8864  0.9359
  0.3419   8111   0.648    980   0.575   9091   0.640  0.691  0.8548  0.8568  0.8335  0.8499
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26617
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0681
Overall R factor                     =     0.1942
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9242
AverageFree Fourier shell correlation=     0.9148
Overall weighted R factor            =     0.1683
Free weighted R factor               =     0.2059
Overall weighted R2 factor           =     0.1989
Free weighted R2 factor              =     0.2349
Average correlation coefficient      =     0.9077
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9349
Cruickshanks DPI for coordinate error=     0.0976
DPI based on free R factor           =     0.1020
Overall figure of merit              =     0.7868
ML based su of positional parameters =     0.0725
ML based su of thermal parameters    =     2.1914
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134603.38       25737.434       900612.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37300935    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    876285.44    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =   -0.0611
Partial structure    1: scale =     0.3859, B  =   48.4158
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1937
Free R factor                        =     0.2384
Average Fourier shell correlation    =     0.9398
AverageFree Fourier shell correlation=     0.9296
Average correlation coefficient      =     0.9087
Overall figure of merit              =     0.8298
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133334.06       9660.4043       876285.44       900612.56    


     CGMAT cycle number =      3

 Weight matrix   0.39056960    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    873592.38    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =   -0.0123
Partial structure    1: scale =     0.3862, B  =   44.4200
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1926
Free R factor                        =     0.2377
Average Fourier shell correlation    =     0.9427
AverageFree Fourier shell correlation=     0.9322
Average correlation coefficient      =     0.9113
Overall figure of merit              =     0.8379
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132988.89       9210.8379       873592.38       876285.44    


     CGMAT cycle number =      4

 Weight matrix   0.39403850    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872843.00    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =    0.0029
Partial structure    1: scale =     0.3861, B  =   43.9339
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1922
Free R factor                        =     0.2371
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9327
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8389
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132885.25       9135.0361       872843.00       873592.38    


     CGMAT cycle number =      5

 Weight matrix   0.35963365    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    794087.31    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =    0.0108
Partial structure    1: scale =     0.3863, B  =   44.1093
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1921
Free R factor                        =     0.2366
Average Fourier shell correlation    =     0.9435
AverageFree Fourier shell correlation=     0.9329
Average correlation coefficient      =     0.9129
Overall figure of merit              =     0.8392
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132834.44       9198.4844       794087.31       872843.00    


     CGMAT cycle number =      6

 Weight matrix   0.32666430    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722699.94    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =    0.0108
Partial structure    1: scale =     0.3862, B  =   44.2656
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1925
Free R factor                        =     0.2364
Average Fourier shell correlation    =     0.9434
AverageFree Fourier shell correlation=     0.9330
Average correlation coefficient      =     0.9128
Overall figure of merit              =     0.8393
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    132872.75       8958.8926       722699.94       794087.31    


     CGMAT cycle number =      7

 Weight matrix   0.32633260    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722661.88    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =    0.0100
Partial structure    1: scale =     0.3860, B  =   44.1552
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1929
Free R factor                        =     0.2364
Average Fourier shell correlation    =     0.9433
AverageFree Fourier shell correlation=     0.9330
Average correlation coefficient      =     0.9123
Overall figure of merit              =     0.8393
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    132926.69       8631.0654       722661.88       722699.94    


     CGMAT cycle number =      8

 Weight matrix   0.32564154    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722737.56    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =    0.0135
Partial structure    1: scale =     0.3862, B  =   44.2012
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1932
Free R factor                        =     0.2365
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9329
Average correlation coefficient      =     0.9123
Overall figure of merit              =     0.8392
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    132956.47       8548.0762       722760.63       722661.88    

 fvalues    132956.47       8548.0762       722741.25       722738.81    
 fvalues    132956.47       8548.0762       722741.25       722738.81    


     CGMAT cycle number =      9

 Weight matrix   0.32589319    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722721.13    

-------------------------------------------------------------------------------
             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 =     0.0440, B  =    0.0096
Partial structure    1: scale =     0.3862, B  =   44.2170
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1932
Free R factor                        =     0.2365
Average Fourier shell correlation    =     0.9433
AverageFree Fourier shell correlation=     0.9329
Average correlation coefficient      =     0.9122
Overall figure of merit              =     0.8392
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    132955.66       8534.7500       722721.13       722738.81    


     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.= 0.879 id.= 3.000 dev= -2.12 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.32538086    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                38.2
Norm of Geom. positional gradient                38.4
Norm of X_ray B-factor gradient                  109.
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.142E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.384E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.7142E+06 GEOM=      8519.     TOTAL=     0.7227E+06
 function value    722748.19    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.772     1.644
Bond angles  : others                          3242     1.504     1.582
Torsion angles, period  1. refined              184     6.805     5.000
Torsion angles, period  2. refined               90    35.954    22.778
Torsion angles, period  3. refined              268    13.046    15.000
Torsion angles, period  4. refined                9    10.850    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.268     0.200
VDW repulsions.others                          1347     0.205     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             791     0.083     0.200
HBOND: refined_atoms                            227     0.195     0.200
HBOND.others                                      1     0.038     0.200
VDW repulsions: symmetry: refined_atoms          10     0.194     0.200
VDW repulsions: symmetry: others                 24     0.186     0.200
HBOND: symmetry: refined_atoms                   21     0.240     0.200
M. chain bond B values: refined atoms           745     1.704     1.501
M. chain bond B values: others                  745     1.701     1.502
M. chain angle B values: refined atoms          926     2.663     2.239
M. chain angle B values: others                 927     2.661     2.239
S. chain bond B values: refined atoms           811     2.956     1.890
S. chain bond B values: others                  810     2.951     1.890
S. chain angle B values: refined atoms         1177     4.567     2.674
S. chain angle B values: others                1178     4.566     2.673
Long range B values: refined atoms             1852     7.762    21.003
Long range B values: others                    1755     7.348    19.407
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0440, B  =    0.0163
Partial structure    1: scale =     0.3863, B  =   44.2345
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3588 100.00   434.4   443.2  0.17  0.18     194   428.6   437.6  0.21  0.22
 0.147    6132  99.97   259.8   243.9  0.17  0.15     312   258.6   243.7  0.20  0.18
 0.244    7807 100.00   168.1   152.2  0.19  0.17     411   166.3   149.7  0.23  0.20
 0.342    9086 100.00    71.6    85.7  0.32  0.26     504    72.2    88.9  0.37  0.29
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2625   0.913    963   0.829   3588   0.890  0.945  0.9580  0.9690  0.8928  0.9339
  0.1468   5160   0.892    972   0.794   6132   0.876  1.027  0.9547  0.9632  0.9096  0.9416
  0.2444   6817   0.879    990   0.770   7807   0.865  1.052  0.9461  0.9581  0.8912  0.9357
  0.3419   8111   0.780    980   0.701   9091   0.772  0.751  0.8990  0.9068  0.8411  0.8639
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26617
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0681
Overall R factor                     =     0.1932
Free R factor                        =     0.2366
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9329
Overall weighted R factor            =     0.1684
Free weighted R factor               =     0.2047
Overall weighted R2 factor           =     0.1996
Free weighted R2 factor              =     0.2350
Average correlation coefficient      =     0.9123
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9356
Cruickshanks DPI for coordinate error=     0.0971
DPI based on free R factor           =     0.1011
Overall figure of merit              =     0.8392
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.8243
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    132960.94       8518.9785       722756.25       722721.13    

 fvalues    132960.94       8518.9785       722742.00       722733.75    
 fvalues    132960.94       8518.9785       722742.00       722733.75    

    ****                              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.= 0.879 id.= 3.000 dev= -2.12 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_R12_1-60A.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     1.771     1.644
Bond angles  : others                          3242     1.504     1.582
Torsion angles, period  1. refined              184     6.805     5.000
Torsion angles, period  2. refined               90    35.949    22.778
Torsion angles, period  3. refined              268    13.043    15.000
Torsion angles, period  4. refined                9    10.852    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   299     0.269     0.200
VDW repulsions.others                          1345     0.205     0.200
VDW; torsion: refined_atoms                     721     0.172     0.200
VDW; torsion.others                             791     0.083     0.200
HBOND: refined_atoms                            227     0.195     0.200
HBOND.others                                      1     0.038     0.200
VDW repulsions: symmetry: refined_atoms          10     0.194     0.200
VDW repulsions: symmetry: others                 24     0.186     0.200
HBOND: symmetry: refined_atoms                   21     0.240     0.200
M. chain bond B values: refined atoms           745     1.704     1.501
M. chain bond B values: others                  745     1.700     1.502
M. chain angle B values: refined atoms          926     2.662     2.239
M. chain angle B values: others                 927     2.661     2.239
S. chain bond B values: refined atoms           811     2.955     1.890
S. chain bond B values: others                  810     2.950     1.890
S. chain angle B values: refined atoms         1177     4.566     2.674
S. chain angle B values: others                1178     4.564     2.673
Long range B values: refined atoms             1850     7.735    20.954
Long range B values: others                    1753     7.318    19.354
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0440, B  =    0.0147
Partial structure    1: scale =     0.3862, B  =   44.2361
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3588 100.00   434.4   443.2  0.17  0.18     194   428.6   437.7  0.21  0.22
 0.147    6132  99.97   259.8   243.9  0.17  0.15     312   258.6   243.8  0.20  0.18
 0.244    7807 100.00   168.1   152.3  0.19  0.17     411   166.3   149.7  0.23  0.20
 0.342    9086 100.00    71.6    85.8  0.32  0.26     504    72.2    89.0  0.37  0.29
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2625   0.913    963   0.829   3588   0.890  0.945  0.9580  0.9690  0.8928  0.9339
  0.1468   5160   0.892    972   0.794   6132   0.876  1.027  0.9547  0.9632  0.9096  0.9415
  0.2444   6817   0.879    990   0.770   7807   0.865  1.052  0.9461  0.9581  0.8912  0.9357
  0.3419   8111   0.780    980   0.701   9091   0.772  0.751  0.8990  0.9068  0.8411  0.8639
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26617
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0681
Overall R factor                     =     0.1932
Free R factor                        =     0.2365
Average Fourier shell correlation    =     0.9432
AverageFree Fourier shell correlation=     0.9329
Overall weighted R factor            =     0.1684
Free weighted R factor               =     0.2047
Overall weighted R2 factor           =     0.1996
Free weighted R2 factor              =     0.2349
Average correlation coefficient      =     0.9123
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9356
Cruickshanks DPI for coordinate error=     0.0971
DPI based on free R factor           =     0.1011
Overall figure of merit              =     0.8392
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.8243
-----------------------------------------------------------------------------
  Time in seconds: CPU =        21.03
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1942   0.2387   0.787      134603.    7339.2   0.0123  0.909   1.763  1.023   0.085
       1   0.1937   0.2384   0.830      133334.    7301.2   0.0123  0.907   1.751  1.017   0.085
       2   0.1926   0.2377   0.838      132989.    7289.6   0.0133  0.986   1.801  1.049   0.087
       3   0.1922   0.2371   0.839      132885.    7284.8   0.0135  1.002   1.827  1.065   0.088
       4   0.1921   0.2366   0.839      132834.    7282.4   0.0136  1.008   1.842  1.075   0.089
       5   0.1925   0.2364   0.839      132873.    7282.2   0.0131  0.967   1.821  1.062   0.087
       6   0.1929   0.2364   0.839      132927.    7282.5   0.0124  0.923   1.785  1.041   0.085
       7   0.1932   0.2365   0.839      132956.    7283.4   0.0124  0.918   1.774  1.035   0.085
       8   0.1932   0.2365   0.839      132956.    7283.4   0.0124  0.917   1.773  1.034   0.085
       9   0.1932   0.2366   0.839      132964.    7283.8   0.0124  0.917   1.772  1.034   0.085
      10   0.1932   0.2365   0.839      132963.    7283.8   0.0124  0.917   1.771  1.033   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1942   0.1932
             R free    0.2387   0.2365
     Rms BondLength    0.0123   0.0124
      Rms BondAngle    1.7634   1.7714
     Rms ChirVolume    0.0849   0.0846
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      53.2s System:    0.2s Elapsed:     0:54