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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: 17:50:15 


 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 7
  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_R07_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R07_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_R07_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:     7
  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_R07_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=   2.041 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=   2.191 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=   1.830 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=   2.208 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=   2.411 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=   2.391 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=   2.076 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                            7
Number of "free" reflections       1396
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.= 0.903 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        :   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   0.30153784    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                41.2
Norm of Geom. positional gradient                79.1
Norm of X_ray B-factor gradient                  122.
Norm of Geom. B-factor gradient                 0.214E+05
Product of X_ray and Geom posit. gradients     -0.135E+08
 Cosine of angle between them                      -0.428
Product of X_ray and Geom B-fact gradients     -0.393E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8740E+06 GEOM=     0.2592E+05 TOTAL=     0.8999E+06
 function value    899898.56    

-------------------------------------------------------------------------------
             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     1.770     1.644
Bond angles  : others                          3242     2.341     1.582
Torsion angles, period  1. refined              184     6.933     5.000
Torsion angles, period  2. refined               90    36.813    22.778
Torsion angles, period  3. refined              268    13.617    15.000
Torsion angles, period  4. refined                9    11.515    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   306     0.267     0.200
VDW repulsions.others                          1352     0.230     0.200
VDW; torsion: refined_atoms                     723     0.172     0.200
VDW; torsion.others                             719     0.081     0.200
HBOND: refined_atoms                            226     0.199     0.200
HBOND.others                                      2     0.090     0.200
VDW repulsions: symmetry: refined_atoms           9     0.209     0.200
VDW repulsions: symmetry: others                 26     0.217     0.200
HBOND: symmetry: refined_atoms                   24     0.258     0.200
M. chain bond B values: refined atoms           745     1.617     1.388
M. chain bond B values: others                  745     1.615     1.388
M. chain angle B values: refined atoms          926     2.591     2.069
M. chain angle B values: others                 927     2.590     2.068
S. chain bond B values: refined atoms           812     2.955     1.783
S. chain bond B values: others                  811     2.949     1.783
S. chain angle B values: refined atoms         1177     4.582     2.511
S. chain angle B values: others                1178     4.580     2.510
Long range B values: refined atoms             1855     7.508    19.605
Long range B values: others                    1757     7.195    18.119
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    1.2353
Partial structure    1: scale =     0.3872, B  =   49.0724
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3591 100.00   435.5   444.8  0.17  0.17     191   388.3   399.9  0.21  0.22
 0.147    6143  99.97   260.0   243.8  0.17  0.15     301   242.7   236.2  0.21  0.18
 0.244    7794 100.00   166.9   151.2  0.19  0.17     424   179.8   159.5  0.23  0.20
 0.342    9110 100.00    71.6    86.0  0.33  0.26     480    69.0    82.5  0.36  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2637   0.917    954   0.819   3591   0.891  0.947  0.9588  0.9703  0.9011  0.9362
  0.1468   5167   0.892    976   0.801   6143   0.878  1.029  0.9522  0.9648  0.9024  0.9429
  0.2444   6791   0.855   1003   0.748   7794   0.842  1.049  0.9449  0.9495  0.9075  0.9324
  0.3419   8140   0.665    975   0.598   9115   0.658  0.701  0.8484  0.8679  0.8062  0.8573
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26642
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.9790
Overall R factor                     =     0.1930
Free R factor                        =     0.2363
Average Fourier shell correlation    =     0.9279
AverageFree Fourier shell correlation=     0.9152
Overall weighted R factor            =     0.1665
Free weighted R factor               =     0.2079
Overall weighted R2 factor           =     0.1957
Free weighted R2 factor              =     0.2457
Average correlation coefficient      =     0.9096
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9341
Cruickshanks DPI for coordinate error=     0.0969
DPI based on free R factor           =     0.1010
Overall figure of merit              =     0.7937
ML based su of positional parameters =     0.0712
ML based su of thermal parameters    =     2.1590
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134466.11       25915.615       899898.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.38534984    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    876413.38    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0702
Partial structure    1: scale =     0.3876, B  =   48.5303
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                     =     0.1924
Free R factor                        =     0.2363
Average Fourier shell correlation    =     0.9416
AverageFree Fourier shell correlation=     0.9292
Average correlation coefficient      =     0.9105
Overall figure of merit              =     0.8320
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133325.20       9845.8525       876413.38       899898.56    


     CGMAT cycle number =      3

 Weight matrix   0.39470997    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    873939.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0223
Partial structure    1: scale =     0.3872, B  =   44.7017
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                     =     0.1913
Free R factor                        =     0.2358
Average Fourier shell correlation    =     0.9440
AverageFree Fourier shell correlation=     0.9312
Average correlation coefficient      =     0.9131
Overall figure of merit              =     0.8383
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    133008.11       9432.5996       873939.13       876413.38    


     CGMAT cycle number =      4

 Weight matrix   0.36047959    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    794714.75    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0090
Partial structure    1: scale =     0.3872, B  =   44.2937
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                     =     0.1910
Free R factor                        =     0.2355
Average Fourier shell correlation    =     0.9444
AverageFree Fourier shell correlation=     0.9316
Average correlation coefficient      =     0.9140
Overall figure of merit              =     0.8393
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132921.44       9311.8604       794714.75       873939.13    


     CGMAT cycle number =      5

 Weight matrix   0.32765761    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723191.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0066
Partial structure    1: scale =     0.3870, B  =   44.0570
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                     =     0.1913
Free R factor                        =     0.2355
Average Fourier shell correlation    =     0.9444
AverageFree Fourier shell correlation=     0.9315
Average correlation coefficient      =     0.9139
Overall figure of merit              =     0.8392
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132944.95       9062.4180       723191.31       794714.75    


     CGMAT cycle number =      6

 Weight matrix   0.32759383    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723216.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0131
Partial structure    1: scale =     0.3865, B  =   43.9587
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                     =     0.1918
Free R factor                        =     0.2357
Average Fourier shell correlation    =     0.9443
AverageFree Fourier shell correlation=     0.9315
Average correlation coefficient      =     0.9136
Overall figure of merit              =     0.8393
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    133005.88       8747.1563       723218.00       723191.31    

 fvalues    133005.88       8747.1563       723220.88       723203.25    
 fvalues    133005.88       8747.1563       723220.88       723203.25    


     CGMAT cycle number =      7

 Weight matrix   0.32775465    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723215.44    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0149
Partial structure    1: scale =     0.3865, B  =   44.0529
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                     =     0.1918
Free R factor                        =     0.2357
Average Fourier shell correlation    =     0.9443
AverageFree Fourier shell correlation=     0.9316
Average correlation coefficient      =     0.9136
Overall figure of merit              =     0.8395
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    133013.13       8725.6094       723239.75       723203.25    

 fvalues    133013.13       8725.6094       723235.00       723220.75    
 fvalues    133013.13       8725.6094       723235.00       723220.75    


     CGMAT cycle number =      8

 Weight matrix   0.32736763    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723240.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0106
Partial structure    1: scale =     0.3865, B  =   44.0607
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                     =     0.1918
Free R factor                        =     0.2356
Average Fourier shell correlation    =     0.9443
AverageFree Fourier shell correlation=     0.9316
Average correlation coefficient      =     0.9136
Overall figure of merit              =     0.8394
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    133015.55       8716.7998       723237.06       723220.75    

 fvalues    133015.55       8716.7998       723231.19       723224.94    
 fvalues    133015.55       8716.7998       723231.19       723224.94    


     CGMAT cycle number =      9

 Weight matrix   0.32763457    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723237.00    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0154
Partial structure    1: scale =     0.3863, B  =   44.0397
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                     =     0.1918
Free R factor                        =     0.2357
Average Fourier shell correlation    =     0.9443
AverageFree Fourier shell correlation=     0.9316
Average correlation coefficient      =     0.9136
Overall figure of merit              =     0.8394
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    133020.86       8714.1875       723259.56       723224.94    

 fvalues    133020.86       8714.1875       723254.13       723250.81    
 fvalues    133020.86       8714.1875       723254.13       723250.81    


     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.= 0.906 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.32764360    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                38.7
Norm of Geom. positional gradient                38.9
Norm of X_ray B-factor gradient                  108.
Norm of Geom. B-factor gradient                  110.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.382E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7145E+06 GEOM=      8713.     TOTAL=     0.7232E+06
 function value    723224.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.789     1.644
Bond angles  : others                          3242     1.504     1.582
Torsion angles, period  1. refined              184     6.911     5.000
Torsion angles, period  2. refined               90    36.495    22.778
Torsion angles, period  3. refined              268    13.383    15.000
Torsion angles, period  4. refined                9    11.600    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   309     0.266     0.200
VDW repulsions.others                          1357     0.207     0.200
VDW; torsion: refined_atoms                     728     0.172     0.200
VDW; torsion.others                             754     0.085     0.200
HBOND: refined_atoms                            223     0.201     0.200
HBOND.others                                      2     0.110     0.200
VDW repulsions: symmetry: refined_atoms          10     0.191     0.200
VDW repulsions: symmetry: others                 25     0.209     0.200
HBOND: symmetry: refined_atoms                   23     0.267     0.200
HBOND: symmetry: others                           1     0.010     0.200
M. chain bond B values: refined atoms           745     1.695     1.506
M. chain bond B values: others                  745     1.692     1.506
M. chain angle B values: refined atoms          926     2.691     2.248
M. chain angle B values: others                 927     2.690     2.247
S. chain bond B values: refined atoms           811     3.079     1.909
S. chain bond B values: others                  810     3.074     1.909
S. chain angle B values: refined atoms         1177     4.727     2.696
S. chain angle B values: others                1178     4.725     2.695
Long range B values: refined atoms             1862     7.540    21.147
Long range B values: others                    1764     7.129    19.610
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0155
Partial structure    1: scale =     0.3863, B  =   44.0377
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3591 100.00   435.9   445.5  0.17  0.17     191   388.6   400.0  0.21  0.22
 0.147    6143  99.97   260.2   243.7  0.16  0.15     301   242.9   236.1  0.21  0.18
 0.244    7794 100.00   167.1   151.4  0.19  0.17     424   180.0   160.2  0.23  0.20
 0.342    9110 100.00    71.7    85.8  0.32  0.25     480    69.0    82.5  0.36  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2637   0.924    954   0.837   3591   0.901  0.948  0.9607  0.9721  0.9000  0.9355
  0.1468   5167   0.897    976   0.806   6143   0.883  1.029  0.9536  0.9661  0.9037  0.9440
  0.2444   6791   0.870   1003   0.765   7794   0.857  1.049  0.9503  0.9550  0.9086  0.9329
  0.3419   8140   0.779    975   0.708   9115   0.771  0.753  0.8896  0.9096  0.8077  0.8680
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26642
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.9790
Overall R factor                     =     0.1918
Free R factor                        =     0.2357
Average Fourier shell correlation    =     0.9443
AverageFree Fourier shell correlation=     0.9316
Overall weighted R factor            =     0.1666
Free weighted R factor               =     0.2074
Overall weighted R2 factor           =     0.1967
Free weighted R2 factor              =     0.2471
Average correlation coefficient      =     0.9136
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9342
Cruickshanks DPI for coordinate error=     0.0963
DPI based on free R factor           =     0.1007
Overall figure of merit              =     0.8394
ML based su of positional parameters =     0.0620
ML based su of thermal parameters    =     1.8292
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    133016.11       8713.1309       723224.25       723250.81    

    ****                              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.= 0.906 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R07_1-60A.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     1.788     1.644
Bond angles  : others                          3242     1.504     1.582
Torsion angles, period  1. refined              184     6.911     5.000
Torsion angles, period  2. refined               90    36.493    22.778
Torsion angles, period  3. refined              268    13.381    15.000
Torsion angles, period  4. refined                9    11.599    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   309     0.266     0.200
VDW repulsions.others                          1357     0.207     0.200
VDW; torsion: refined_atoms                     727     0.172     0.200
VDW; torsion.others                             754     0.085     0.200
HBOND: refined_atoms                            223     0.201     0.200
HBOND.others                                      2     0.110     0.200
VDW repulsions: symmetry: refined_atoms          10     0.191     0.200
VDW repulsions: symmetry: others                 25     0.209     0.200
HBOND: symmetry: refined_atoms                   23     0.267     0.200
HBOND: symmetry: others                           1     0.010     0.200
M. chain bond B values: refined atoms           745     1.695     1.506
M. chain bond B values: others                  745     1.692     1.506
M. chain angle B values: refined atoms          926     2.691     2.248
M. chain angle B values: others                 927     2.690     2.247
S. chain bond B values: refined atoms           811     3.078     1.909
S. chain bond B values: others                  810     3.074     1.908
S. chain angle B values: refined atoms         1177     4.726     2.696
S. chain angle B values: others                1178     4.724     2.695
Long range B values: refined atoms             1861     7.541    21.151
Long range B values: others                    1763     7.130    19.613
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0159
Partial structure    1: scale =     0.3863, B  =   44.1381
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3591 100.00   435.9   445.5  0.17  0.17     191   388.7   400.0  0.21  0.22
 0.147    6143  99.97   260.2   243.8  0.16  0.15     301   242.9   236.1  0.21  0.18
 0.244    7794 100.00   167.1   151.4  0.19  0.17     424   180.0   160.2  0.23  0.20
 0.342    9110 100.00    71.7    85.8  0.32  0.25     480    69.0    82.5  0.36  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2637   0.924    954   0.837   3591   0.901  0.948  0.9607  0.9721  0.9000  0.9355
  0.1468   5167   0.897    976   0.806   6143   0.883  1.029  0.9536  0.9661  0.9037  0.9440
  0.2444   6791   0.870   1003   0.765   7794   0.857  1.049  0.9503  0.9550  0.9086  0.9329
  0.3419   8140   0.779    975   0.708   9115   0.771  0.753  0.8896  0.9096  0.8077  0.8680
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26642
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.9790
Overall R factor                     =     0.1918
Free R factor                        =     0.2356
Average Fourier shell correlation    =     0.9443
AverageFree Fourier shell correlation=     0.9316
Overall weighted R factor            =     0.1666
Free weighted R factor               =     0.2074
Overall weighted R2 factor           =     0.1967
Free weighted R2 factor              =     0.2471
Average correlation coefficient      =     0.9136
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9342
Cruickshanks DPI for coordinate error=     0.0963
DPI based on free R factor           =     0.1007
Overall figure of merit              =     0.8394
ML based su of positional parameters =     0.0620
ML based su of thermal parameters    =     1.8292
-----------------------------------------------------------------------------
  Time in seconds: CPU =        24.58
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1930   0.2363   0.794      134466.    7189.7   0.0123  0.920   1.770  1.026   0.087
       1   0.1924   0.2363   0.832      133325.    7154.5   0.0126  0.936   1.767  1.025   0.088
       2   0.1913   0.2358   0.838      133008.    7148.3   0.0137  1.016   1.820  1.058   0.090
       3   0.1910   0.2355   0.839      132921.    7145.7   0.0138  1.025   1.841  1.071   0.091
       4   0.1913   0.2355   0.839      132945.    7146.0   0.0132  0.985   1.824  1.060   0.089
       5   0.1918   0.2357   0.839      133008.    7147.4   0.0126  0.940   1.792  1.041   0.087
       6   0.1918   0.2357   0.839      133012.    7147.7   0.0126  0.939   1.790  1.040   0.087
       7   0.1918   0.2356   0.839      133018.    7147.9   0.0126  0.938   1.789  1.039   0.087
       8   0.1918   0.2357   0.839      133018.    7148.0   0.0126  0.938   1.789  1.039   0.087
       9   0.1918   0.2357   0.839      133016.    7148.3   0.0126  0.938   1.789  1.039   0.087
      10   0.1918   0.2356   0.839      133016.    7148.3   0.0126  0.938   1.788  1.039   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1930   0.1918
             R free    0.2363   0.2356
     Rms BondLength    0.0123   0.0126
      Rms BondAngle    1.7704   1.7884
     Rms ChirVolume    0.0866   0.0869
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      56.9s System:    0.2s Elapsed:     0:57