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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: 19:19:14 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.50     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 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_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R07_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R07_1-50A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:     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  1.5000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R07_1-60A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.052 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=   2.187 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=   1.822 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.203 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.409 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=   2.393 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=   2.093 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       1698
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.893 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.28349644    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                39.2
Norm of Geom. positional gradient                80.0
Norm of X_ray B-factor gradient                  109.
Norm of Geom. B-factor gradient                 0.219E+05
Product of X_ray and Geom posit. gradients     -0.141E+08
 Cosine of angle between them                      -0.464
Product of X_ray and Geom B-fact gradients     -0.352E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.9782E+06 GEOM=     0.2614E+05 TOTAL=     0.1004E+07
 function value    1004300.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.789     1.644
Bond angles  : others                          3242     2.346     1.582
Torsion angles, period  1. refined              184     6.910     5.000
Torsion angles, period  2. refined               90    36.490    22.778
Torsion angles, period  3. refined              268    13.385    15.000
Torsion angles, period  4. refined                9    11.606    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                   309     0.266     0.200
VDW repulsions.others                          1347     0.230     0.200
VDW; torsion: refined_atoms                     729     0.172     0.200
VDW; torsion.others                             724     0.081     0.200
HBOND: refined_atoms                            223     0.201     0.200
HBOND.others                                      2     0.092     0.200
VDW repulsions: symmetry: refined_atoms          10     0.191     0.200
VDW repulsions: symmetry: others                 24     0.229     0.200
HBOND: symmetry: refined_atoms                   22     0.273     0.200
HBOND: symmetry: others                           1     0.002     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     2.692     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             1863     7.539    21.150
Long range B values: others                    1765     7.128    19.614
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =    1.1422
Partial structure    1: scale =     0.3908, B  =   46.9114
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4321 100.00   409.1   418.4  0.17  0.18     226   363.8   375.9  0.21  0.22
 0.167    7416  99.97   228.8   208.2  0.18  0.16     382   225.9   210.3  0.22  0.19
 0.278    9410 100.00   124.0   114.4  0.21  0.19     500   127.3   115.1  0.25  0.22
 0.389   11051 100.00    50.4    62.9  0.41  0.36     590    48.9    59.9  0.43  0.39
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3231   0.912   1090   0.811   4321   0.886  0.946  0.9571  0.9692  0.9024  0.9345
  0.1670   6301   0.880   1115   0.779   7416   0.865  1.064  0.9519  0.9614  0.8988  0.9388
  0.2780   8275   0.829   1135   0.752   9410   0.820  1.016  0.9317  0.9406  0.8941  0.9271
  0.3890   9942   0.552   1121   0.487  11063   0.546  0.559  0.7375  0.7648  0.7334  0.7701
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32210
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0077
Overall R factor                     =     0.2075
Free R factor                        =     0.2482
Average Fourier shell correlation    =     0.8888
AverageFree Fourier shell correlation=     0.8722
Overall weighted R factor            =     0.1754
Free weighted R factor               =     0.2146
Overall weighted R2 factor           =     0.2037
Free weighted R2 factor              =     0.2549
Average correlation coefficient      =     0.8769
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9381
Cruickshanks DPI for coordinate error=     0.0860
DPI based on free R factor           =     0.0904
Overall figure of merit              =     0.7450
ML based su of positional parameters =     0.0720
ML based su of thermal parameters    =     2.1225
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156514.59       26135.594       1004300.0      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35613117    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    981283.44    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0589
Partial structure    1: scale =     0.3907, B  =   46.1431
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2072
Free R factor                        =     0.2478
Average Fourier shell correlation    =     0.9022
AverageFree Fourier shell correlation=     0.8858
Average correlation coefficient      =     0.8773
Overall figure of merit              =     0.7708
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155443.11       9815.4141       981283.44       1004300.0    


     CGMAT cycle number =      3

 Weight matrix   0.36838314    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978643.44    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0201
Partial structure    1: scale =     0.3912, B  =   42.1374
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2061
Free R factor                        =     0.2472
Average Fourier shell correlation    =     0.9075
AverageFree Fourier shell correlation=     0.8912
Average correlation coefficient      =     0.8792
Overall figure of merit              =     0.7828
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155111.02       9250.9355       978643.44       981283.44    


     CGMAT cycle number =      4

 Weight matrix   0.33416095    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    890064.00    

-------------------------------------------------------------------------------
             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 =     0.0455, B  =   -0.0299
Partial structure    1: scale =     0.3913, B  =   40.3779
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2059
Free R factor                        =     0.2467
Average Fourier shell correlation    =     0.9070
AverageFree Fourier shell correlation=     0.8905
Average correlation coefficient      =     0.8801
Overall figure of merit              =     0.7801
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    155068.38       9040.3730       890064.00       978643.44    


     CGMAT cycle number =      5

 Weight matrix   0.30155814    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    810098.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0153
Partial structure    1: scale =     0.3914, B  =   40.3403
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2061
Free R factor                        =     0.2465
Average Fourier shell correlation    =     0.9059
AverageFree Fourier shell correlation=     0.8891
Average correlation coefficient      =     0.8800
Overall figure of merit              =     0.7765
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    155145.67       8768.4648       810098.19       890064.00    


     CGMAT cycle number =      6

 Weight matrix   0.30409130    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809820.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0170
Partial structure    1: scale =     0.3916, B  =   40.2300
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2065
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.9076
AverageFree Fourier shell correlation=     0.8912
Average correlation coefficient      =     0.8796
Overall figure of merit              =     0.7826
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    155153.64       8449.0781       809820.00       810098.19    


     CGMAT cycle number =      7

 Weight matrix   0.30141783    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    810072.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0144
Partial structure    1: scale =     0.3916, B  =   40.1231
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2465
Average Fourier shell correlation    =     0.9061
AverageFree Fourier shell correlation=     0.8894
Average correlation coefficient      =     0.8796
Overall figure of merit              =     0.7780
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    155250.84       8370.6875       809911.44       809820.00    
 fvalues    155250.84       8370.6875       809911.44       810243.69    


     CGMAT cycle number =      8

 Weight matrix   0.30388793    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809966.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0153
Partial structure    1: scale =     0.3901, B  =   40.1524
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2070
Free R factor                        =     0.2460
Average Fourier shell correlation    =     0.9077
AverageFree Fourier shell correlation=     0.8912
Average correlation coefficient      =     0.8794
Overall figure of merit              =     0.7831
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    155204.95       8330.9102       809966.88       810243.69    


     CGMAT cycle number =      9

 Weight matrix   0.30116591    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    810187.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0166
Partial structure    1: scale =     0.3902, B  =   40.1375
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2070
Free R factor                        =     0.2462
Average Fourier shell correlation    =     0.9063
AverageFree Fourier shell correlation=     0.8896
Average correlation coefficient      =     0.8794
Overall figure of merit              =     0.7788
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    155287.36       8309.4980       810022.56       809966.88    
 fvalues    155287.36       8309.4980       810022.56       810371.06    


     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.= 0.913 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        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.30278274    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                38.1
Norm of Geom. positional gradient                38.1
Norm of X_ray B-factor gradient                  99.1
Norm of Geom. B-factor gradient                  99.9
Product of X_ray and Geom posit. gradients     -0.140E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.319E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.8017E+06 GEOM=      8300.     TOTAL=     0.8100E+06
 function value    810048.88    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.757     1.644
Bond angles  : others                          3242     1.490     1.582
Torsion angles, period  1. refined              184     6.936     5.000
Torsion angles, period  2. refined               90    36.293    22.778
Torsion angles, period  3. refined              268    13.305    15.000
Torsion angles, period  4. refined                9    11.753    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.266     0.200
VDW repulsions.others                          1370     0.202     0.200
VDW; torsion: refined_atoms                     728     0.172     0.200
VDW; torsion.others                             787     0.083     0.200
HBOND: refined_atoms                            222     0.197     0.200
HBOND.others                                      2     0.101     0.200
VDW repulsions: symmetry: refined_atoms          10     0.185     0.200
VDW repulsions: symmetry: others                 24     0.213     0.200
HBOND: symmetry: refined_atoms                   22     0.275     0.200
HBOND: symmetry: others                           1     0.008     0.200
M. chain bond B values: refined atoms           745     1.722     1.620
M. chain bond B values: others                  745     1.720     1.620
M. chain angle B values: refined atoms          926     2.709     2.418
M. chain angle B values: others                 927     2.707     2.418
S. chain bond B values: refined atoms           811     3.107     2.026
S. chain bond B values: others                  810     3.102     2.026
S. chain angle B values: refined atoms         1177     4.767     2.871
S. chain angle B values: others                1178     4.765     2.871
Long range B values: refined atoms             1857     7.479    22.463
Long range B values: others                    1760     7.050    20.887
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0167
Partial structure    1: scale =     0.3904, B  =   40.1611
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4321 100.00   409.5   419.0  0.17  0.18     226   364.1   375.8  0.21  0.22
 0.167    7416  99.97   229.0   208.4  0.18  0.16     382   226.2   210.7  0.22  0.19
 0.278    9410 100.00   124.1   114.6  0.21  0.19     500   127.4   115.6  0.25  0.22
 0.389   11051 100.00    50.4    62.8  0.41  0.36     590    48.9    59.7  0.43  0.38
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3231   0.921   1090   0.832   4321   0.899  0.948  0.9594  0.9714  0.9017  0.9336
  0.1670   6301   0.895   1115   0.797   7416   0.880  1.067  0.9558  0.9647  0.8998  0.9389
  0.2780   8275   0.854   1135   0.778   9410   0.845  1.022  0.9407  0.9492  0.8953  0.9280
  0.3890   9942   0.624   1121   0.558  11063   0.617  0.594  0.7800  0.8082  0.7356  0.7769
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32210
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0077
Overall R factor                     =     0.2070
Free R factor                        =     0.2463
Average Fourier shell correlation    =     0.9073
AverageFree Fourier shell correlation=     0.8907
Overall weighted R factor            =     0.1758
Free weighted R factor               =     0.2130
Overall weighted R2 factor           =     0.2048
Free weighted R2 factor              =     0.2562
Average correlation coefficient      =     0.8794
Overall correlation coefficient      =     0.9590
Free correlation coefficient         =     0.9384
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0897
Overall figure of merit              =     0.7821
ML based su of positional parameters =     0.0632
ML based su of thermal parameters    =     1.8399
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    155226.80       8300.1289       810048.88       810371.06    

    ****                              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.= 0.913 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_1-50A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.756     1.644
Bond angles  : others                          3242     1.490     1.582
Torsion angles, period  1. refined              184     6.939     5.000
Torsion angles, period  2. refined               90    36.289    22.778
Torsion angles, period  3. refined              268    13.307    15.000
Torsion angles, period  4. refined                9    11.747    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                   305     0.265     0.200
VDW repulsions.others                          1371     0.202     0.200
VDW; torsion: refined_atoms                     728     0.172     0.200
VDW; torsion.others                             789     0.083     0.200
HBOND: refined_atoms                            222     0.197     0.200
HBOND.others                                      2     0.100     0.200
VDW repulsions: symmetry: refined_atoms          10     0.185     0.200
VDW repulsions: symmetry: others                 24     0.213     0.200
HBOND: symmetry: refined_atoms                   22     0.275     0.200
HBOND: symmetry: others                           1     0.008     0.200
M. chain bond B values: refined atoms           745     1.722     1.619
M. chain bond B values: others                  745     1.719     1.619
M. chain angle B values: refined atoms          926     2.707     2.418
M. chain angle B values: others                 927     2.706     2.418
S. chain bond B values: refined atoms           811     3.105     2.026
S. chain bond B values: others                  810     3.100     2.025
S. chain angle B values: refined atoms         1177     4.765     2.871
S. chain angle B values: others                1178     4.763     2.870
Long range B values: refined atoms             1858     7.504    22.483
Long range B values: others                    1761     7.079    20.910
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0455, B  =   -0.0001
Partial structure    1: scale =     0.3904, B  =   40.1610
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4321 100.00   409.5   418.9  0.17  0.18     226   364.1   375.7  0.21  0.22
 0.167    7416  99.97   229.0   208.3  0.18  0.16     382   226.2   210.5  0.22  0.19
 0.278    9410 100.00   124.1   114.5  0.21  0.19     500   127.4   115.5  0.25  0.22
 0.389   11051 100.00    50.4    62.7  0.41  0.36     590    48.9    59.6  0.42  0.38
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3231   0.921   1090   0.832   4321   0.899  0.948  0.9592  0.9714  0.9012  0.9336
  0.1670   6301   0.895   1115   0.797   7416   0.880  1.067  0.9557  0.9647  0.8998  0.9389
  0.2780   8275   0.854   1135   0.777   9410   0.845  1.022  0.9406  0.9491  0.8953  0.9280
  0.3890   9942   0.610   1121   0.546  11063   0.604  0.586  0.7751  0.8039  0.7356  0.7770
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32210
Percentage observed                  =    99.9912
Percentage of free reflections       =     5.0077
Overall R factor                     =     0.2070
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.9058
AverageFree Fourier shell correlation=     0.8890
Overall weighted R factor            =     0.1759
Free weighted R factor               =     0.2133
Overall weighted R2 factor           =     0.2049
Free weighted R2 factor              =     0.2568
Average correlation coefficient      =     0.8794
Overall correlation coefficient      =     0.9590
Free correlation coefficient         =     0.9382
Cruickshanks DPI for coordinate error=     0.0858
DPI based on free R factor           =     0.0898
Overall figure of merit              =     0.7773
ML based su of positional parameters =     0.0632
ML based su of thermal parameters    =     1.8399
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.82
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2075   0.2482   0.745      156515.    8390.3   0.0126  0.939   1.789  1.039   0.087
       1   0.2072   0.2478   0.771      155443.    8360.4   0.0124  0.928   1.764  1.024   0.087
       2   0.2061   0.2472   0.783      155111.    8351.6   0.0135  1.009   1.814  1.054   0.090
       3   0.2059   0.2467   0.780      155068.    8350.9   0.0136  1.016   1.831  1.064   0.091
       4   0.2061   0.2465   0.776      155146.    8353.9   0.0130  0.974   1.810  1.052   0.090
       5   0.2065   0.2464   0.783      155154.    8352.4   0.0124  0.928   1.776  1.031   0.087
       6   0.2066   0.2465   0.778      155218.    8355.9   0.0123  0.923   1.765  1.025   0.087
       7   0.2070   0.2460   0.783      155205.    8353.9   0.0123  0.920   1.760  1.022   0.087
       8   0.2070   0.2462   0.779      155252.    8356.8   0.0123  0.920   1.758  1.021   0.087
       9   0.2070   0.2463   0.782      155227.    8355.7   0.0122  0.919   1.757  1.020   0.087
      10   0.2070   0.2464   0.777      155274.    8358.6   0.0122  0.918   1.756  1.020   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2075   0.2070
             R free    0.2482   0.2464
     Rms BondLength    0.0126   0.0122
      Rms BondAngle    1.7889   1.7558
     Rms ChirVolume    0.0868   0.0866
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      56.1s System:    0.2s Elapsed:     0:56