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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: 20:44:54 


 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 1.42     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 4
  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_R04_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R04_1-42A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R04_1-42A.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       0.1240
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4200
  Estimated number of reflections :      51186
  Free R exclusion - flag equals:     4
  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  1.4200

  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_R04_1-50A.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=   2.062 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=   2.192 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=   1.825 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=   2.215 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.392 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.392 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=   2.081 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                            4
Number of "free" reflections       2053
Number of   all  reflections      39817
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          39817

   Current auto weighting coefficient =    6.0498405    

 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.= 0.889 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  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.25115243    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                39.2
Norm of Geom. positional gradient                80.3
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                 0.222E+05
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.471
Product of X_ray and Geom B-fact gradients     -0.308E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1065E+07 GEOM=     0.2605E+05 TOTAL=     0.1091E+07
 function value    1090956.0    

-------------------------------------------------------------------------------
             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     1.788     1.644
Bond angles  : others                          3242     2.344     1.582
Torsion angles, period  1. refined              184     6.838     5.000
Torsion angles, period  2. refined               90    35.687    22.778
Torsion angles, period  3. refined              268    13.316    15.000
Torsion angles, period  4. refined                9    11.474    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   316     0.265     0.200
VDW repulsions.others                          1357     0.230     0.200
VDW; torsion: refined_atoms                     725     0.171     0.200
VDW; torsion.others                             716     0.081     0.200
HBOND: refined_atoms                            209     0.206     0.200
HBOND.others                                      3     0.083     0.200
VDW repulsions: symmetry: refined_atoms           8     0.226     0.200
VDW repulsions: symmetry: others                 23     0.203     0.200
HBOND: symmetry: refined_atoms                   24     0.194     0.200
M. chain bond B values: refined atoms           745     1.740     1.622
M. chain bond B values: others                  745     1.736     1.622
M. chain angle B values: refined atoms          926     2.716     2.421
M. chain angle B values: others                 927     2.715     2.421
S. chain bond B values: refined atoms           811     3.132     2.032
S. chain bond B values: others                  810     3.126     2.031
S. chain angle B values: refined atoms         1177     4.843     2.878
S. chain angle B values: others                1178     4.841     2.877
Long range B values: refined atoms             1852     7.378    22.414
Long range B values: others                    1765     7.121    21.043
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.7800
Partial structure    1: scale =     0.3954, B  =   46.0037
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5055 100.00   380.7   390.0  0.17  0.18     274   373.7   383.1  0.20  0.21
 0.186    8706  99.98   206.0   181.7  0.19  0.17     437   208.3   188.0  0.23  0.20
 0.310   10997 100.00    92.1    88.8  0.23  0.20     650    89.8    86.8  0.27  0.23
 0.434   12813  98.63    38.7    48.0  0.47  0.46     682    39.5    49.3  0.48  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3820   0.912   1235   0.806   5055   0.886  0.953  0.9657  0.9690  0.9266  0.9352
  0.1863   7460   0.863   1246   0.761   8706   0.848  1.095  0.9466  0.9556  0.8957  0.9341
  0.3102   9763   0.811   1234   0.739  10997   0.803  0.953  0.9255  0.9362  0.8883  0.9145
  0.4340  11567   0.316   1246   0.278  12813   0.312  0.320  0.5809  0.5739  0.6039  0.6429
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37571
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.1573
Overall R factor                     =     0.2187
Free R factor                        =     0.2499
Average Fourier shell correlation    =     0.8216
AverageFree Fourier shell correlation=     0.8204
Overall weighted R factor            =     0.1823
Free weighted R factor               =     0.2118
Overall weighted R2 factor           =     0.2093
Free weighted R2 factor              =     0.2544
Average correlation coefficient      =     0.8292
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9493
Cruickshanks DPI for coordinate error=     0.0780
DPI based on free R factor           =     0.0800
Overall figure of merit              =     0.6572
ML based su of positional parameters =     0.0752
ML based su of thermal parameters    =     2.1822
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176022.03       26050.699       1090956.0      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.32253140    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067851.3    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0576
Partial structure    1: scale =     0.3951, B  =   45.3971
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2187
Free R factor                        =     0.2493
Average Fourier shell correlation    =     0.8442
AverageFree Fourier shell correlation=     0.8431
Average correlation coefficient      =     0.8286
Overall figure of merit              =     0.6986
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    174842.92       10079.521       1067851.3       1090956.0    


     CGMAT cycle number =      3

 Weight matrix   0.31791669    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065966.4    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0171
Partial structure    1: scale =     0.3954, B  =   41.6885
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2176
Free R factor                        =     0.2492
Average Fourier shell correlation    =     0.8398
AverageFree Fourier shell correlation=     0.8389
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.6835
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174666.02       9264.8701       1065966.4       1067851.3    


     CGMAT cycle number =      4

 Weight matrix   0.31974939    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065307.9    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0076
Partial structure    1: scale =     0.3953, B  =   38.8882
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2174
Free R factor                        =     0.2491
Average Fourier shell correlation    =     0.8409
AverageFree Fourier shell correlation=     0.8399
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.6845
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174609.45       8948.5303       1065307.9       1065966.4    


     CGMAT cycle number =      5

 Weight matrix   0.32042429    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065169.9    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0004
Partial structure    1: scale =     0.3953, B  =   38.8816
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2173
Free R factor                        =     0.2491
Average Fourier shell correlation    =     0.8411
AverageFree Fourier shell correlation=     0.8400
Average correlation coefficient      =     0.8305
Overall figure of merit              =     0.6848
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    174591.36       8919.9502       1065169.9       1065307.9    


     CGMAT cycle number =      6

 Weight matrix   0.30159426    
 Actual weight    5.4998550      is applied to the X-ray term


 function value    968831.50    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0015
Partial structure    1: scale =     0.3953, B  =   38.8730
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2173
Free R factor                        =     0.2491
Average Fourier shell correlation    =     0.8493
AverageFree Fourier shell correlation=     0.8477
Average correlation coefficient      =     0.8306
Overall figure of merit              =     0.7039
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    174531.02       8936.2090       968831.50       1065169.9    


     CGMAT cycle number =      7

 Weight matrix   0.26427677    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    881851.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0009
Partial structure    1: scale =     0.3953, B  =   38.8574
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2177
Free R factor                        =     0.2491
Average Fourier shell correlation    =     0.8409
AverageFree Fourier shell correlation=     0.8400
Average correlation coefficient      =     0.8304
Overall figure of merit              =     0.6845
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    174646.91       8640.1465       881851.56       968831.50    


     CGMAT cycle number =      8

 Weight matrix   0.26340285    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    881967.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0001
Partial structure    1: scale =     0.3953, B  =   38.7616
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2181
Free R factor                        =     0.2492
Average Fourier shell correlation    =     0.8406
AverageFree Fourier shell correlation=     0.8398
Average correlation coefficient      =     0.8298
Overall figure of merit              =     0.6843
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    174741.45       8287.1846       881984.50       881851.56    

 fvalues    174741.45       8287.1846       881970.19       881971.38    
 fvalues    174741.45       8287.1846       881970.19       881971.38    


     CGMAT cycle number =      9

 Weight matrix   0.26326478    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    881985.75    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =    0.0019
Partial structure    1: scale =     0.3956, B  =   38.7936
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2182
Free R factor                        =     0.2492
Average Fourier shell correlation    =     0.8406
AverageFree Fourier shell correlation=     0.8398
Average correlation coefficient      =     0.8297
Overall figure of merit              =     0.6843
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    174753.50       8250.0098       881995.25       881971.38    

 fvalues    174753.50       8250.0098       881995.44       881994.44    
 fvalues    174753.50       8250.0098       881995.44       881994.44    


     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.= 0.909 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  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.26320171    
 Actual weight    4.9998679      is applied to the X-ray term
Norm of X_ray positional gradient                38.2
Norm of Geom. positional gradient                38.4
Norm of X_ray B-factor gradient                  93.7
Norm of Geom. B-factor gradient                  94.9
Product of X_ray and Geom posit. gradients     -0.142E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.287E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.8738E+06 GEOM=      8242.     TOTAL=     0.8820E+06
 function value    882003.06    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.781     1.644
Bond angles  : others                          3242     1.487     1.582
Torsion angles, period  1. refined              184     6.820     5.000
Torsion angles, period  2. refined               90    35.503    22.778
Torsion angles, period  3. refined              268    12.959    15.000
Torsion angles, period  4. refined                9    11.400    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   315     0.265     0.200
VDW repulsions.others                          1371     0.203     0.200
VDW; torsion: refined_atoms                     727     0.171     0.200
VDW; torsion.others                             781     0.083     0.200
HBOND: refined_atoms                            213     0.201     0.200
HBOND.others                                      2     0.108     0.200
VDW repulsions: symmetry: refined_atoms           8     0.224     0.200
VDW repulsions: symmetry: others                 21     0.210     0.200
HBOND: symmetry: refined_atoms                   23     0.198     0.200
M. chain bond B values: refined atoms           745     1.770     1.698
M. chain bond B values: others                  745     1.766     1.698
M. chain angle B values: refined atoms          926     2.748     2.534
M. chain angle B values: others                 927     2.747     2.534
S. chain bond B values: refined atoms           811     3.168     2.112
S. chain bond B values: others                  810     3.162     2.111
S. chain angle B values: refined atoms         1177     4.894     2.996
S. chain angle B values: others                1178     4.892     2.996
Long range B values: refined atoms             1856     7.523    23.499
Long range B values: others                    1766     7.241    22.048
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =    0.0020
Partial structure    1: scale =     0.3957, B  =   38.7960
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5055 100.00   381.1   390.4  0.17  0.18     274   374.1   383.5  0.20  0.21
 0.186    8706  99.98   206.2   182.1  0.19  0.17     437   208.6   188.4  0.23  0.20
 0.310   10997 100.00    92.2    89.0  0.23  0.20     650    89.9    87.0  0.26  0.23
 0.434   12813  98.63    38.7    48.0  0.47  0.46     682    39.6    49.4  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3820   0.927   1235   0.831   5055   0.904  0.955  0.9695  0.9727  0.9267  0.9351
  0.1863   7460   0.885   1246   0.784   8706   0.870  1.099  0.9516  0.9607  0.8961  0.9345
  0.3102   9763   0.834   1234   0.764  10997   0.826  0.959  0.9339  0.9437  0.8897  0.9153
  0.4340  11567   0.353   1246   0.317  12813   0.350  0.338  0.6262  0.6183  0.6046  0.6434
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37571
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.1573
Overall R factor                     =     0.2182
Free R factor                        =     0.2492
Average Fourier shell correlation    =     0.8406
AverageFree Fourier shell correlation=     0.8398
Overall weighted R factor            =     0.1820
Free weighted R factor               =     0.2112
Overall weighted R2 factor           =     0.2093
Free weighted R2 factor              =     0.2543
Average correlation coefficient      =     0.8297
Overall correlation coefficient      =     0.9597
Free correlation coefficient         =     0.9495
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0798
Overall figure of merit              =     0.6843
ML based su of positional parameters =     0.0668
ML based su of thermal parameters    =     1.9304
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    174756.50       8241.6445       882013.19       881994.44    

 fvalues    174756.50       8241.6445       881998.44       882001.06    
 fvalues    174756.50       8241.6445       881998.44       882001.06    

    ****                              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.= 0.909 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
          28          24          36  0.70425701      2.37302221E-02  0.70425248    
          36           8          36  0.70425701      2.37302221E-02  0.70425248    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R04_1-42A.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     1.780     1.644
Bond angles  : others                          3242     1.487     1.582
Torsion angles, period  1. refined              184     6.819     5.000
Torsion angles, period  2. refined               90    35.499    22.778
Torsion angles, period  3. refined              268    12.955    15.000
Torsion angles, period  4. refined                9    11.398    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   315     0.265     0.200
VDW repulsions.others                          1372     0.203     0.200
VDW; torsion: refined_atoms                     727     0.171     0.200
VDW; torsion.others                             780     0.083     0.200
HBOND: refined_atoms                            213     0.201     0.200
HBOND.others                                      2     0.108     0.200
VDW repulsions: symmetry: refined_atoms           8     0.224     0.200
VDW repulsions: symmetry: others                 21     0.210     0.200
HBOND: symmetry: refined_atoms                   23     0.198     0.200
M. chain bond B values: refined atoms           745     1.769     1.698
M. chain bond B values: others                  745     1.765     1.698
M. chain angle B values: refined atoms          926     2.747     2.534
M. chain angle B values: others                 927     2.746     2.534
S. chain bond B values: refined atoms           811     3.167     2.111
S. chain bond B values: others                  810     3.160     2.111
S. chain angle B values: refined atoms         1177     4.891     2.996
S. chain angle B values: others                1178     4.889     2.995
Long range B values: refined atoms             1856     7.521    23.499
Long range B values: others                    1766     7.239    22.047
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =    0.0023
Partial structure    1: scale =     0.3957, B  =   38.7804
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5055 100.00   381.1   390.4  0.17  0.18     274   374.1   383.5  0.20  0.21
 0.186    8706  99.98   206.2   182.1  0.19  0.17     437   208.6   188.4  0.23  0.20
 0.310   10997 100.00    92.2    89.0  0.23  0.20     650    89.9    87.0  0.26  0.23
 0.434   12813  98.63    38.7    48.0  0.47  0.46     682    39.6    49.4  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3820   0.927   1235   0.831   5055   0.904  0.955  0.9695  0.9727  0.9266  0.9351
  0.1863   7460   0.885   1246   0.784   8706   0.870  1.099  0.9516  0.9607  0.8961  0.9345
  0.3102   9763   0.834   1234   0.764  10997   0.826  0.959  0.9339  0.9437  0.8898  0.9152
  0.4340  11567   0.353   1246   0.317  12813   0.350  0.338  0.6262  0.6183  0.6046  0.6434
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37571
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.1573
Overall R factor                     =     0.2182
Free R factor                        =     0.2492
Average Fourier shell correlation    =     0.8406
AverageFree Fourier shell correlation=     0.8398
Overall weighted R factor            =     0.1821
Free weighted R factor               =     0.2113
Overall weighted R2 factor           =     0.2093
Free weighted R2 factor              =     0.2545
Average correlation coefficient      =     0.8297
Overall correlation coefficient      =     0.9598
Free correlation coefficient         =     0.9495
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0798
Overall figure of merit              =     0.6843
ML based su of positional parameters =     0.0668
ML based su of thermal parameters    =     1.9304
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.99
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2187   0.2499   0.657      176022.    9719.7   0.0123  0.921   1.788  1.041   0.088
       1   0.2187   0.2493   0.699      174843.    9680.5   0.0121  0.907   1.768  1.030   0.088
       2   0.2176   0.2492   0.683      174666.    9677.6   0.0133  0.992   1.825  1.064   0.091
       3   0.2174   0.2491   0.685      174609.    9674.7   0.0133  0.998   1.844  1.075   0.092
       4   0.2173   0.2491   0.685      174591.    9673.6   0.0134  1.002   1.854  1.081   0.093
       5   0.2173   0.2491   0.704      174531.    9670.6   0.0134  1.003   1.860  1.084   0.093
       6   0.2177   0.2491   0.685      174647.    9674.1   0.0128  0.958   1.828  1.065   0.091
       7   0.2181   0.2492   0.684      174741.    9676.3   0.0121  0.910   1.786  1.040   0.088
       8   0.2182   0.2492   0.684      174752.    9676.6   0.0121  0.908   1.782  1.037   0.088
       9   0.2182   0.2492   0.684      174757.    9676.9   0.0121  0.908   1.781  1.037   0.088
      10   0.2182   0.2492   0.684      174759.    9677.0   0.0121  0.907   1.780  1.036   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2187   0.2182
             R free    0.2499   0.2492
     Rms BondLength    0.0123   0.0121
      Rms BondAngle    1.7878   1.7800
     Rms ChirVolume    0.0880   0.0881
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      62.0s System:    0.3s Elapsed:     1:03