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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: 21:06:55 


 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 8
  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_R08_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R08_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_R08_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:     8
  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_R08_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=   2.183 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=   1.827 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.208 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.391 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=   2.386 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=   2.031 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  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  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:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            8
Number of "free" reflections       1982
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.= 0.893 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  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   0.26505741    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                39.6
Norm of Geom. positional gradient                80.2
Norm of X_ray B-factor gradient                  104.
Norm of Geom. B-factor gradient                  96.9
Product of X_ray and Geom posit. gradients     -0.142E+08
 Cosine of angle between them                      -0.463
Product of X_ray and Geom B-fact gradients     -0.301E+08
 Cosine of angle between them                      -0.922


Residuals: XRAY=     0.1065E+07 GEOM=     0.1267E+05 TOTAL=     0.1078E+07
 function value    1077885.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.756     1.644
Bond angles  : others                          3238     2.351     1.580
Torsion angles, period  1. refined              185     6.864     5.000
Torsion angles, period  2. refined               90    35.706    22.778
Torsion angles, period  3. refined              268    13.000    15.000
Torsion angles, period  4. refined                9    11.416    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   293     0.245     0.200
VDW repulsions.others                          1326     0.221     0.200
VDW; torsion: refined_atoms                     725     0.172     0.200
VDW; torsion.others                             719     0.080     0.200
HBOND: refined_atoms                            212     0.198     0.200
HBOND.others                                      1     0.027     0.200
VDW repulsions: symmetry: refined_atoms           9     0.189     0.200
VDW repulsions: symmetry: others                 24     0.191     0.200
HBOND: symmetry: refined_atoms                   24     0.170     0.200
M. chain bond B values: refined atoms           746     1.757     1.623
M. chain bond B values: others                  746     1.754     1.623
M. chain angle B values: refined atoms          929     2.740     2.427
M. chain angle B values: others                 930     2.739     2.427
S. chain bond B values: refined atoms           811     3.124     2.024
S. chain bond B values: others                  810     3.116     2.024
S. chain angle B values: refined atoms         1177     4.766     2.868
S. chain angle B values: others                1178     4.764     2.868
Long range B values: refined atoms             1832     7.001    22.178
Long range B values: others                    1737     6.728    20.619
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.7745
Partial structure    1: scale =     0.3945, B  =   38.0982
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5057 100.00   380.0   390.1  0.18  0.18     272   377.7   388.4  0.21  0.22
 0.186    8694  99.98   206.0   182.1  0.19  0.17     449   204.1   179.7  0.23  0.20
 0.310   11074 100.00    91.9    88.6  0.23  0.20     573    92.4    88.3  0.26  0.22
 0.434   12816  98.63    38.7    48.0  0.47  0.46     679    39.4    48.4  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3818   0.907   1239   0.794   5057   0.879  0.946  0.9601  0.9672  0.9033  0.9348
  0.1863   7432   0.865   1262   0.762   8694   0.850  1.095  0.9430  0.9566  0.8899  0.9361
  0.3102   9821   0.810   1253   0.735  11074   0.802  0.952  0.9271  0.9353  0.8920  0.9135
  0.4340  11588   0.373   1228   0.335  12816   0.370  0.362  0.6279  0.6221  0.6393  0.6435
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37641
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9806
Overall R factor                     =     0.2191
Free R factor                        =     0.2517
Average Fourier shell correlation    =     0.8378
AverageFree Fourier shell correlation=     0.8323
Overall weighted R factor            =     0.1835
Free weighted R factor               =     0.2169
Overall weighted R2 factor           =     0.2135
Free weighted R2 factor              =     0.2458
Average correlation coefficient      =     0.8296
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9432
Cruickshanks DPI for coordinate error=     0.0780
DPI based on free R factor           =     0.0804
Overall figure of merit              =     0.6761
ML based su of positional parameters =     0.0732
ML based su of thermal parameters    =     2.1055
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176073.73       12667.492       1077885.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.32034478    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066973.6    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0522
Partial structure    1: scale =     0.3948, B  =   38.2460
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                     =     0.2190
Free R factor                        =     0.2507
Average Fourier shell correlation    =     0.8462
AverageFree Fourier shell correlation=     0.8401
Average correlation coefficient      =     0.8297
Overall figure of merit              =     0.6911
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175043.92       7985.8491       1066973.6       1077885.5    


     CGMAT cycle number =      3

 Weight matrix   0.32314500    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066571.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0000
Partial structure    1: scale =     0.3948, B  =   38.2460
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                     =     0.2180
Free R factor                        =     0.2508
Average Fourier shell correlation    =     0.8472
AverageFree Fourier shell correlation=     0.8403
Average correlation coefficient      =     0.8307
Overall figure of merit              =     0.6907
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174884.84       8546.4063       1066571.8       1066973.6    


     CGMAT cycle number =      4

 Weight matrix   0.32303920    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066203.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0046
Partial structure    1: scale =     0.3949, B  =   38.2086
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                     =     0.2178
Free R factor                        =     0.2509
Average Fourier shell correlation    =     0.8467
AverageFree Fourier shell correlation=     0.8394
Average correlation coefficient      =     0.8310
Overall figure of merit              =     0.6892
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174803.19       8672.3271       1066203.8       1066571.8    


     CGMAT cycle number =      5

 Weight matrix   0.32877889    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066040.1    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.0002
Partial structure    1: scale =     0.3949, B  =   38.2224
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                        =     0.2510
Average Fourier shell correlation    =     0.8508
AverageFree Fourier shell correlation=     0.8447
Average correlation coefficient      =     0.8311
Overall figure of merit              =     0.6970
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    174765.95       8734.0078       1066040.1       1066203.8    


     CGMAT cycle number =      6

 Weight matrix   0.29621932    
 Actual weight    5.4998550      is applied to the X-ray term


 function value    970204.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0002
Partial structure    1: scale =     0.3949, B  =   38.2257
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                        =     0.2510
Average Fourier shell correlation    =     0.8482
AverageFree Fourier shell correlation=     0.8415
Average correlation coefficient      =     0.8313
Overall figure of merit              =     0.6921
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    174813.30       8757.0850       970204.88       1066040.1    


     CGMAT cycle number =      7

 Weight matrix   0.27101374    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    882531.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0004
Partial structure    1: scale =     0.3949, B  =   38.2298
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                     =     0.2180
Free R factor                        =     0.2511
Average Fourier shell correlation    =     0.8503
AverageFree Fourier shell correlation=     0.8442
Average correlation coefficient      =     0.8308
Overall figure of merit              =     0.6963
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    174818.30       8463.0273       882531.38       970204.88    


     CGMAT cycle number =      8

 Weight matrix   0.26800737    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883002.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0132
Partial structure    1: scale =     0.3945, B  =   38.3305
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                     =     0.2185
Free R factor                        =     0.2514
Average Fourier shell correlation    =     0.8476
AverageFree Fourier shell correlation=     0.8409
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.6914
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    174941.55       8128.1436       883073.88       882531.38    

 fvalues    174941.55       8128.1436       883068.75       882812.75    
 fvalues    174941.55       8128.1436       883068.75       882812.75    


     CGMAT cycle number =      9

 Weight matrix   0.26767972    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883076.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0109
Partial structure    1: scale =     0.3944, B  =   38.3388
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                     =     0.2185
Free R factor                        =     0.2513
Average Fourier shell correlation    =     0.8475
AverageFree Fourier shell correlation=     0.8409
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.6913
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    174951.27       8109.1094       883108.88       882812.75    

 fvalues    174951.27       8109.1094       883114.81       882842.38    
 fvalues    174951.27       8109.1094       883114.81       882842.38    


     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.= 0.910 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   0.26693851    
 Actual weight    4.9998679      is applied to the X-ray term
Norm of X_ray positional gradient                38.0
Norm of Geom. positional gradient                38.4
Norm of X_ray B-factor gradient                  95.2
Norm of Geom. B-factor gradient                  96.6
Product of X_ray and Geom posit. gradients     -0.141E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.296E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.8750E+06 GEOM=      8103.     TOTAL=     0.8831E+06
 function value    883113.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.763     1.644
Bond angles  : others                          3238     1.494     1.580
Torsion angles, period  1. refined              185     6.870     5.000
Torsion angles, period  2. refined               90    35.644    22.778
Torsion angles, period  3. refined              268    13.017    15.000
Torsion angles, period  4. refined                9    11.300    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   294     0.245     0.200
VDW repulsions.others                          1351     0.193     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             785     0.083     0.200
HBOND: refined_atoms                            210     0.201     0.200
HBOND.others                                      1     0.067     0.200
VDW repulsions: symmetry: refined_atoms           9     0.186     0.200
VDW repulsions: symmetry: others                 22     0.187     0.200
HBOND: symmetry: refined_atoms                   22     0.169     0.200
M. chain bond B values: refined atoms           746     1.806     1.700
M. chain bond B values: others                  746     1.803     1.700
M. chain angle B values: refined atoms          929     2.794     2.542
M. chain angle B values: others                 930     2.793     2.542
S. chain bond B values: refined atoms           811     3.181     2.107
S. chain bond B values: others                  810     3.173     2.106
S. chain angle B values: refined atoms         1177     4.852     2.990
S. chain angle B values: others                1178     4.850     2.989
Long range B values: refined atoms             1828     7.012    22.980
Long range B values: others                    1735     6.742    21.419
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0000
Partial structure    1: scale =     0.3944, B  =   38.3387
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5057 100.00   380.5   390.3  0.17  0.18     272   378.1   389.1  0.21  0.22
 0.186    8694  99.98   206.2   182.2  0.19  0.17     449   204.3   179.7  0.23  0.20
 0.310   11074 100.00    92.0    88.7  0.23  0.20     573    92.5    88.4  0.26  0.22
 0.434   12816  98.63    38.7    47.9  0.47  0.46     679    39.4    48.3  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3818   0.923   1239   0.826   5057   0.899  0.949  0.9658  0.9723  0.9028  0.9354
  0.1863   7432   0.885   1262   0.782   8694   0.870  1.098  0.9487  0.9614  0.8914  0.9360
  0.3102   9821   0.829   1253   0.755  11074   0.821  0.956  0.9346  0.9427  0.8927  0.9140
  0.4340  11588   0.378   1228   0.342  12816   0.375  0.361  0.6397  0.6381  0.6389  0.6448
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37641
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9806
Overall R factor                     =     0.2185
Free R factor                        =     0.2513
Average Fourier shell correlation    =     0.8473
AverageFree Fourier shell correlation=     0.8406
Overall weighted R factor            =     0.1830
Free weighted R factor               =     0.2167
Overall weighted R2 factor           =     0.2128
Free weighted R2 factor              =     0.2463
Average correlation coefficient      =     0.8303
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9433
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0803
Overall figure of merit              =     0.6908
ML based su of positional parameters =     0.0663
ML based su of thermal parameters    =     1.9107
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    174958.41       8102.5410       882856.69       882842.38    
 fvalues    174958.41       8102.5410       882856.69       882871.50    

    ****                              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.= 0.910 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_R08_1-42A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.761     1.644
Bond angles  : others                          3238     1.494     1.580
Torsion angles, period  1. refined              185     6.870     5.000
Torsion angles, period  2. refined               90    35.641    22.778
Torsion angles, period  3. refined              268    13.014    15.000
Torsion angles, period  4. refined                9    11.293    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   294     0.245     0.200
VDW repulsions.others                          1351     0.193     0.200
VDW; torsion: refined_atoms                     723     0.172     0.200
VDW; torsion.others                             786     0.083     0.200
HBOND: refined_atoms                            210     0.201     0.200
HBOND.others                                      1     0.067     0.200
VDW repulsions: symmetry: refined_atoms           9     0.186     0.200
VDW repulsions: symmetry: others                 23     0.183     0.200
HBOND: symmetry: refined_atoms                   22     0.169     0.200
M. chain bond B values: refined atoms           746     1.805     1.699
M. chain bond B values: others                  746     1.802     1.700
M. chain angle B values: refined atoms          929     2.792     2.542
M. chain angle B values: others                 930     2.791     2.541
S. chain bond B values: refined atoms           811     3.178     2.106
S. chain bond B values: others                  810     3.170     2.106
S. chain angle B values: refined atoms         1177     4.848     2.989
S. chain angle B values: others                1178     4.845     2.988
Long range B values: refined atoms             1829     7.010    22.990
Long range B values: others                    1736     6.740    21.430
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0113
Partial structure    1: scale =     0.3944, B  =   38.3015
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5057 100.00   380.5   390.4  0.17  0.18     272   378.1   389.2  0.22  0.22
 0.186    8694  99.98   206.2   182.4  0.19  0.17     449   204.3   179.9  0.23  0.20
 0.310   11074 100.00    92.0    88.8  0.23  0.20     573    92.5    88.5  0.26  0.22
 0.434   12816  98.63    38.7    48.0  0.47  0.46     679    39.4    48.4  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3818   0.923   1239   0.826   5057   0.899  0.949  0.9657  0.9723  0.9028  0.9354
  0.1863   7432   0.885   1262   0.782   8694   0.870  1.098  0.9488  0.9614  0.8914  0.9360
  0.3102   9821   0.830   1253   0.756  11074   0.821  0.956  0.9346  0.9428  0.8927  0.9140
  0.4340  11588   0.391   1228   0.354  12816   0.388  0.372  0.6489  0.6454  0.6388  0.6447
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37641
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9806
Overall R factor                     =     0.2185
Free R factor                        =     0.2514
Average Fourier shell correlation    =     0.8498
AverageFree Fourier shell correlation=     0.8438
Overall weighted R factor            =     0.1830
Free weighted R factor               =     0.2167
Overall weighted R2 factor           =     0.2127
Free weighted R2 factor              =     0.2464
Average correlation coefficient      =     0.8302
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9433
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0803
Overall figure of merit              =     0.6954
ML based su of positional parameters =     0.0663
ML based su of thermal parameters    =     1.9107
-----------------------------------------------------------------------------
  Time in seconds: CPU =        30.11
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2191   0.2517   0.676      176074.    9385.4   0.0122  0.918   1.756  1.024   0.087
       1   0.2190   0.2507   0.691      175044.    9358.3   0.0121  0.909   1.746  1.019   0.087
       2   0.2180   0.2508   0.691      174885.    9356.5   0.0132  0.991   1.803  1.052   0.090
       3   0.2178   0.2509   0.689      174803.    9355.0   0.0133  0.998   1.823  1.063   0.091
       4   0.2177   0.2510   0.697      174766.    9351.1   0.0133  1.002   1.833  1.068   0.091
       5   0.2177   0.2510   0.692      174813.    9353.8   0.0134  1.004   1.839  1.071   0.091
       6   0.2180   0.2511   0.696      174818.    9351.6   0.0127  0.958   1.807  1.052   0.089
       7   0.2185   0.2514   0.691      174980.    9358.1   0.0121  0.912   1.766  1.028   0.087
       8   0.2185   0.2513   0.691      174998.    9358.9   0.0121  0.911   1.764  1.027   0.087
       9   0.2185   0.2513   0.691      175007.    9359.3   0.0121  0.911   1.763  1.026   0.087
      10   0.2185   0.2514   0.695      174955.    9356.5   0.0121  0.910   1.761  1.025   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2191   0.2185
             R free    0.2517   0.2514
     Rms BondLength    0.0122   0.0121
      Rms BondAngle    1.7561   1.7614
     Rms ChirVolume    0.0874   0.0865
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      62.2s System:    0.2s Elapsed:     1:03