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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: 20:39:20 


 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 3
  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_R03_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R03_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_R03_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:     3
  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_R03_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=   2.050 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=   2.198 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=   1.816 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=   2.217 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=   2.382 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=   2.383 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=   2.084 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                            3
Number of "free" reflections       1923
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.= 0.879 id.= 3.000 dev= -2.12 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.25974092    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                40.1
Norm of Geom. positional gradient                80.5
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  94.4
Product of X_ray and Geom posit. gradients     -0.145E+08
 Cosine of angle between them                      -0.465
Product of X_ray and Geom B-fact gradients     -0.286E+08
 Cosine of angle between them                      -0.888


Residuals: XRAY=     0.1067E+07 GEOM=     0.1271E+05 TOTAL=     0.1080E+07
 function value    1079770.3    

-------------------------------------------------------------------------------
             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     1.762     1.644
Bond angles  : others                          3238     2.348     1.580
Torsion angles, period  1. refined              185     6.855     5.000
Torsion angles, period  2. refined               90    36.113    22.778
Torsion angles, period  3. refined              268    13.292    15.000
Torsion angles, period  4. refined                9    12.063    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                   299     0.242     0.200
VDW repulsions.others                          1334     0.221     0.200
VDW; torsion: refined_atoms                     727     0.171     0.200
VDW; torsion.others                             698     0.082     0.200
HBOND: refined_atoms                            218     0.193     0.200
HBOND.others                                      2     0.027     0.200
VDW repulsions: symmetry: refined_atoms           8     0.219     0.200
VDW repulsions: symmetry: others                 27     0.167     0.200
HBOND: symmetry: refined_atoms                   20     0.186     0.200
HBOND: symmetry: others                           1     0.024     0.200
M. chain bond B values: refined atoms           746     1.736     1.625
M. chain bond B values: others                  746     1.733     1.625
M. chain angle B values: refined atoms          929     2.707     2.429
M. chain angle B values: others                 930     2.706     2.429
S. chain bond B values: refined atoms           811     3.177     2.041
S. chain bond B values: others                  810     3.170     2.041
S. chain angle B values: refined atoms         1177     4.906     2.889
S. chain angle B values: others                1178     4.904     2.889
Long range B values: refined atoms             1844     7.257    22.356
Long range B values: others                    1750     6.971    20.804
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0468, B  =    0.7643
Partial structure    1: scale =     0.3951, B  =   38.8681
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5078 100.00   378.2   388.8  0.17  0.18     251   394.8   393.6  0.20  0.20
 0.186    8715  99.98   205.4   181.6  0.19  0.17     428   205.7   184.5  0.21  0.19
 0.310   11082 100.00    91.3    88.0  0.23  0.20     565    98.2    93.9  0.26  0.23
 0.434   12825  98.63    38.6    47.9  0.47  0.46     670    39.4    48.0  0.46  0.44
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3840   0.908   1238   0.791   5078   0.880  0.947  0.9627  0.9683  0.9007  0.9362
  0.1863   7459   0.870   1256   0.773   8715   0.856  1.096  0.9490  0.9590  0.9002  0.9372
  0.3102   9826   0.797   1256   0.722  11082   0.788  0.948  0.9278  0.9281  0.8990  0.9100
  0.4340  11573   0.366   1252   0.326  12825   0.362  0.362  0.6307  0.6085  0.6407  0.6421
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37700
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.8316
Overall R factor                     =     0.2188
Free R factor                        =     0.2404
Average Fourier shell correlation    =     0.8320
AverageFree Fourier shell correlation=     0.8331
Overall weighted R factor            =     0.1824
Free weighted R factor               =     0.2040
Overall weighted R2 factor           =     0.2110
Free weighted R2 factor              =     0.2388
Average correlation coefficient      =     0.8287
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9458
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0767
Overall figure of merit              =     0.6714
ML based su of positional parameters =     0.0740
ML based su of thermal parameters    =     2.1619
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176378.09       12710.881       1079770.3      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31441149    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068088.4    

-------------------------------------------------------------------------------
             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 =     0.0468, B  =   -0.0783
Partial structure    1: scale =     0.3952, B  =   38.7927
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                        =     0.2408
Average Fourier shell correlation    =     0.8467
AverageFree Fourier shell correlation=     0.8466
Average correlation coefficient      =     0.8284
Overall figure of merit              =     0.6934
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175215.56       8062.0859       1068088.4       1079770.3    


     CGMAT cycle number =      3

 Weight matrix   0.32221606    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067145.3    

-------------------------------------------------------------------------------
             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 =     0.0468, B  =   -0.0359
Partial structure    1: scale =     0.3952, B  =   39.0119
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                        =     0.2400
Average Fourier shell correlation    =     0.8507
AverageFree Fourier shell correlation=     0.8499
Average correlation coefficient      =     0.8294
Overall figure of merit              =     0.6980
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174974.98       8574.5400       1067145.3       1068088.4    


     CGMAT cycle number =      4

 Weight matrix   0.32389483    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066893.5    

-------------------------------------------------------------------------------
             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 =     0.0468, B  =   -0.0365
Partial structure    1: scale =     0.3949, B  =   38.9512
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                        =     0.2398
Average Fourier shell correlation    =     0.8516
AverageFree Fourier shell correlation=     0.8507
Average correlation coefficient      =     0.8299
Overall figure of merit              =     0.6992
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174912.42       8701.2119       1066893.5       1067145.3    


     CGMAT cycle number =      5

 Weight matrix   0.32346472    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066935.3    

-------------------------------------------------------------------------------
             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 =     0.0468, B  =   -0.0256
Partial structure    1: scale =     0.3948, B  =   38.9328
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                     =     0.2175
Free R factor                        =     0.2398
Average Fourier shell correlation    =     0.8516
AverageFree Fourier shell correlation=     0.8506
Average correlation coefficient      =     0.8301
Overall figure of merit              =     0.6991
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    174914.97       8759.1699       1066857.3       1066893.5    
 fvalues    174914.97       8759.1699       1066857.3       1066966.8    


     CGMAT cycle number =      6

 Weight matrix   0.29462871    
 Actual weight    5.4998550      is applied to the X-ray term


 function value    970715.38    

-------------------------------------------------------------------------------
             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 =     0.0468, B  =   -0.0277
Partial structure    1: scale =     0.3948, B  =   38.8214
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                     =     0.2175
Free R factor                        =     0.2398
Average Fourier shell correlation    =     0.8517
AverageFree Fourier shell correlation=     0.8506
Average correlation coefficient      =     0.8302
Overall figure of merit              =     0.6992
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    174902.30       8778.1074       970715.38       1066966.8    


     CGMAT cycle number =      7

 Weight matrix   0.26731154    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883295.00    

-------------------------------------------------------------------------------
             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 =     0.0468, B  =   -0.0343
Partial structure    1: scale =     0.3949, B  =   38.8173
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                        =     0.2400
Average Fourier shell correlation    =     0.8515
AverageFree Fourier shell correlation=     0.8504
Average correlation coefficient      =     0.8298
Overall figure of merit              =     0.6991
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    174966.41       8486.0791       883295.00       970715.38    


     CGMAT cycle number =      8

 Weight matrix   0.26618928    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883403.38    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0393
Partial structure    1: scale =     0.3949, B  =   38.7315
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                     =     0.2183
Free R factor                        =     0.2404
Average Fourier shell correlation    =     0.8512
AverageFree Fourier shell correlation=     0.8501
Average correlation coefficient      =     0.8293
Overall figure of merit              =     0.6988
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    175057.20       8148.3887       883472.56       883295.00    

 fvalues    175057.20       8148.3887       883485.44       883411.25    
 fvalues    175057.20       8148.3887       883485.44       883411.25    


     CGMAT cycle number =      9

 Weight matrix   0.26607424    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883418.94    

-------------------------------------------------------------------------------
             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  =   -0.0391
Partial structure    1: scale =     0.3950, B  =   38.8007
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                     =     0.2183
Free R factor                        =     0.2404
Average Fourier shell correlation    =     0.8512
AverageFree Fourier shell correlation=     0.8501
Average correlation coefficient      =     0.8293
Overall figure of merit              =     0.6988
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    175063.05       8128.2295       883460.38       883411.25    

 fvalues    175063.05       8128.2295       883464.88       883420.38    
 fvalues    175063.05       8128.2295       883464.88       883420.38    


     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.= 0.902 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.26593930    
 Actual weight    4.9998679      is applied to the X-ray term
Norm of X_ray positional gradient                37.6
Norm of Geom. positional gradient                38.0
Norm of X_ray B-factor gradient                  90.3
Norm of Geom. B-factor gradient                  93.7
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.272E+08
 Cosine of angle between them                      -0.994


Residuals: XRAY=     0.8753E+06 GEOM=      8121.     TOTAL=     0.8834E+06
 function value    883439.00    

-------------------------------------------------------------------------------
             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     1.760     1.644
Bond angles  : others                          3238     1.480     1.580
Torsion angles, period  1. refined              185     6.843     5.000
Torsion angles, period  2. refined               90    35.860    22.778
Torsion angles, period  3. refined              268    13.133    15.000
Torsion angles, period  4. refined                9    11.838    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                   299     0.243     0.200
VDW repulsions.others                          1352     0.194     0.200
VDW; torsion: refined_atoms                     731     0.171     0.200
VDW; torsion.others                             783     0.083     0.200
HBOND: refined_atoms                            214     0.195     0.200
HBOND.others                                      1     0.072     0.200
VDW repulsions: symmetry: refined_atoms           8     0.217     0.200
VDW repulsions: symmetry: others                 24     0.168     0.200
HBOND: symmetry: refined_atoms                   17     0.204     0.200
HBOND: symmetry: others                           1     0.024     0.200
M. chain bond B values: refined atoms           746     1.771     1.704
M. chain bond B values: others                  746     1.767     1.704
M. chain angle B values: refined atoms          929     2.749     2.547
M. chain angle B values: others                 930     2.748     2.547
S. chain bond B values: refined atoms           811     3.252     2.127
S. chain bond B values: others                  810     3.245     2.126
S. chain angle B values: refined atoms         1177     5.000     3.016
S. chain angle B values: others                1178     4.997     3.015
Long range B values: refined atoms             1845     7.411    23.324
Long range B values: others                    1753     7.191    21.827
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0383
Partial structure    1: scale =     0.3950, B  =   38.7829
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5078 100.00   378.5   389.0  0.17  0.18     251   395.1   393.6  0.20  0.20
 0.186    8715  99.98   205.5   181.8  0.19  0.17     428   205.9   184.9  0.21  0.19
 0.310   11082 100.00    91.4    88.1  0.23  0.20     565    98.2    94.0  0.26  0.23
 0.434   12825  98.63    38.6    47.9  0.47  0.46     670    39.4    48.0  0.46  0.44
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3840   0.925   1238   0.821   5078   0.900  0.951  0.9676  0.9729  0.9014  0.9363
  0.1863   7459   0.893   1256   0.796   8715   0.879  1.101  0.9536  0.9644  0.9000  0.9383
  0.3102   9826   0.811   1256   0.739  11082   0.803  0.951  0.9352  0.9362  0.8981  0.9100
  0.4340  11573   0.411   1252   0.371  12825   0.407  0.384  0.6680  0.6525  0.6389  0.6430
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37700
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.8316
Overall R factor                     =     0.2183
Free R factor                        =     0.2405
Average Fourier shell correlation    =     0.8511
AverageFree Fourier shell correlation=     0.8500
Overall weighted R factor            =     0.1819
Free weighted R factor               =     0.2042
Overall weighted R2 factor           =     0.2106
Free weighted R2 factor              =     0.2392
Average correlation coefficient      =     0.8293
Overall correlation coefficient      =     0.9602
Free correlation coefficient         =     0.9459
Cruickshanks DPI for coordinate error=     0.0776
DPI based on free R factor           =     0.0767
Overall figure of merit              =     0.6987
ML based su of positional parameters =     0.0664
ML based su of thermal parameters    =     1.9430
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    175068.91       8121.0176       883481.94       883420.38    

 fvalues    175068.91       8121.0176       883429.75       883442.44    
 fvalues    175068.91       8121.0176       883429.75       883442.44    

    ****                              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.= 0.902 id.= 3.000 dev= -2.10 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_R03_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     1.760     1.644
Bond angles  : others                          3238     1.480     1.580
Torsion angles, period  1. refined              185     6.843     5.000
Torsion angles, period  2. refined               90    35.858    22.778
Torsion angles, period  3. refined              268    13.131    15.000
Torsion angles, period  4. refined                9    11.835    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                   299     0.243     0.200
VDW repulsions.others                          1352     0.194     0.200
VDW; torsion: refined_atoms                     731     0.171     0.200
VDW; torsion.others                             783     0.083     0.200
HBOND: refined_atoms                            214     0.195     0.200
HBOND.others                                      1     0.072     0.200
VDW repulsions: symmetry: refined_atoms           8     0.217     0.200
VDW repulsions: symmetry: others                 24     0.168     0.200
HBOND: symmetry: refined_atoms                   17     0.204     0.200
HBOND: symmetry: others                           1     0.025     0.200
M. chain bond B values: refined atoms           746     1.770     1.704
M. chain bond B values: others                  746     1.767     1.704
M. chain angle B values: refined atoms          929     2.748     2.547
M. chain angle B values: others                 930     2.747     2.547
S. chain bond B values: refined atoms           811     3.250     2.126
S. chain bond B values: others                  810     3.244     2.126
S. chain angle B values: refined atoms         1177     4.997     3.016
S. chain angle B values: others                1178     4.995     3.015
Long range B values: refined atoms             1845     7.410    23.324
Long range B values: others                    1753     7.190    21.826
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0382
Partial structure    1: scale =     0.3950, B  =   38.7886
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5078 100.00   378.4   389.0  0.17  0.18     251   395.1   393.6  0.20  0.20
 0.186    8715  99.98   205.5   181.8  0.19  0.17     428   205.8   184.9  0.21  0.19
 0.310   11082 100.00    91.4    88.1  0.23  0.20     565    98.2    94.0  0.26  0.23
 0.434   12825  98.63    38.6    47.9  0.47  0.46     670    39.4    48.0  0.46  0.44
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3840   0.925   1238   0.821   5078   0.900  0.951  0.9676  0.9729  0.9014  0.9363
  0.1863   7459   0.893   1256   0.796   8715   0.879  1.101  0.9536  0.9644  0.9000  0.9383
  0.3102   9826   0.811   1256   0.739  11082   0.803  0.951  0.9352  0.9362  0.8981  0.9100
  0.4340  11573   0.411   1252   0.371  12825   0.407  0.384  0.6680  0.6525  0.6388  0.6430
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37700
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.8316
Overall R factor                     =     0.2183
Free R factor                        =     0.2405
Average Fourier shell correlation    =     0.8512
AverageFree Fourier shell correlation=     0.8500
Overall weighted R factor            =     0.1819
Free weighted R factor               =     0.2042
Overall weighted R2 factor           =     0.2106
Free weighted R2 factor              =     0.2392
Average correlation coefficient      =     0.8292
Overall correlation coefficient      =     0.9602
Free correlation coefficient         =     0.9459
Cruickshanks DPI for coordinate error=     0.0776
DPI based on free R factor           =     0.0767
Overall figure of merit              =     0.6987
ML based su of positional parameters =     0.0664
ML based su of thermal parameters    =     1.9430
-----------------------------------------------------------------------------
  Time in seconds: CPU =        33.21
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2188   0.2404   0.671      176378.    9096.8   0.0122  0.914   1.762  1.025   0.087
       1   0.2185   0.2408   0.693      175216.    9070.9   0.0123  0.920   1.751  1.021   0.088
       2   0.2177   0.2400   0.698      174975.    9064.5   0.0133  0.993   1.802  1.050   0.090
       3   0.2176   0.2398   0.699      174912.    9061.8   0.0133  1.000   1.821  1.061   0.091
       4   0.2175   0.2398   0.699      174910.    9061.8   0.0134  1.004   1.830  1.066   0.091
       5   0.2175   0.2398   0.699      174902.    9061.7   0.0134  1.005   1.834  1.069   0.091
       6   0.2178   0.2400   0.699      174966.    9063.3   0.0128  0.959   1.804  1.051   0.089
       7   0.2183   0.2404   0.699      175056.    9066.5   0.0121  0.912   1.764  1.027   0.087
       8   0.2183   0.2404   0.699      175063.    9066.8   0.0121  0.911   1.761  1.026   0.087
       9   0.2183   0.2405   0.699      175068.    9067.0   0.0121  0.911   1.760  1.026   0.087
      10   0.2183   0.2405   0.699      175065.    9066.9   0.0121  0.911   1.760  1.025   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2188   0.2183
             R free    0.2404   0.2405
     Rms BondLength    0.0122   0.0121
      Rms BondAngle    1.7620   1.7598
     Rms ChirVolume    0.0865   0.0869
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      65.3s System:    0.2s Elapsed:     1:06