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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 21:34:35 


 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 13
  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_R13_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R13_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_R13_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:    13
  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_R13_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=   2.064 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=   2.201 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=   1.831 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=   2.207 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.392 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.386 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=   2.064 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                           13
Number of "free" reflections       1930
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.= 0.898 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   0.27893773    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                39.9
Norm of Geom. positional gradient                80.9
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  98.1
Product of X_ray and Geom posit. gradients     -0.148E+08
 Cosine of angle between them                      -0.472
Product of X_ray and Geom B-fact gradients     -0.307E+08
 Cosine of angle between them                      -0.910


Residuals: XRAY=     0.1066E+07 GEOM=     0.1294E+05 TOTAL=     0.1079E+07
 function value    1078725.9    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.798     1.644
Bond angles  : others                          3238     2.352     1.580
Torsion angles, period  1. refined              185     6.917     5.000
Torsion angles, period  2. refined               90    35.784    22.778
Torsion angles, period  3. refined              268    13.546    15.000
Torsion angles, period  4. refined                9    10.799    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                   301     0.247     0.200
VDW repulsions.others                          1342     0.222     0.200
VDW; torsion: refined_atoms                     724     0.173     0.200
VDW; torsion.others                             726     0.081     0.200
HBOND: refined_atoms                            224     0.199     0.200
HBOND.others                                      2     0.062     0.200
VDW repulsions: symmetry: refined_atoms           9     0.190     0.200
VDW repulsions: symmetry: others                 25     0.189     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           746     1.794     1.619
M. chain bond B values: others                  746     1.791     1.619
M. chain angle B values: refined atoms          929     2.784     2.420
M. chain angle B values: others                 930     2.783     2.420
S. chain bond B values: refined atoms           811     3.190     2.039
S. chain bond B values: others                  810     3.184     2.039
S. chain angle B values: refined atoms         1177     4.932     2.885
S. chain angle B values: others                1178     4.930     2.884
Long range B values: refined atoms             1850     7.690    22.517
Long range B values: others                    1751     7.212    20.881
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.7982
Partial structure    1: scale =     0.3938, B  =   38.9917
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5064 100.00   379.6   389.7  0.17  0.18     265   383.4   389.4  0.18  0.19
 0.186    8679  99.98   206.0   182.2  0.19  0.17     464   202.0   173.7  0.22  0.19
 0.310   11113 100.00    91.8    88.5  0.23  0.20     534    93.9    91.6  0.26  0.22
 0.434   12839  98.63    38.7    48.1  0.47  0.46     656    38.7    46.7  0.46  0.44
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3831   0.917   1233   0.821   5064   0.894  0.950  0.9684  0.9711  0.9265  0.9356
  0.1863   7420   0.871   1259   0.773   8679   0.857  1.098  0.9495  0.9584  0.9189  0.9359
  0.3102   9857   0.792   1256   0.717  11113   0.783  0.943  0.9260  0.9324  0.8814  0.9118
  0.4340  11598   0.453   1241   0.411  12839   0.449  0.420  0.6479  0.6557  0.6517  0.6440
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37695
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.8442
Overall R factor                     =     0.2191
Free R factor                        =     0.2352
Average Fourier shell correlation    =     0.8494
AverageFree Fourier shell correlation=     0.8425
Overall weighted R factor            =     0.1824
Free weighted R factor               =     0.1969
Overall weighted R2 factor           =     0.2103
Free weighted R2 factor              =     0.2182
Average correlation coefficient      =     0.8294
Overall correlation coefficient      =     0.9598
Free correlation coefficient         =     0.9535
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0751
Overall figure of merit              =     0.7013
ML based su of positional parameters =     0.0714
ML based su of thermal parameters    =     2.0653
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176167.33       12941.575       1078725.9      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.34680808    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067384.3    

-------------------------------------------------------------------------------
             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  =   -0.0480
Partial structure    1: scale =     0.3940, B  =   39.3803
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2190
Free R factor                        =     0.2347
Average Fourier shell correlation    =     0.8605
AverageFree Fourier shell correlation=     0.8527
Average correlation coefficient      =     0.8296
Overall figure of merit              =     0.7236
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175077.56       8192.8652       1067384.3       1078725.9    


     CGMAT cycle number =      3

 Weight matrix   0.35094860    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066899.8    

-------------------------------------------------------------------------------
             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  =   -0.0112
Partial structure    1: scale =     0.3942, B  =   39.3272
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2181
Free R factor                        =     0.2344
Average Fourier shell correlation    =     0.8628
AverageFree Fourier shell correlation=     0.8546
Average correlation coefficient      =     0.8306
Overall figure of merit              =     0.7259
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174904.47       8755.5781       1066899.8       1067384.3    


     CGMAT cycle number =      4

 Weight matrix   0.31960121    
 Actual weight    5.4998550      is applied to the X-ray term


 function value    970665.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.014     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0116
Partial structure    1: scale =     0.3946, B  =   39.3620
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2179
Free R factor                        =     0.2343
Average Fourier shell correlation    =     0.8631
AverageFree Fourier shell correlation=     0.8548
Average correlation coefficient      =     0.8310
Overall figure of merit              =     0.7262
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174871.78       8895.8896       970665.31       1066899.8    


     CGMAT cycle number =      5

 Weight matrix   0.28988266    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883246.50    

-------------------------------------------------------------------------------
             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  =   -0.0149
Partial structure    1: scale =     0.3949, B  =   39.3475
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2181
Free R factor                        =     0.2344
Average Fourier shell correlation    =     0.8630
AverageFree Fourier shell correlation=     0.8547
Average correlation coefficient      =     0.8308
Overall figure of merit              =     0.7261
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    174921.16       8663.7813       883246.50       970665.31    


     CGMAT cycle number =      6

 Weight matrix   0.28884438    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883342.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0190
Partial structure    1: scale =     0.3950, B  =   39.3008
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2185
Free R factor                        =     0.2346
Average Fourier shell correlation    =     0.8628
AverageFree Fourier shell correlation=     0.8546
Average correlation coefficient      =     0.8304
Overall figure of merit              =     0.7260
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    175009.50       8343.3916       883401.81       883246.50    

 fvalues    175009.50       8343.3916       883386.63       883367.75    
 fvalues    175009.50       8343.3916       883386.63       883367.75    


     CGMAT cycle number =      7

 Weight matrix   0.28865030    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883380.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0192
Partial structure    1: scale =     0.3949, B  =   39.2806
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2185
Free R factor                        =     0.2346
Average Fourier shell correlation    =     0.8628
AverageFree Fourier shell correlation=     0.8545
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.7260
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05

 fvalues    175012.63       8323.2383       883363.25       883367.75    


     CGMAT cycle number =      8

 Weight matrix   0.28849652    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883394.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0184
Partial structure    1: scale =     0.3949, B  =   39.3137
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2186
Free R factor                        =     0.2346
Average Fourier shell correlation    =     0.8628
AverageFree Fourier shell correlation=     0.8545
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.7260
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    175025.70       8290.6289       883427.13       883363.25    

 fvalues    175025.70       8290.6289       883393.63       883396.00    
 fvalues    175025.70       8290.6289       883393.63       883396.00    


     CGMAT cycle number =      9

 Weight matrix   0.28900442    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883390.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0176
Partial structure    1: scale =     0.3949, B  =   39.3136
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2186
Free R factor                        =     0.2346
Average Fourier shell correlation    =     0.8631
AverageFree Fourier shell correlation=     0.8549
Average correlation coefficient      =     0.8302
Overall figure of merit              =     0.7267
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    175026.75       8280.2559       883390.88       883396.00    


     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.= 0.917 id.= 3.000 dev= -2.08 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   0.28870431    
 Actual weight    4.9998679      is applied to the X-ray term
Norm of X_ray positional gradient                38.5
Norm of Geom. positional gradient                38.7
Norm of X_ray B-factor gradient                  94.1
Norm of Geom. B-factor gradient                  96.3
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.292E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.8751E+06 GEOM=      8268.     TOTAL=     0.8834E+06
 function value    883392.81    

-------------------------------------------------------------------------------
             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     1.788     1.644
Bond angles  : others                          3238     1.492     1.580
Torsion angles, period  1. refined              185     6.908     5.000
Torsion angles, period  2. refined               90    35.643    22.778
Torsion angles, period  3. refined              268    13.517    15.000
Torsion angles, period  4. refined                9    10.612    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.244     0.200
VDW repulsions.others                          1361     0.196     0.200
VDW; torsion: refined_atoms                     723     0.173     0.200
VDW; torsion.others                             777     0.083     0.200
HBOND: refined_atoms                            228     0.196     0.200
HBOND.others                                      1     0.102     0.200
VDW repulsions: symmetry: refined_atoms           9     0.185     0.200
VDW repulsions: symmetry: others                 28     0.174     0.200
HBOND: symmetry: refined_atoms                   24     0.186     0.200
M. chain bond B values: refined atoms           746     1.817     1.699
M. chain bond B values: others                  746     1.813     1.699
M. chain angle B values: refined atoms          929     2.801     2.539
M. chain angle B values: others                 930     2.799     2.539
S. chain bond B values: refined atoms           811     3.225     2.121
S. chain bond B values: others                  810     3.219     2.121
S. chain angle B values: refined atoms         1177     4.974     3.008
S. chain angle B values: others                1178     4.972     3.007
Long range B values: refined atoms             1859     7.810    23.663
Long range B values: others                    1761     7.334    22.031
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0165
Partial structure    1: scale =     0.3949, B  =   39.3031
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5064 100.00   379.9   389.8  0.17  0.18     265   383.7   389.1  0.19  0.19
 0.186    8679  99.98   206.2   182.5  0.19  0.17     464   202.1   174.2  0.22  0.19
 0.310   11113 100.00    91.9    88.6  0.23  0.20     534    93.9    91.7  0.26  0.22
 0.434   12839  98.63    38.7    48.1  0.47  0.46     656    38.7    46.8  0.45  0.44
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3831   0.928   1233   0.838   5064   0.906  0.950  0.9706  0.9737  0.9263  0.9355
  0.1863   7420   0.895   1259   0.797   8679   0.880  1.101  0.9559  0.9642  0.9196  0.9368
  0.3102   9857   0.820   1256   0.746  11113   0.811  0.954  0.9323  0.9398  0.8814  0.9126
  0.4340  11598   0.482   1241   0.440  12839   0.478  0.437  0.6730  0.6840  0.6497  0.6453
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37695
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.8442
Overall R factor                     =     0.2186
Free R factor                        =     0.2346
Average Fourier shell correlation    =     0.8629
AverageFree Fourier shell correlation=     0.8547
Overall weighted R factor            =     0.1820
Free weighted R factor               =     0.1964
Overall weighted R2 factor           =     0.2100
Free weighted R2 factor              =     0.2176
Average correlation coefficient      =     0.8302
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9536
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0749
Overall figure of merit              =     0.7262
ML based su of positional parameters =     0.0637
ML based su of thermal parameters    =     1.8427
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    175028.64       8268.1348       883388.19       883390.88    

    ****                              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.= 0.917 id.= 3.000 dev= -2.08 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_R13_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     1.786     1.644
Bond angles  : others                          3238     1.491     1.580
Torsion angles, period  1. refined              185     6.908     5.000
Torsion angles, period  2. refined               90    35.632    22.778
Torsion angles, period  3. refined              268    13.514    15.000
Torsion angles, period  4. refined                9    10.604    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   305     0.244     0.200
VDW repulsions.others                          1359     0.196     0.200
VDW; torsion: refined_atoms                     724     0.173     0.200
VDW; torsion.others                             782     0.083     0.200
HBOND: refined_atoms                            227     0.196     0.200
HBOND.others                                      1     0.102     0.200
VDW repulsions: symmetry: refined_atoms           9     0.185     0.200
VDW repulsions: symmetry: others                 27     0.177     0.200
HBOND: symmetry: refined_atoms                   24     0.186     0.200
M. chain bond B values: refined atoms           746     1.815     1.699
M. chain bond B values: others                  746     1.812     1.699
M. chain angle B values: refined atoms          929     2.798     2.539
M. chain angle B values: others                 930     2.797     2.539
S. chain bond B values: refined atoms           811     3.222     2.121
S. chain bond B values: others                  810     3.216     2.121
S. chain angle B values: refined atoms         1177     4.970     3.007
S. chain angle B values: others                1178     4.968     3.007
Long range B values: refined atoms             1859     7.804    23.656
Long range B values: others                    1761     7.327    22.024
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0173
Partial structure    1: scale =     0.3949, B  =   39.2722
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5064 100.00   379.9   389.8  0.17  0.18     265   383.7   389.1  0.19  0.19
 0.186    8679  99.98   206.2   182.5  0.19  0.17     464   202.2   174.2  0.22  0.19
 0.310   11113 100.00    91.9    88.6  0.23  0.20     534    93.9    91.7  0.26  0.22
 0.434   12839  98.63    38.7    48.1  0.47  0.46     656    38.7    46.8  0.45  0.44
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3831   0.928   1233   0.838   5064   0.906  0.950  0.9706  0.9737  0.9263  0.9355
  0.1863   7420   0.895   1259   0.797   8679   0.880  1.101  0.9559  0.9642  0.9196  0.9367
  0.3102   9857   0.820   1256   0.746  11113   0.811  0.954  0.9323  0.9398  0.8814  0.9126
  0.4340  11598   0.482   1241   0.440  12839   0.478  0.437  0.6730  0.6840  0.6497  0.6454
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37695
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.8442
Overall R factor                     =     0.2186
Free R factor                        =     0.2347
Average Fourier shell correlation    =     0.8629
AverageFree Fourier shell correlation=     0.8547
Overall weighted R factor            =     0.1820
Free weighted R factor               =     0.1963
Overall weighted R2 factor           =     0.2100
Free weighted R2 factor              =     0.2175
Average correlation coefficient      =     0.8302
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9536
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0749
Overall figure of merit              =     0.7262
ML based su of positional parameters =     0.0637
ML based su of thermal parameters    =     1.8427
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.56
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2191   0.2352   0.701      176167.    9099.7   0.0125  0.943   1.798  1.042   0.087
       1   0.2190   0.2347   0.724      175078.    9068.9   0.0123  0.930   1.780  1.032   0.086
       2   0.2181   0.2344   0.726      174904.    9065.0   0.0135  1.017   1.836  1.065   0.090
       3   0.2179   0.2343   0.726      174872.    9064.7   0.0135  1.024   1.856  1.076   0.090
       4   0.2181   0.2344   0.726      174921.    9066.2   0.0129  0.981   1.834  1.063   0.088
       5   0.2185   0.2346   0.726      175004.    9068.6   0.0123  0.935   1.797  1.041   0.086
       6   0.2185   0.2346   0.726      175016.    9069.2   0.0123  0.934   1.795  1.040   0.086
       7   0.2186   0.2346   0.726      175025.    9070.0   0.0123  0.932   1.790  1.037   0.086
       8   0.2186   0.2346   0.727      175027.    9070.1   0.0123  0.931   1.789  1.037   0.086
       9   0.2186   0.2346   0.726      175030.    9070.0   0.0123  0.930   1.788  1.036   0.086
      10   0.2186   0.2347   0.726      175033.    9070.2   0.0123  0.930   1.786  1.035   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2191   0.2186
             R free    0.2352   0.2347
     Rms BondLength    0.0125   0.0123
      Rms BondAngle    1.7977   1.7861
     Rms ChirVolume    0.0866   0.0859
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      61.9s System:    0.2s Elapsed:     1:02