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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: 22:02:17 


 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 18
  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_R18_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R18_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_R18_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:    18
  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_R18_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=   2.057 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=   2.180 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=   1.815 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=   2.212 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=   2.383 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=   2.381 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.093 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                           18
Number of "free" reflections       2035
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.= 0.882 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   0.26245165    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                37.6
Norm of Geom. positional gradient                82.8
Norm of X_ray B-factor gradient                  97.6
Norm of Geom. B-factor gradient                 0.237E+05
Product of X_ray and Geom posit. gradients     -0.150E+08
 Cosine of angle between them                      -0.496
Product of X_ray and Geom B-fact gradients     -0.302E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1064E+07 GEOM=     0.2752E+05 TOTAL=     0.1092E+07
 function value    1091695.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.838     1.644
Bond angles  : others                          3242     2.358     1.582
Torsion angles, period  1. refined              184     6.897     5.000
Torsion angles, period  2. refined               90    35.524    22.778
Torsion angles, period  3. refined              268    12.939    15.000
Torsion angles, period  4. refined                9    11.879    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   311     0.268     0.200
VDW repulsions.others                          1341     0.231     0.200
VDW; torsion: refined_atoms                     724     0.173     0.200
VDW; torsion.others                             721     0.081     0.200
HBOND: refined_atoms                            218     0.200     0.200
HBOND.others                                      2     0.090     0.200
VDW repulsions: symmetry: refined_atoms          10     0.204     0.200
VDW repulsions: symmetry: others                 26     0.185     0.200
HBOND: symmetry: refined_atoms                   20     0.250     0.200
HBOND: symmetry: others                           1     0.015     0.200
M. chain bond B values: refined atoms           745     1.811     1.616
M. chain bond B values: others                  745     1.806     1.616
M. chain angle B values: refined atoms          926     2.786     2.412
M. chain angle B values: others                 927     2.785     2.411
S. chain bond B values: refined atoms           811     3.243     2.031
S. chain bond B values: others                  810     3.239     2.030
S. chain angle B values: refined atoms         1177     4.960     2.874
S. chain angle B values: others                1178     4.957     2.873
Long range B values: refined atoms             1853     7.510    22.444
Long range B values: others                    1756     7.201    20.855
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.7806
Partial structure    1: scale =     0.3928, B  =   45.2668
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5050 100.00   378.9   387.9  0.18  0.18     279   410.1   424.1  0.20  0.21
 0.186    8648  99.98   206.5   182.3  0.19  0.17     495   201.5   180.3  0.24  0.21
 0.310   11101 100.00    92.2    88.9  0.23  0.20     546    89.9    87.1  0.26  0.23
 0.434   12793  98.63    38.8    48.2  0.47  0.46     702    38.3    48.7  0.48  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3826   0.894   1224   0.779   5050   0.866  0.944  0.9625  0.9642  0.9192  0.9345
  0.1863   7414   0.865   1234   0.764   8648   0.851  1.096  0.9434  0.9572  0.8849  0.9379
  0.3102   9852   0.808   1249   0.730  11101   0.799  0.951  0.9224  0.9356  0.8819  0.9139
  0.4340  11544   0.405   1249   0.364  12793   0.401  0.384  0.6409  0.6393  0.6434  0.6476
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37592
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.1043
Overall R factor                     =     0.2189
Free R factor                        =     0.2474
Average Fourier shell correlation    =     0.8436
AverageFree Fourier shell correlation=     0.8353
Overall weighted R factor            =     0.1825
Free weighted R factor               =     0.2153
Overall weighted R2 factor           =     0.2103
Free weighted R2 factor              =     0.2523
Average correlation coefficient      =     0.8316
Overall correlation coefficient      =     0.9597
Free correlation coefficient         =     0.9499
Cruickshanks DPI for coordinate error=     0.0781
DPI based on free R factor           =     0.0792
Overall figure of merit              =     0.6844
ML based su of positional parameters =     0.0736
ML based su of thermal parameters    =     2.1044
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    175901.28       27520.791       1091695.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31439808    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068470.4    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0574
Partial structure    1: scale =     0.3928, B  =   44.5537
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                     =     0.2195
Free R factor                        =     0.2475
Average Fourier shell correlation    =     0.8567
AverageFree Fourier shell correlation=     0.8500
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.7040
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    174933.88       10148.402       1068470.4       1091695.4    


     CGMAT cycle number =      3

 Weight matrix   0.32183024    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066313.0    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0342
Partial structure    1: scale =     0.3930, B  =   41.0641
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                        =     0.2471
Average Fourier shell correlation    =     0.8606
AverageFree Fourier shell correlation=     0.8541
Average correlation coefficient      =     0.8316
Overall figure of merit              =     0.7087
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174750.69       9099.2314       1066313.0       1068470.4    


     CGMAT cycle number =      4

 Weight matrix   0.32323048    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065687.3    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0242
Partial structure    1: scale =     0.3930, B  =   38.1514
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                     =     0.2184
Free R factor                        =     0.2470
Average Fourier shell correlation    =     0.8617
AverageFree Fourier shell correlation=     0.8552
Average correlation coefficient      =     0.8322
Overall figure of merit              =     0.7099
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174710.36       8717.5352       1065687.3       1066313.0    


     CGMAT cycle number =      5

 Weight matrix   0.32369354    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065559.1    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0137
Partial structure    1: scale =     0.3929, B  =   37.7887
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                        =     0.2467
Average Fourier shell correlation    =     0.8619
AverageFree Fourier shell correlation=     0.8554
Average correlation coefficient      =     0.8325
Overall figure of merit              =     0.7102
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    174699.97       8652.1738       1065559.1       1065687.3    


     CGMAT cycle number =      6

 Weight matrix   0.32342908    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065582.8    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0084
Partial structure    1: scale =     0.3927, B  =   37.7366
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                        =     0.2467
Average Fourier shell correlation    =     0.8620
AverageFree Fourier shell correlation=     0.8554
Average correlation coefficient      =     0.8326
Overall figure of merit              =     0.7102
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    174704.52       8658.3799       1065612.0       1065559.1    

 fvalues    174704.52       8658.3799       1065585.5       1065592.9    
 fvalues    174704.52       8658.3799       1065585.5       1065592.9    


     CGMAT cycle number =      7

 Weight matrix   0.32294634    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065603.1    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0000
Partial structure    1: scale =     0.3926, B  =   37.7174
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                        =     0.2466
Average Fourier shell correlation    =     0.8620
AverageFree Fourier shell correlation=     0.8554
Average correlation coefficient      =     0.8326
Overall figure of merit              =     0.7102
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    174706.45       8657.5938       1065606.1       1065592.9    

 fvalues    174706.45       8657.5938       1065585.8       1065603.8    
 fvalues    174706.45       8657.5938       1065585.8       1065603.8    


     CGMAT cycle number =      8

 Weight matrix   0.32363695    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065591.5    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0106
Partial structure    1: scale =     0.3925, B  =   37.6899
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                        =     0.2467
Average Fourier shell correlation    =     0.8621
AverageFree Fourier shell correlation=     0.8555
Average correlation coefficient      =     0.8326
Overall figure of merit              =     0.7104
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    174705.16       8653.1816       1065591.5       1065603.8    


     CGMAT cycle number =      9

 Weight matrix   0.32304591    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065612.3    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0015
Partial structure    1: scale =     0.3925, B  =   37.6895
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2182
Free R factor                        =     0.2466
Average Fourier shell correlation    =     0.8620
AverageFree Fourier shell correlation=     0.8554
Average correlation coefficient      =     0.8326
Overall figure of merit              =     0.7103
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    174706.94       8654.2646       1065605.3       1065591.5    

 fvalues    174706.94       8654.2646       1065619.9       1065603.4    
 fvalues    174706.94       8654.2646       1065619.9       1065603.4    


     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.= 0.901 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   0.32364917    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                42.7
Norm of Geom. positional gradient                42.7
Norm of X_ray B-factor gradient                  101.
Norm of Geom. B-factor gradient                  101.
Product of X_ray and Geom posit. gradients     -0.177E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.329E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.1057E+07 GEOM=      8654.     TOTAL=     0.1066E+07
 function value    1065603.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.820     1.644
Bond angles  : others                          3242     1.503     1.582
Torsion angles, period  1. refined              184     6.888     5.000
Torsion angles, period  2. refined               90    35.438    22.778
Torsion angles, period  3. refined              268    12.936    15.000
Torsion angles, period  4. refined                9    11.909    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   308     0.268     0.200
VDW repulsions.others                          1374     0.204     0.200
VDW; torsion: refined_atoms                     727     0.173     0.200
VDW; torsion.others                             766     0.084     0.200
HBOND: refined_atoms                            214     0.199     0.200
HBOND.others                                      2     0.088     0.200
VDW repulsions: symmetry: refined_atoms           9     0.211     0.200
VDW repulsions: symmetry: others                 23     0.182     0.200
HBOND: symmetry: refined_atoms                   20     0.271     0.200
HBOND: symmetry: others                           1     0.006     0.200
M. chain bond B values: refined atoms           745     1.826     1.689
M. chain bond B values: others                  745     1.822     1.690
M. chain angle B values: refined atoms          926     2.794     2.523
M. chain angle B values: others                 927     2.793     2.523
S. chain bond B values: refined atoms           811     3.265     2.108
S. chain bond B values: others                  810     3.260     2.108
S. chain angle B values: refined atoms         1177     4.994     2.989
S. chain angle B values: others                1178     4.992     2.989
Long range B values: refined atoms             1848     7.518    23.187
Long range B values: others                    1754     7.238    21.628
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0110
Partial structure    1: scale =     0.3927, B  =   37.7017
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5050 100.00   379.7   388.5  0.17  0.18     279   410.9   424.8  0.20  0.21
 0.186    8648  99.98   206.9   182.7  0.19  0.17     495   201.9   180.6  0.24  0.21
 0.310   11101 100.00    92.3    89.2  0.23  0.20     546    90.1    87.3  0.26  0.23
 0.434   12793  98.63    38.9    48.2  0.47  0.46     702    38.4    48.8  0.47  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3826   0.914   1224   0.814   5050   0.890  0.947  0.9676  0.9700  0.9202  0.9349
  0.1863   7414   0.884   1234   0.783   8648   0.869  1.099  0.9482  0.9615  0.8853  0.9378
  0.3102   9852   0.819   1249   0.743  11101   0.810  0.953  0.9277  0.9411  0.8826  0.9149
  0.4340  11544   0.449   1249   0.412  12793   0.446  0.407  0.6894  0.6837  0.6444  0.6497
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37592
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.1043
Overall R factor                     =     0.2182
Free R factor                        =     0.2467
Average Fourier shell correlation    =     0.8621
AverageFree Fourier shell correlation=     0.8555
Overall weighted R factor            =     0.1821
Free weighted R factor               =     0.2146
Overall weighted R2 factor           =     0.2100
Free weighted R2 factor              =     0.2507
Average correlation coefficient      =     0.8326
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9503
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0789
Overall figure of merit              =     0.7104
ML based su of positional parameters =     0.0662
ML based su of thermal parameters    =     1.8935
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    174706.91       8654.1133       1065603.0       1065603.4    

    ****                              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.= 0.901 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_R18_1-42A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.820     1.644
Bond angles  : others                          3242     1.503     1.582
Torsion angles, period  1. refined              184     6.888     5.000
Torsion angles, period  2. refined               90    35.437    22.778
Torsion angles, period  3. refined              268    12.936    15.000
Torsion angles, period  4. refined                9    11.910    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   308     0.268     0.200
VDW repulsions.others                          1374     0.204     0.200
VDW; torsion: refined_atoms                     727     0.173     0.200
VDW; torsion.others                             768     0.084     0.200
HBOND: refined_atoms                            214     0.199     0.200
HBOND.others                                      2     0.088     0.200
VDW repulsions: symmetry: refined_atoms           9     0.211     0.200
VDW repulsions: symmetry: others                 23     0.182     0.200
HBOND: symmetry: refined_atoms                   20     0.271     0.200
HBOND: symmetry: others                           1     0.006     0.200
M. chain bond B values: refined atoms           745     1.827     1.689
M. chain bond B values: others                  745     1.822     1.690
M. chain angle B values: refined atoms          926     2.795     2.523
M. chain angle B values: others                 927     2.793     2.523
S. chain bond B values: refined atoms           811     3.265     2.108
S. chain bond B values: others                  810     3.261     2.108
S. chain angle B values: refined atoms         1177     4.994     2.989
S. chain angle B values: others                1178     4.992     2.989
Long range B values: refined atoms             1848     7.516    23.187
Long range B values: others                    1754     7.237    21.628
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0081
Partial structure    1: scale =     0.3926, B  =   37.6861
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5050 100.00   379.7   388.4  0.17  0.18     279   410.9   424.8  0.20  0.21
 0.186    8648  99.98   206.9   182.7  0.19  0.17     495   201.9   180.6  0.24  0.21
 0.310   11101 100.00    92.4    89.2  0.23  0.20     546    90.1    87.3  0.26  0.23
 0.434   12793  98.63    38.9    48.2  0.47  0.46     702    38.4    48.8  0.47  0.47
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3826   0.914   1224   0.814   5050   0.890  0.947  0.9676  0.9700  0.9202  0.9349
  0.1863   7414   0.884   1234   0.783   8648   0.869  1.099  0.9482  0.9615  0.8853  0.9378
  0.3102   9852   0.819   1249   0.743  11101   0.810  0.953  0.9277  0.9411  0.8826  0.9149
  0.4340  11544   0.449   1249   0.411  12793   0.445  0.407  0.6893  0.6836  0.6444  0.6498
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37592
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.1043
Overall R factor                     =     0.2182
Free R factor                        =     0.2466
Average Fourier shell correlation    =     0.8620
AverageFree Fourier shell correlation=     0.8554
Overall weighted R factor            =     0.1821
Free weighted R factor               =     0.2146
Overall weighted R2 factor           =     0.2100
Free weighted R2 factor              =     0.2508
Average correlation coefficient      =     0.8326
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9503
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0789
Overall figure of merit              =     0.7103
ML based su of positional parameters =     0.0662
ML based su of thermal parameters    =     1.8935
-----------------------------------------------------------------------------
  Time in seconds: CPU =        31.48
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2189   0.2474   0.684      175901.    9649.1   0.0133  0.998   1.838  1.075   0.092
       1   0.2195   0.2475   0.704      174934.    9618.8   0.0120  0.905   1.765  1.030   0.090
       2   0.2185   0.2471   0.709      174751.    9613.7   0.0129  0.974   1.800  1.051   0.091
       3   0.2184   0.2470   0.710      174710.    9612.4   0.0130  0.981   1.811  1.058   0.092
       4   0.2183   0.2467   0.710      174700.    9611.1   0.0130  0.984   1.816  1.061   0.092
       5   0.2183   0.2467   0.710      174703.    9611.4   0.0130  0.986   1.819  1.063   0.092
       6   0.2183   0.2466   0.710      174706.    9611.6   0.0130  0.986   1.820  1.063   0.092
       7   0.2183   0.2467   0.710      174705.    9611.8   0.0130  0.985   1.820  1.063   0.092
       8   0.2182   0.2466   0.710      174708.    9611.8   0.0130  0.986   1.820  1.064   0.092
       9   0.2182   0.2467   0.710      174707.    9611.9   0.0130  0.986   1.820  1.064   0.092
      10   0.2182   0.2466   0.710      174711.    9612.1   0.0130  0.986   1.820  1.064   0.092
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2189   0.2182
             R free    0.2474   0.2466
     Rms BondLength    0.0133   0.0130
      Rms BondAngle    1.8385   1.8205
     Rms ChirVolume    0.0924   0.0921
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      63.6s System:    0.3s Elapsed:     1:04