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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: 16:52:28 


 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 1.74     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 0
  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_step0-01A_R00_1-75A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-74A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-01A_R00_1-74A.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       0.0826
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7400
  Estimated number of reflections :      28726
  Free R exclusion - flag equals:     0
  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  1.7400

  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_step0-01A_R00_1-75A.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=   2.047 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=   2.205 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=   1.841 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=   2.210 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=   2.409 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=   2.405 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=   2.095 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:22-OCT-19
  --------------------------------
  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                            0
Number of "free" reflections       1120
Number of   all  reflections      21950
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          21950

   Current auto weighting coefficient =    6.8496723    

 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.= 0.903 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        :   120  120  256
 Maximuum H,K,L                 :    34   34   71
 Minimum acceptable grid spacing:    78   78  164
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   71
 Minimum acceptable grid spacing:    78   78  164
 Weight matrix   0.28034595    
 Actual weight    6.8496723      is applied to the X-ray term
Norm of X_ray positional gradient                35.6
Norm of Geom. positional gradient                80.4
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.127E+08
 Cosine of angle between them                      -0.457
Product of X_ray and Geom B-fact gradients     -0.392E+08
 Cosine of angle between them                      -0.931


Residuals: XRAY=     0.7496E+06 GEOM=     0.1340E+05 TOTAL=     0.7630E+06
 function value    763034.00    

-------------------------------------------------------------------------------
             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     1.811     1.644
Bond angles  : others                          3238     2.357     1.580
Torsion angles, period  1. refined              185     6.844     5.000
Torsion angles, period  2. refined               90    35.586    22.778
Torsion angles, period  3. refined              268    13.350    15.000
Torsion angles, period  4. refined                9    12.317    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   292     0.247     0.200
VDW repulsions.others                          1323     0.220     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             718     0.080     0.200
HBOND: refined_atoms                            216     0.201     0.200
HBOND.others                                      1     0.075     0.200
VDW repulsions: symmetry: refined_atoms           8     0.213     0.200
VDW repulsions: symmetry: others                 22     0.196     0.200
HBOND: symmetry: refined_atoms                   24     0.181     0.200
M. chain bond B values: refined atoms           746     1.652     1.341
M. chain bond B values: others                  746     1.649     1.341
M. chain angle B values: refined atoms          929     2.607     1.998
M. chain angle B values: others                 930     2.605     1.998
S. chain bond B values: refined atoms           811     2.930     1.727
S. chain bond B values: others                  810     2.924     1.726
S. chain angle B values: refined atoms         1177     4.535     2.427
S. chain angle B values: others                1178     4.533     2.426
Long range B values: refined atoms             1833     7.041    18.623
Long range B values: others                    1741     6.692    17.162
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0421, B  =    0.0443
Partial structure    1: scale =     0.3850, B  =   43.9828
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.042    2847 100.00   462.8   471.1  0.16  0.17     129   455.4   466.5  0.20  0.21
 0.124    4787 100.00   313.7   300.2  0.17  0.15     274   316.4   294.7  0.22  0.20
 0.207    6082  99.97   212.2   198.2  0.16  0.14     327   215.9   204.1  0.20  0.17
 0.289    7107 100.00   121.3   130.9  0.22  0.17     388   124.0   133.3  0.27  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0418   2024   0.913    823   0.814   2847   0.884  0.952  0.9624  0.9703  0.9108  0.9408
  0.1242   3958   0.876    829   0.771   4787   0.858  0.996  0.9470  0.9606  0.8918  0.9425
  0.2066   5247   0.879    835   0.768   6082   0.864  1.032  0.9521  0.9599  0.9086  0.9407
  0.2891   6286   0.796    826   0.722   7112   0.787  0.862  0.9272  0.9358  0.8737  0.9157
 $$
Resolution limits                    =     41.964     1.740
Number of used reflections           =      20828
Percentage observed                  =    99.9863
Percentage of free reflections       =     5.1030
Overall R factor                     =     0.1731
Free R factor                        =     0.2208
Average Fourier shell correlation    =     0.9533
AverageFree Fourier shell correlation=     0.9434
Overall weighted R factor            =     0.1560
Free weighted R factor               =     0.1968
Overall weighted R2 factor           =     0.1880
Free weighted R2 factor              =     0.2321
Average correlation coefficient      =     0.9326
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9293
Cruickshanks DPI for coordinate error=     0.1131
DPI based on free R factor           =     0.1161
Overall figure of merit              =     0.8390
ML based su of positional parameters =     0.0758
ML based su of thermal parameters    =     2.3758
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    109440.77       13400.567       763034.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31988850    
 Actual weight    6.8496723      is applied to the X-ray term


 function value    754777.31    

-------------------------------------------------------------------------------
             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 =     0.0421, B  =   -0.0741
Partial structure    1: scale =     0.3851, B  =   44.2877
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1733
Free R factor                        =     0.2200
Average Fourier shell correlation    =     0.9569
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9324
Overall figure of merit              =     0.8552
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    108931.63       8631.3770       754777.31       763034.00    


     CGMAT cycle number =      3

 Weight matrix   0.32311520    
 Actual weight    6.8496723      is applied to the X-ray term


 function value    754426.94    

-------------------------------------------------------------------------------
             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 =     0.0420, B  =   -0.0610
Partial structure    1: scale =     0.3850, B  =   44.1983
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1729
Free R factor                        =     0.2196
Average Fourier shell correlation    =     0.9573
AverageFree Fourier shell correlation=     0.9476
Average correlation coefficient      =     0.9330
Overall figure of merit              =     0.8563
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    108847.38       8858.0576       754426.94       754777.31    


     CGMAT cycle number =      4

 Weight matrix   0.32401600    
 Actual weight    6.8496723      is applied to the X-ray term


 function value    754293.94    

-------------------------------------------------------------------------------
             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 =     0.0421, B  =   -0.0419
Partial structure    1: scale =     0.3850, B  =   44.0050
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1729
Free R factor                        =     0.2194
Average Fourier shell correlation    =     0.9574
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9331
Overall figure of merit              =     0.8566
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    108817.95       8926.6270       754293.94       754426.94    


     CGMAT cycle number =      5

 Weight matrix   0.32431498    
 Actual weight    6.8496723      is applied to the X-ray term


 function value    754236.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0421, B  =   -0.0411
Partial structure    1: scale =     0.3849, B  =   43.9021
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1728
Free R factor                        =     0.2193
Average Fourier shell correlation    =     0.9574
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9332
Overall figure of merit              =     0.8567
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    108806.48       8947.5947       754236.38       754293.94    


     CGMAT cycle number =      6

 Weight matrix   0.32432246    
 Actual weight    6.8496723      is applied to the X-ray term


 function value    754219.31    

-------------------------------------------------------------------------------
             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 =     0.0421, B  =   -0.0383
Partial structure    1: scale =     0.3849, B  =   43.8338
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1728
Free R factor                        =     0.2192
Average Fourier shell correlation    =     0.9575
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9332
Overall figure of merit              =     0.8567
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    108802.97       8954.6094       754219.31       754236.38    


     CGMAT cycle number =      7

 Weight matrix   0.32456174    
 Actual weight    6.8496723      is applied to the X-ray term


 function value    754199.63    

-------------------------------------------------------------------------------
             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 =     0.0421, B  =   -0.0403
Partial structure    1: scale =     0.3847, B  =   43.7608
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1728
Free R factor                        =     0.2192
Average Fourier shell correlation    =     0.9575
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9332
Overall figure of merit              =     0.8568
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    108800.35       8952.8926       754199.63       754219.31    


     CGMAT cycle number =      8

 Weight matrix   0.32459605    
 Actual weight    6.8496723      is applied to the X-ray term


 function value    754160.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0421, B  =   -0.0390
Partial structure    1: scale =     0.3847, B  =   43.8753
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1729
Free R factor                        =     0.2191
Average Fourier shell correlation    =     0.9575
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9332
Overall figure of merit              =     0.8568
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    108794.58       8953.0674       754160.25       754199.63    


     CGMAT cycle number =      9

 Weight matrix   0.32474133    
 Actual weight    6.8496723      is applied to the X-ray term


 function value    754125.19    

-------------------------------------------------------------------------------
             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 =     0.0421, B  =   -0.0413
Partial structure    1: scale =     0.3846, B  =   43.8044
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1729
Free R factor                        =     0.2190
Average Fourier shell correlation    =     0.9575
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9332
Overall figure of merit              =     0.8569
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    108790.63       8945.0234       754125.19       754160.25    


     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.= 0.907 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   71
 Minimum acceptable grid spacing:    78   78  164
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   71
 Minimum acceptable grid spacing:    78   78  164
 Weight matrix   0.32460263    
 Actual weight    6.8496723      is applied to the X-ray term
Norm of X_ray positional gradient                39.8
Norm of Geom. positional gradient                39.8
Norm of X_ray B-factor gradient                  122.
Norm of Geom. B-factor gradient                  124.
Product of X_ray and Geom posit. gradients     -0.153E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.485E+08
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.7452E+06 GEOM=      8950.     TOTAL=     0.7541E+06
 function value    754139.44    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.812     1.644
Bond angles  : others                          3238     1.493     1.580
Torsion angles, period  1. refined              185     6.848     5.000
Torsion angles, period  2. refined               90    35.475    22.778
Torsion angles, period  3. refined              268    13.351    15.000
Torsion angles, period  4. refined                9    12.270    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   288     0.250     0.200
VDW repulsions.others                          1360     0.191     0.200
VDW; torsion: refined_atoms                     715     0.173     0.200
VDW; torsion.others                             787     0.084     0.200
HBOND: refined_atoms                            207     0.203     0.200
HBOND.others                                      1     0.004     0.200
VDW repulsions: symmetry: refined_atoms           8     0.208     0.200
VDW repulsions: symmetry: others                 24     0.175     0.200
HBOND: symmetry: refined_atoms                   24     0.182     0.200
M. chain bond B values: refined atoms           746     1.658     1.350
M. chain bond B values: others                  746     1.656     1.350
M. chain angle B values: refined atoms          929     2.621     2.012
M. chain angle B values: others                 930     2.619     2.012
S. chain bond B values: refined atoms           811     2.956     1.739
S. chain bond B values: others                  810     2.949     1.739
S. chain angle B values: refined atoms         1177     4.570     2.444
S. chain angle B values: others                1178     4.568     2.444
Long range B values: refined atoms             1819     7.005    18.627
Long range B values: others                    1730     6.695    17.214
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0421, B  =   -0.0404
Partial structure    1: scale =     0.3846, B  =   43.7962
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.042    2847 100.00   463.1   471.8  0.16  0.17     129   455.7   467.1  0.20  0.21
 0.124    4787 100.00   313.9   300.1  0.16  0.15     274   316.6   294.5  0.22  0.20
 0.207    6082  99.97   212.3   198.3  0.16  0.14     327   216.0   204.1  0.20  0.17
 0.289    7107 100.00   121.4   130.9  0.22  0.17     388   124.1   133.1  0.27  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0418   2024   0.925    823   0.831   2847   0.898  0.952  0.9657  0.9728  0.9115  0.9406
  0.1242   3958   0.878    829   0.774   4787   0.860  0.996  0.9483  0.9614  0.8940  0.9429
  0.2066   5247   0.885    835   0.776   6082   0.870  1.032  0.9543  0.9617  0.9110  0.9410
  0.2891   6286   0.836    826   0.762   7112   0.827  0.873  0.9363  0.9451  0.8759  0.9170
 $$
Resolution limits                    =     41.964     1.740
Number of used reflections           =      20828
Percentage observed                  =    99.9863
Percentage of free reflections       =     5.1030
Overall R factor                     =     0.1729
Free R factor                        =     0.2189
Average Fourier shell correlation    =     0.9575
AverageFree Fourier shell correlation=     0.9479
Overall weighted R factor            =     0.1561
Free weighted R factor               =     0.1954
Overall weighted R2 factor           =     0.1883
Free weighted R2 factor              =     0.2300
Average correlation coefficient      =     0.9332
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9305
Cruickshanks DPI for coordinate error=     0.1130
DPI based on free R factor           =     0.1151
Overall figure of merit              =     0.8569
ML based su of positional parameters =     0.0703
ML based su of thermal parameters    =     2.1746
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    108788.64       8949.7529       754116.31       754125.19    

    ****                              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.= 0.907 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-74A.mtz 




-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.813     1.644
Bond angles  : others                          3238     1.493     1.580
Torsion angles, period  1. refined              185     6.847     5.000
Torsion angles, period  2. refined               90    35.468    22.778
Torsion angles, period  3. refined              268    13.352    15.000
Torsion angles, period  4. refined                9    12.261    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   288     0.250     0.200
VDW repulsions.others                          1365     0.191     0.200
VDW; torsion: refined_atoms                     715     0.173     0.200
VDW; torsion.others                             786     0.084     0.200
HBOND: refined_atoms                            207     0.203     0.200
HBOND.others                                      1     0.006     0.200
VDW repulsions: symmetry: refined_atoms           8     0.208     0.200
VDW repulsions: symmetry: others                 24     0.175     0.200
HBOND: symmetry: refined_atoms                   24     0.183     0.200
M. chain bond B values: refined atoms           746     1.658     1.349
M. chain bond B values: others                  746     1.656     1.349
M. chain angle B values: refined atoms          929     2.620     2.011
M. chain angle B values: others                 930     2.619     2.011
S. chain bond B values: refined atoms           811     2.957     1.739
S. chain bond B values: others                  810     2.950     1.739
S. chain angle B values: refined atoms         1177     4.571     2.444
S. chain angle B values: others                1178     4.569     2.444
Long range B values: refined atoms             1819     7.006    18.624
Long range B values: others                    1730     6.696    17.211
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0421, B  =   -0.0405
Partial structure    1: scale =     0.3847, B  =   43.8056
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.042    2847 100.00   463.1   471.8  0.16  0.17     129   455.7   467.1  0.20  0.21
 0.124    4787 100.00   313.9   300.1  0.16  0.15     274   316.6   294.5  0.22  0.20
 0.207    6082  99.97   212.3   198.3  0.16  0.14     327   216.0   204.2  0.20  0.17
 0.289    7107 100.00   121.4   131.0  0.22  0.17     388   124.1   133.1  0.27  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0418   2024   0.925    823   0.831   2847   0.898  0.952  0.9657  0.9728  0.9115  0.9407
  0.1242   3958   0.878    829   0.774   4787   0.860  0.996  0.9483  0.9614  0.8940  0.9429
  0.2066   5247   0.885    835   0.776   6082   0.870  1.032  0.9543  0.9617  0.9110  0.9410
  0.2891   6286   0.836    826   0.762   7112   0.827  0.873  0.9363  0.9451  0.8759  0.9170
 $$
Resolution limits                    =     41.964     1.740
Number of used reflections           =      20828
Percentage observed                  =    99.9863
Percentage of free reflections       =     5.1030
Overall R factor                     =     0.1729
Free R factor                        =     0.2189
Average Fourier shell correlation    =     0.9575
AverageFree Fourier shell correlation=     0.9479
Overall weighted R factor            =     0.1561
Free weighted R factor               =     0.1954
Overall weighted R2 factor           =     0.1883
Free weighted R2 factor              =     0.2301
Average correlation coefficient      =     0.9332
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9305
Cruickshanks DPI for coordinate error=     0.1130
DPI based on free R factor           =     0.1151
Overall figure of merit              =     0.8569
ML based su of positional parameters =     0.0703
ML based su of thermal parameters    =     2.1746
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.65
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1731   0.2208   0.839      109441.    6055.7   0.0126  0.937   1.811  1.050   0.088
       1   0.1733   0.2200   0.855      108932.    6044.1   0.0118  0.884   1.770  1.026   0.086
       2   0.1729   0.2196   0.856      108847.    6041.6   0.0125  0.934   1.797  1.042   0.089
       3   0.1729   0.2194   0.857      108818.    6039.9   0.0126  0.940   1.805  1.048   0.089
       4   0.1728   0.2193   0.857      108806.    6039.2   0.0126  0.942   1.809  1.050   0.089
       5   0.1728   0.2192   0.857      108803.    6039.0   0.0127  0.944   1.811  1.051   0.089
       6   0.1728   0.2192   0.857      108800.    6038.9   0.0127  0.944   1.811  1.052   0.089
       7   0.1729   0.2191   0.857      108795.    6038.7   0.0127  0.944   1.812  1.052   0.089
       8   0.1729   0.2190   0.857      108791.    6038.4   0.0127  0.944   1.812  1.052   0.089
       9   0.1729   0.2189   0.857      108792.    6038.3   0.0127  0.945   1.812  1.052   0.089
      10   0.1729   0.2189   0.857      108791.    6038.3   0.0127  0.945   1.813  1.052   0.089
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1731   0.1729
             R free    0.2208   0.2189
     Rms BondLength    0.0126   0.0127
      Rms BondAngle    1.8110   1.8125
     Rms ChirVolume    0.0882   0.0890
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.8s System:    0.1s Elapsed:     0:47