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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 27/ 5/2020 Run time: 06:19:41 


 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 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_1-43A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_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_step0-01A_R00_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:     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  1.4200

  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_step0-01A_R00_1-43A.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=   2.054 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=   2.195 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.831 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.220 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=   2.404 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=   2.385 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=   2.101 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       2004
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.= 0.896 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   0.25276729    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                36.0
Norm of Geom. positional gradient                82.4
Norm of X_ray B-factor gradient                  88.6
Norm of Geom. B-factor gradient                  97.8
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.500
Product of X_ray and Geom B-fact gradients     -0.255E+08
 Cosine of angle between them                      -0.911


Residuals: XRAY=     0.1066E+07 GEOM=     0.1304E+05 TOTAL=     0.1079E+07
 function value    1079403.4    

-------------------------------------------------------------------------------
             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     1.834     1.644
Bond angles  : others                          3238     2.363     1.580
Torsion angles, period  1. refined              185     6.730     5.000
Torsion angles, period  2. refined               90    34.571    22.778
Torsion angles, period  3. refined              268    13.353    15.000
Torsion angles, period  4. refined                9    12.335    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   305     0.243     0.200
VDW repulsions.others                          1335     0.220     0.200
VDW; torsion: refined_atoms                     728     0.173     0.200
VDW; torsion.others                             717     0.081     0.200
HBOND: refined_atoms                            204     0.200     0.200
HBOND.others                                      1     0.074     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 23     0.205     0.200
HBOND: symmetry: refined_atoms                   19     0.176     0.200
M. chain bond B values: refined atoms           746     1.834     1.687
M. chain bond B values: others                  746     1.828     1.687
M. chain angle B values: refined atoms          929     2.820     2.521
M. chain angle B values: others                 930     2.819     2.521
S. chain bond B values: refined atoms           811     3.266     2.105
S. chain bond B values: others                  810     3.261     2.105
S. chain angle B values: refined atoms         1177     4.962     2.985
S. chain angle B values: others                1178     4.960     2.985
Long range B values: refined atoms             1840     7.769    22.952
Long range B values: others                    1756     7.499    21.570
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0830
Partial structure    1: scale =     0.3933, B  =   37.2618
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5089 100.00   380.3   390.0  0.17  0.18     240   375.4   379.5  0.22  0.22
 0.186    8652  99.98   205.5   181.7  0.19  0.17     491   214.2   190.5  0.22  0.20
 0.310   11047 100.00    91.9    88.5  0.23  0.20     600    92.1    89.1  0.27  0.24
 0.434   12831  98.63    38.7    48.0  0.47  0.46     664    39.1    48.9  0.47  0.46
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.893   1243   0.781   5089   0.866  0.946  0.9551  0.9650  0.8982  0.9354
  0.1863   7407   0.862   1245   0.762   8652   0.848  1.094  0.9468  0.9553  0.9003  0.9362
  0.3102   9814   0.801   1233   0.722  11047   0.792  0.951  0.9250  0.9319  0.8867  0.9136
  0.4340  11579   0.430   1252   0.381  12831   0.426  0.405  0.6589  0.6373  0.6798  0.6456
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37619
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0361
Overall R factor                     =     0.2186
Free R factor                        =     0.2530
Average Fourier shell correlation    =     0.8413
AverageFree Fourier shell correlation=     0.8454
Overall weighted R factor            =     0.1828
Free weighted R factor               =     0.2173
Overall weighted R2 factor           =     0.2113
Free weighted R2 factor              =     0.2527
Average correlation coefficient      =     0.8303
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9414
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0809
Overall figure of merit              =     0.6899
ML based su of positional parameters =     0.0750
ML based su of thermal parameters    =     2.1394
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176262.80       13041.622       1079403.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.32054558    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067678.0    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0554
Partial structure    1: scale =     0.3931, B  =   37.2035
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2190
Free R factor                        =     0.2523
Average Fourier shell correlation    =     0.8535
AverageFree Fourier shell correlation=     0.8572
Average correlation coefficient      =     0.8291
Overall figure of merit              =     0.7113
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175152.17       8035.3096       1067678.0       1079403.4    


     CGMAT cycle number =      3

 Weight matrix   0.32615921    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067096.8    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0053
Partial structure    1: scale =     0.3933, B  =   37.1685
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                        =     0.2523
Average Fourier shell correlation    =     0.8566
AverageFree Fourier shell correlation=     0.8597
Average correlation coefficient      =     0.8298
Overall figure of merit              =     0.7145
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174984.56       8468.0986       1067096.8       1067678.0    


     CGMAT cycle number =      4

 Weight matrix   0.32715213    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066967.1    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0003
Partial structure    1: scale =     0.3933, B  =   37.1620
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                        =     0.2524
Average Fourier shell correlation    =     0.8574
AverageFree Fourier shell correlation=     0.8603
Average correlation coefficient      =     0.8301
Overall figure of merit              =     0.7155
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174950.45       8544.7520       1066967.1       1067096.8    


     CGMAT cycle number =      5

 Weight matrix   0.32689390    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066994.9    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0004
Partial structure    1: scale =     0.3934, B  =   37.1754
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                        =     0.2525
Average Fourier shell correlation    =     0.8574
AverageFree Fourier shell correlation=     0.8603
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.7155
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    174950.42       8574.4590       1067025.4       1066967.1    

 fvalues    174950.42       8574.4590       1066996.1       1066996.6    
 fvalues    174950.42       8574.4590       1066996.1       1066996.6    


     CGMAT cycle number =      6

 Weight matrix   0.32680562    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067031.4    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0007
Partial structure    1: scale =     0.3934, B  =   37.1721
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                        =     0.2526
Average Fourier shell correlation    =     0.8575
AverageFree Fourier shell correlation=     0.8603
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.7155
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    174957.55       8577.6396       1067042.8       1066996.6    
 fvalues    174957.55       8577.6396       1067042.8       1067042.9    


     CGMAT cycle number =      7

 Weight matrix   0.32675549    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067043.9    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =    0.0000
Partial structure    1: scale =     0.3935, B  =   37.1686
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                        =     0.2526
Average Fourier shell correlation    =     0.8574
AverageFree Fourier shell correlation=     0.8603
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.7155
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    174957.61       8578.0986       1067083.8       1067042.9    

 fvalues    174957.61       8578.0986       1067050.0       1067043.8    
 fvalues    174957.61       8578.0986       1067050.0       1067043.8    


     CGMAT cycle number =      8

 Weight matrix   0.32668108    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067048.1    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0001
Partial structure    1: scale =     0.3935, B  =   37.1659
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                        =     0.2526
Average Fourier shell correlation    =     0.8574
AverageFree Fourier shell correlation=     0.8603
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.7155
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    174958.63       8575.9473       1067064.8       1067043.8    

 fvalues    174958.63       8575.9473       1067059.8       1067047.8    
 fvalues    174958.63       8575.9473       1067059.8       1067047.8    


     CGMAT cycle number =      9

 Weight matrix   0.32661611    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067055.5    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0012
Partial structure    1: scale =     0.3936, B  =   37.1330
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                        =     0.2526
Average Fourier shell correlation    =     0.8574
AverageFree Fourier shell correlation=     0.8603
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.7155
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    174960.53       8576.0723       1067056.1       1067047.8    
 fvalues    174960.53       8576.0723       1067056.1       1067059.4    


     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.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.32659599    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                43.3
Norm of Geom. positional gradient                43.3
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                  102.
Product of X_ray and Geom posit. gradients     -0.181E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.339E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.1058E+07 GEOM=      8576.     TOTAL=     0.1067E+07
 function value    1067059.4    

-------------------------------------------------------------------------------
             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     1.840     1.644
Bond angles  : others                          3238     1.511     1.580
Torsion angles, period  1. refined              185     6.724     5.000
Torsion angles, period  2. refined               90    34.596    22.778
Torsion angles, period  3. refined              268    13.370    15.000
Torsion angles, period  4. refined                9    12.357    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.244     0.200
VDW repulsions.others                          1365     0.194     0.200
VDW; torsion: refined_atoms                     729     0.173     0.200
VDW; torsion.others                             750     0.086     0.200
HBOND: refined_atoms                            203     0.201     0.200
HBOND.others                                      1     0.006     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 24     0.186     0.200
HBOND: symmetry: refined_atoms                   20     0.168     0.200
M. chain bond B values: refined atoms           746     1.845     1.693
M. chain bond B values: others                  746     1.840     1.694
M. chain angle B values: refined atoms          929     2.827     2.531
M. chain angle B values: others                 930     2.826     2.531
S. chain bond B values: refined atoms           811     3.273     2.112
S. chain bond B values: others                  810     3.268     2.112
S. chain angle B values: refined atoms         1177     4.976     2.995
S. chain angle B values: others                1178     4.973     2.994
Long range B values: refined atoms             1837     7.760    22.996
Long range B values: others                    1753     7.485    21.610
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0011
Partial structure    1: scale =     0.3936, B  =   37.1257
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5089 100.00   380.9   390.4  0.17  0.18     240   376.0   380.1  0.22  0.22
 0.186    8652  99.98   205.8   182.1  0.19  0.17     491   214.5   190.7  0.22  0.20
 0.310   11047 100.00    92.1    88.7  0.23  0.20     600    92.3    89.3  0.26  0.23
 0.434   12831  98.63    38.8    48.1  0.47  0.46     664    39.2    48.9  0.47  0.46
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.909   1243   0.807   5089   0.884  0.949  0.9599  0.9694  0.8989  0.9354
  0.1863   7407   0.882   1245   0.782   8652   0.868  1.096  0.9512  0.9600  0.9007  0.9361
  0.3102   9814   0.830   1233   0.754  11047   0.822  0.961  0.9344  0.9415  0.8882  0.9150
  0.4340  11579   0.459   1252   0.412  12831   0.455  0.420  0.6902  0.6714  0.6787  0.6441
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37619
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0361
Overall R factor                     =     0.2182
Free R factor                        =     0.2526
Average Fourier shell correlation    =     0.8574
AverageFree Fourier shell correlation=     0.8603
Overall weighted R factor            =     0.1826
Free weighted R factor               =     0.2170
Overall weighted R2 factor           =     0.2110
Free weighted R2 factor              =     0.2520
Average correlation coefficient      =     0.8303
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9417
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0807
Overall figure of merit              =     0.7155
ML based su of positional parameters =     0.0659
ML based su of thermal parameters    =     1.8759
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    174960.52       8576.1484       1067059.4       1067059.4    

    ****                              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.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS
          28          24          36  0.70425701      2.37302221E-02  0.70425248    
          36           8          36  0.70425701      2.37302221E-02  0.70425248    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-42A.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     1.840     1.644
Bond angles  : others                          3238     1.511     1.580
Torsion angles, period  1. refined              185     6.724     5.000
Torsion angles, period  2. refined               90    34.596    22.778
Torsion angles, period  3. refined              268    13.371    15.000
Torsion angles, period  4. refined                9    12.357    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.244     0.200
VDW repulsions.others                          1363     0.194     0.200
VDW; torsion: refined_atoms                     729     0.173     0.200
VDW; torsion.others                             752     0.086     0.200
HBOND: refined_atoms                            203     0.201     0.200
HBOND.others                                      1     0.006     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 24     0.186     0.200
HBOND: symmetry: refined_atoms                   20     0.168     0.200
M. chain bond B values: refined atoms           746     1.846     1.693
M. chain bond B values: others                  746     1.840     1.693
M. chain angle B values: refined atoms          929     2.827     2.531
M. chain angle B values: others                 930     2.826     2.531
S. chain bond B values: refined atoms           811     3.273     2.112
S. chain bond B values: others                  810     3.268     2.112
S. chain angle B values: refined atoms         1177     4.976     2.995
S. chain angle B values: others                1178     4.973     2.994
Long range B values: refined atoms             1837     7.760    22.995
Long range B values: others                    1753     7.486    21.610
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0001
Partial structure    1: scale =     0.3936, B  =   37.1261
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5089 100.00   380.9   390.4  0.17  0.18     240   376.0   380.1  0.22  0.22
 0.186    8652  99.98   205.8   182.1  0.19  0.17     491   214.5   190.7  0.22  0.20
 0.310   11047 100.00    92.1    88.8  0.23  0.20     600    92.3    89.3  0.26  0.23
 0.434   12831  98.63    38.8    48.1  0.47  0.46     664    39.2    48.9  0.47  0.46
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3846   0.909   1243   0.807   5089   0.884  0.949  0.9599  0.9694  0.8989  0.9354
  0.1863   7407   0.882   1245   0.782   8652   0.868  1.096  0.9512  0.9600  0.9007  0.9361
  0.3102   9814   0.830   1233   0.754  11047   0.822  0.961  0.9344  0.9415  0.8882  0.9151
  0.4340  11579   0.459   1252   0.412  12831   0.455  0.420  0.6902  0.6715  0.6787  0.6441
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37619
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0361
Overall R factor                     =     0.2182
Free R factor                        =     0.2526
Average Fourier shell correlation    =     0.8574
AverageFree Fourier shell correlation=     0.8603
Overall weighted R factor            =     0.1826
Free weighted R factor               =     0.2170
Overall weighted R2 factor           =     0.2110
Free weighted R2 factor              =     0.2520
Average correlation coefficient      =     0.8302
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9417
Cruickshanks DPI for coordinate error=     0.0778
DPI based on free R factor           =     0.0807
Overall figure of merit              =     0.7155
ML based su of positional parameters =     0.0659
ML based su of thermal parameters    =     1.8759
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.75
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2186   0.2530   0.690      176263.    9512.8   0.0129  0.976   1.834  1.067   0.090
       1   0.2190   0.2523   0.711      175152.    9480.9   0.0117  0.885   1.766  1.028   0.087
       2   0.2183   0.2523   0.715      174985.    9477.8   0.0129  0.972   1.815  1.057   0.089
       3   0.2183   0.2524   0.715      174950.    9477.3   0.0130  0.978   1.830  1.066   0.090
       4   0.2182   0.2525   0.715      174950.    9477.7   0.0130  0.981   1.836  1.069   0.090
       5   0.2182   0.2526   0.716      174956.    9478.1   0.0130  0.982   1.838  1.070   0.090
       6   0.2182   0.2526   0.716      174958.    9478.4   0.0130  0.982   1.839  1.071   0.090
       7   0.2182   0.2526   0.716      174959.    9478.5   0.0130  0.982   1.840  1.071   0.090
       8   0.2182   0.2526   0.716      174960.    9478.5   0.0130  0.982   1.840  1.071   0.090
       9   0.2182   0.2526   0.716      174961.    9478.6   0.0130  0.982   1.840  1.071   0.090
      10   0.2182   0.2526   0.716      174961.    9478.6   0.0130  0.982   1.840  1.071   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2186   0.2182
             R free    0.2530   0.2526
     Rms BondLength    0.0129   0.0130
      Rms BondAngle    1.8343   1.8401
     Rms ChirVolume    0.0902   0.0904
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      60.3s System:    0.2s Elapsed:     1:01