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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: 05:45:51 


 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 1.43     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_1-44A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-43A.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_1-43A.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       0.1223
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4300
  Estimated number of reflections :      50598
  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  1.4300

  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_1-44A.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=   2.056 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=   2.193 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=   2.216 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=   2.408 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.386 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.105 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       1960
Number of   all  reflections      39006
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          39006

   Current auto weighting coefficient =    6.0746651    

 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.= 0.895 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   86
 Minimum acceptable grid spacing:    90   90  191
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   86
 Minimum acceptable grid spacing:    90   90  191
 Weight matrix   0.24439637    
 Actual weight    6.0746651      is applied to the X-ray term
Norm of X_ray positional gradient                35.9
Norm of Geom. positional gradient                82.4
Norm of X_ray B-factor gradient                  89.9
Norm of Geom. B-factor gradient                  98.7
Product of X_ray and Geom posit. gradients     -0.143E+08
 Cosine of angle between them                      -0.499
Product of X_ray and Geom B-fact gradients     -0.259E+08
 Cosine of angle between them                      -0.905


Residuals: XRAY=     0.1058E+07 GEOM=     0.1307E+05 TOTAL=     0.1072E+07
 function value    1071524.8    

-------------------------------------------------------------------------------
             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     1.838     1.644
Bond angles  : others                          3238     2.363     1.580
Torsion angles, period  1. refined              185     6.729     5.000
Torsion angles, period  2. refined               90    34.597    22.778
Torsion angles, period  3. refined              268    13.340    15.000
Torsion angles, period  4. refined                9    12.414    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     0.244     0.200
VDW repulsions.others                          1341     0.219     0.200
VDW; torsion: refined_atoms                     727     0.174     0.200
VDW; torsion.others                             721     0.081     0.200
HBOND: refined_atoms                            204     0.200     0.200
HBOND.others                                      1     0.077     0.200
VDW repulsions: symmetry: refined_atoms           8     0.196     0.200
VDW repulsions: symmetry: others                 23     0.204     0.200
HBOND: symmetry: refined_atoms                   20     0.168     0.200
M. chain bond B values: refined atoms           746     1.832     1.678
M. chain bond B values: others                  746     1.826     1.678
M. chain angle B values: refined atoms          929     2.818     2.507
M. chain angle B values: others                 930     2.817     2.507
S. chain bond B values: refined atoms           811     3.264     2.095
S. chain bond B values: others                  810     3.259     2.095
S. chain angle B values: refined atoms         1177     4.961     2.970
S. chain angle B values: others                1178     4.959     2.970
Long range B values: refined atoms             1840     7.707    22.850
Long range B values: others                    1756     7.438    21.471
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =    0.1023
Partial structure    1: scale =     0.3936, B  =   37.2409
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    4982 100.00   383.2   392.9  0.17  0.18     234   378.2   381.4  0.22  0.22
 0.184    8484  99.98   208.4   185.0  0.19  0.17     483   217.9   195.0  0.22  0.20
 0.306   10809 100.00    95.7    91.4  0.22  0.20     588    95.4    91.6  0.27  0.24
 0.428   12743  99.90    40.0    49.6  0.46  0.44     654    40.2    50.2  0.46  0.44
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0616   3757   0.893   1225   0.780   4982   0.865  0.946  0.9552  0.9652  0.8981  0.9355
  0.1837   7257   0.864   1227   0.767   8484   0.850  1.089  0.9477  0.9556  0.8998  0.9356
  0.3059   9594   0.803   1215   0.721  10809   0.794  0.961  0.9239  0.9335  0.8824  0.9174
  0.4280  11508   0.387   1248   0.346  12756   0.383  0.375  0.6482  0.6362  0.6932  0.6664
 $$
Resolution limits                    =     41.964     1.430
Number of used reflections           =      37030
Percentage observed                  =    99.9590
Percentage of free reflections       =     5.0269
Overall R factor                     =     0.2173
Free R factor                        =     0.2522
Average Fourier shell correlation    =     0.8404
AverageFree Fourier shell correlation=     0.8413
Overall weighted R factor            =     0.1819
Free weighted R factor               =     0.2168
Overall weighted R2 factor           =     0.2106
Free weighted R2 factor              =     0.2524
Average correlation coefficient      =     0.8376
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9410
Cruickshanks DPI for coordinate error=     0.0786
DPI based on free R factor           =     0.0817
Overall figure of merit              =     0.6750
ML based su of positional parameters =     0.0764
ML based su of thermal parameters    =     2.1974
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    174241.05       13068.706       1071524.8      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31723639    
 Actual weight    6.0746651      is applied to the X-ray term


 function value    1059563.8    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0582
Partial structure    1: scale =     0.3933, B  =   37.3350
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2177
Free R factor                        =     0.2512
Average Fourier shell correlation    =     0.8604
AverageFree Fourier shell correlation=     0.8610
Average correlation coefficient      =     0.8359
Overall figure of merit              =     0.7119
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    173100.02       8039.0781       1059563.8       1071524.8    


     CGMAT cycle number =      3

 Weight matrix   0.32138592    
 Actual weight    6.0746651      is applied to the X-ray term


 function value    1058966.8    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0020
Partial structure    1: scale =     0.3936, B  =   37.3613
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                     =     0.2171
Free R factor                        =     0.2511
Average Fourier shell correlation    =     0.8628
AverageFree Fourier shell correlation=     0.8629
Average correlation coefficient      =     0.8369
Overall figure of merit              =     0.7136
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    172934.09       8449.9893       1058966.8       1059563.8    


     CGMAT cycle number =      4

 Weight matrix   0.32128131    
 Actual weight    6.0746651      is applied to the X-ray term


 function value    1058878.8    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =    0.0028
Partial structure    1: scale =     0.3937, B  =   37.2437
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                     =     0.2170
Free R factor                        =     0.2511
Average Fourier shell correlation    =     0.8632
AverageFree Fourier shell correlation=     0.8630
Average correlation coefficient      =     0.8374
Overall figure of merit              =     0.7135
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    172908.33       8518.6514       1058878.8       1058966.8    


     CGMAT cycle number =      5

 Weight matrix   0.32244328    
 Actual weight    6.0746651      is applied to the X-ray term


 function value    1058848.0    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =    0.0063
Partial structure    1: scale =     0.3937, B  =   37.2081
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                     =     0.2170
Free R factor                        =     0.2512
Average Fourier shell correlation    =     0.8638
AverageFree Fourier shell correlation=     0.8636
Average correlation coefficient      =     0.8375
Overall figure of merit              =     0.7147
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    172898.28       8548.8896       1058848.0       1058878.8    


     CGMAT cycle number =      6

 Weight matrix   0.32130739    
 Actual weight    6.0746651      is applied to the X-ray term


 function value    1058883.3    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =    0.0072
Partial structure    1: scale =     0.3936, B  =   37.1862
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                     =     0.2170
Free R factor                        =     0.2513
Average Fourier shell correlation    =     0.8633
AverageFree Fourier shell correlation=     0.8631
Average correlation coefficient      =     0.8376
Overall figure of merit              =     0.7137
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    172903.42       8554.8477       1058890.0       1058848.0    

 fvalues    172903.42       8554.8477       1058893.9       1058885.3    
 fvalues    172903.42       8554.8477       1058893.9       1058885.3    


     CGMAT cycle number =      7

 Weight matrix   0.32121804    
 Actual weight    6.0746651      is applied to the X-ray term


 function value    1058894.8    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =    0.0078
Partial structure    1: scale =     0.3936, B  =   37.1771
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                     =     0.2170
Free R factor                        =     0.2513
Average Fourier shell correlation    =     0.8633
AverageFree Fourier shell correlation=     0.8631
Average correlation coefficient      =     0.8376
Overall figure of merit              =     0.7137
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    172904.97       8553.7627       1058891.8       1058885.3    
 fvalues    172904.97       8553.7627       1058891.8       1058893.5    


     CGMAT cycle number =      8

 Weight matrix   0.32095167    
 Actual weight    6.0746651      is applied to the X-ray term


 function value    1058917.1    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =    0.0088
Partial structure    1: scale =     0.3936, B  =   37.2798
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                     =     0.2170
Free R factor                        =     0.2513
Average Fourier shell correlation    =     0.8633
AverageFree Fourier shell correlation=     0.8631
Average correlation coefficient      =     0.8376
Overall figure of merit              =     0.7136
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    172908.30       8548.1338       1058915.1       1058893.5    

 fvalues    172908.30       8548.1338       1058908.1       1058908.1    
 fvalues    172908.30       8548.1338       1058908.1       1058908.1    


     CGMAT cycle number =      9

 Weight matrix   0.32097247    
 Actual weight    6.0746651      is applied to the X-ray term


 function value    1058918.9    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =    0.0090
Partial structure    1: scale =     0.3936, B  =   37.2814
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                     =     0.2170
Free R factor                        =     0.2513
Average Fourier shell correlation    =     0.8633
AverageFree Fourier shell correlation=     0.8631
Average correlation coefficient      =     0.8376
Overall figure of merit              =     0.7136
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    172908.58       8547.6475       1058903.6       1058908.1    
 fvalues    172908.58       8547.6475       1058903.6       1058909.4    


     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   86
 Minimum acceptable grid spacing:    90   90  191
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   86
 Minimum acceptable grid spacing:    90   90  191
 Weight matrix   0.32092914    
 Actual weight    6.0746651      is applied to the X-ray term
Norm of X_ray positional gradient                42.8
Norm of Geom. positional gradient                42.8
Norm of X_ray B-factor gradient                  103.
Norm of Geom. B-factor gradient                  102.
Product of X_ray and Geom posit. gradients     -0.177E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.341E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.1050E+07 GEOM=      8547.     TOTAL=     0.1059E+07
 function value    1058922.8    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.835     1.644
Bond angles  : others                          3238     1.510     1.580
Torsion angles, period  1. refined              185     6.727     5.000
Torsion angles, period  2. refined               90    34.574    22.778
Torsion angles, period  3. refined              268    13.350    15.000
Torsion angles, period  4. refined                9    12.350    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                   305     0.243     0.200
VDW repulsions.others                          1366     0.193     0.200
VDW; torsion: refined_atoms                     728     0.173     0.200
VDW; torsion.others                             754     0.086     0.200
HBOND: refined_atoms                            202     0.201     0.200
HBOND.others                                      1     0.016     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 24     0.187     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     4.963     2.985
S. chain angle B values: others                1178     4.960     2.985
Long range B values: refined atoms             1838     7.764    22.933
Long range B values: others                    1754     7.493    21.548
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =    0.0100
Partial structure    1: scale =     0.3936, B  =   37.2806
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    4982 100.00   383.7   393.4  0.17  0.18     234   378.6   382.2  0.22  0.22
 0.184    8484  99.98   208.6   185.3  0.19  0.17     483   218.1   195.2  0.22  0.20
 0.306   10809 100.00    95.8    91.6  0.22  0.20     588    95.5    91.8  0.27  0.24
 0.428   12743  99.90    40.0    49.5  0.46  0.44     654    40.3    50.2  0.46  0.44
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0616   3757   0.909   1225   0.805   4982   0.883  0.948  0.9599  0.9694  0.8987  0.9354
  0.1837   7257   0.883   1227   0.786   8484   0.869  1.091  0.9517  0.9601  0.9007  0.9362
  0.3059   9594   0.828   1215   0.748  10809   0.819  0.968  0.9323  0.9415  0.8832  0.9169
  0.4280  11508   0.459   1248   0.417  12756   0.455  0.423  0.7011  0.6913  0.6942  0.6664
 $$
Resolution limits                    =     41.964     1.430
Number of used reflections           =      37030
Percentage observed                  =    99.9590
Percentage of free reflections       =     5.0269
Overall R factor                     =     0.2170
Free R factor                        =     0.2513
Average Fourier shell correlation    =     0.8633
AverageFree Fourier shell correlation=     0.8631
Overall weighted R factor            =     0.1818
Free weighted R factor               =     0.2160
Overall weighted R2 factor           =     0.2105
Free weighted R2 factor              =     0.2516
Average correlation coefficient      =     0.8376
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9414
Cruickshanks DPI for coordinate error=     0.0785
DPI based on free R factor           =     0.0814
Overall figure of merit              =     0.7137
ML based su of positional parameters =     0.0666
ML based su of thermal parameters    =     1.9016
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    172912.84       8546.9971       1058908.9       1058909.4    
 fvalues    172912.84       8546.9971       1058908.9       1058934.6    

    ****                              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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-43A.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     1.835     1.644
Bond angles  : others                          3238     1.510     1.580
Torsion angles, period  1. refined              185     6.726     5.000
Torsion angles, period  2. refined               90    34.570    22.778
Torsion angles, period  3. refined              268    13.352    15.000
Torsion angles, period  4. refined                9    12.349    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                   305     0.243     0.200
VDW repulsions.others                          1368     0.193     0.200
VDW; torsion: refined_atoms                     728     0.173     0.200
VDW; torsion.others                             759     0.085     0.200
HBOND: refined_atoms                            203     0.200     0.200
HBOND.others                                      1     0.016     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 24     0.187     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             1839     7.769    22.940
Long range B values: others                    1755     7.498    21.556
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =    0.0037
Partial structure    1: scale =     0.3936, B  =   37.2578
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    4982 100.00   383.7   393.4  0.17  0.18     234   378.6   382.2  0.22  0.22
 0.184    8484  99.98   208.6   185.4  0.19  0.17     483   218.1   195.3  0.22  0.20
 0.306   10809 100.00    95.8    91.7  0.22  0.20     588    95.5    91.8  0.27  0.24
 0.428   12743  99.90    40.0    49.6  0.46  0.44     654    40.3    50.2  0.46  0.44
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0616   3757   0.909   1225   0.805   4982   0.883  0.948  0.9599  0.9694  0.8988  0.9354
  0.1837   7257   0.883   1227   0.786   8484   0.869  1.091  0.9517  0.9601  0.9007  0.9362
  0.3059   9594   0.828   1215   0.748  10809   0.819  0.968  0.9323  0.9415  0.8832  0.9169
  0.4280  11508   0.462   1248   0.420  12756   0.458  0.426  0.7025  0.6926  0.6941  0.6664
 $$
Resolution limits                    =     41.964     1.430
Number of used reflections           =      37030
Percentage observed                  =    99.9590
Percentage of free reflections       =     5.0269
Overall R factor                     =     0.2170
Free R factor                        =     0.2513
Average Fourier shell correlation    =     0.8638
AverageFree Fourier shell correlation=     0.8636
Overall weighted R factor            =     0.1818
Free weighted R factor               =     0.2160
Overall weighted R2 factor           =     0.2105
Free weighted R2 factor              =     0.2515
Average correlation coefficient      =     0.8376
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9414
Cruickshanks DPI for coordinate error=     0.0785
DPI based on free R factor           =     0.0814
Overall figure of merit              =     0.7147
ML based su of positional parameters =     0.0666
ML based su of thermal parameters    =     1.9016
-----------------------------------------------------------------------------
  Time in seconds: CPU =        32.99
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2173   0.2522   0.675      174241.    9394.7   0.0130  0.978   1.838  1.069   0.090
       1   0.2177   0.2512   0.712      173100.    9359.1   0.0117  0.883   1.766  1.027   0.087
       2   0.2171   0.2511   0.714      172934.    9355.5   0.0128  0.966   1.811  1.054   0.089
       3   0.2170   0.2511   0.713      172908.    9355.1   0.0129  0.971   1.824  1.062   0.090
       4   0.2170   0.2512   0.715      172898.    9355.0   0.0129  0.974   1.830  1.065   0.090
       5   0.2170   0.2513   0.714      172903.    9355.6   0.0129  0.975   1.833  1.067   0.090
       6   0.2170   0.2513   0.714      172905.    9355.7   0.0129  0.975   1.834  1.067   0.090
       7   0.2170   0.2513   0.714      172910.    9356.1   0.0129  0.975   1.834  1.067   0.090
       8   0.2170   0.2513   0.714      172910.    9356.1   0.0129  0.975   1.834  1.068   0.090
       9   0.2170   0.2513   0.714      172911.    9356.2   0.0129  0.975   1.835  1.068   0.090
      10   0.2170   0.2513   0.715      172908.    9356.0   0.0129  0.975   1.835  1.068   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2173   0.2170
             R free    0.2522   0.2513
     Rms BondLength    0.0130   0.0129
      Rms BondAngle    1.8380   1.8351
     Rms ChirVolume    0.0900   0.0902
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      64.9s System:    0.2s Elapsed:     1:06