###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 27/ 5/2020 Run time: 03:36:34 


 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 1.47     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_1-48A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-47A.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_1-47A.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       0.1157
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4700
  Estimated number of reflections :      47040
  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  1.4700

  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_1-48A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.057 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.192 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=   1.830 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=   2.218 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=   2.407 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=   2.103 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       1804
Number of   all  reflections      35965
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          35965

   Current auto weighting coefficient =    6.1746435    

 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.= 0.893 id.= 3.000 dev= -2.11 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  280
 Maximuum H,K,L                 :    40   40   84
 Minimum acceptable grid spacing:    88   88  187
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    40   40   84
 Minimum acceptable grid spacing:    88   88  187
 Weight matrix   0.27216440    
 Actual weight    6.1746435      is applied to the X-ray term
Norm of X_ray positional gradient                36.3
Norm of Geom. positional gradient                82.7
Norm of X_ray B-factor gradient                  93.8
Norm of Geom. B-factor gradient                  102.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.502
Product of X_ray and Geom B-fact gradients     -0.273E+08
 Cosine of angle between them                      -0.883


Residuals: XRAY=     0.1011E+07 GEOM=     0.1324E+05 TOTAL=     0.1024E+07
 function value    1023768.2    

-------------------------------------------------------------------------------
             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     1.851     1.644
Bond angles  : others                          3238     2.365     1.580
Torsion angles, period  1. refined              185     6.751     5.000
Torsion angles, period  2. refined               90    34.629    22.778
Torsion angles, period  3. refined              268    13.317    15.000
Torsion angles, period  4. refined                9    12.433    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   305     0.244     0.200
VDW repulsions.others                          1336     0.220     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             728     0.081     0.200
HBOND: refined_atoms                            211     0.198     0.200
HBOND.others                                      1     0.078     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 23     0.200     0.200
HBOND: symmetry: refined_atoms                   22     0.166     0.200
M. chain bond B values: refined atoms           746     1.820     1.640
M. chain bond B values: others                  746     1.814     1.640
M. chain angle B values: refined atoms          929     2.807     2.450
M. chain angle B values: others                 930     2.807     2.450
S. chain bond B values: refined atoms           811     3.264     2.057
S. chain bond B values: others                  810     3.259     2.057
S. chain angle B values: refined atoms         1177     4.963     2.913
S. chain angle B values: others                1178     4.960     2.912
Long range B values: refined atoms             1847     7.733    22.477
Long range B values: others                    1761     7.462    21.072
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0460, B  =    0.1123
Partial structure    1: scale =     0.3920, B  =   38.0351
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.058    4597 100.00   397.0   406.6  0.17  0.18     214   391.7   397.2  0.21  0.21
 0.174    7833  99.98   219.1   197.7  0.18  0.16     439   230.4   207.8  0.22  0.20
 0.289    9951 100.00   111.7   104.1  0.21  0.19     555   112.0   105.3  0.25  0.22
 0.405   11763 100.00    45.4    56.7  0.43  0.39     596    45.7    57.0  0.44  0.41
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0583   3446   0.898   1151   0.789   4597   0.871  0.946  0.9579  0.9666  0.9030  0.9359
  0.1739   6670   0.867   1163   0.766   7833   0.852  1.071  0.9458  0.9553  0.8917  0.9336
  0.2894   8803   0.821   1148   0.738   9951   0.811  0.998  0.9328  0.9418  0.8932  0.9269
  0.4050  10595   0.539   1183   0.476  11778   0.533  0.529  0.7301  0.7381  0.7186  0.7421
 $$
Resolution limits                    =     41.964     1.470
Number of used reflections           =      34159
Percentage observed                  =    99.9917
Percentage of free reflections       =     5.0163
Overall R factor                     =     0.2113
Free R factor                        =     0.2473
Average Fourier shell correlation    =     0.8780
AverageFree Fourier shell correlation=     0.8720
Overall weighted R factor            =     0.1783
Free weighted R factor               =     0.2131
Overall weighted R2 factor           =     0.2073
Free weighted R2 factor              =     0.2492
Average correlation coefficient      =     0.8660
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9398
Cruickshanks DPI for coordinate error=     0.0827
DPI based on free R factor           =     0.0857
Overall figure of merit              =     0.7325
ML based su of positional parameters =     0.0730
ML based su of thermal parameters    =     2.1056
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    163656.97       13244.743       1023768.2      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.34285930    
 Actual weight    6.1746435      is applied to the X-ray term


 function value    1011972.5    

-------------------------------------------------------------------------------
             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 =     0.0460, B  =   -0.0730
Partial structure    1: scale =     0.3917, B  =   38.1363
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2118
Free R factor                        =     0.2459
Average Fourier shell correlation    =     0.8932
AverageFree Fourier shell correlation=     0.8880
Average correlation coefficient      =     0.8645
Overall figure of merit              =     0.7597
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    162565.84       8186.3594       1011972.5       1023768.2    


     CGMAT cycle number =      3

 Weight matrix   0.35007060    
 Actual weight    6.1746435      is applied to the X-ray term


 function value    1011295.4    

-------------------------------------------------------------------------------
             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 =     0.0460, B  =   -0.0116
Partial structure    1: scale =     0.3917, B  =   38.0408
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2112
Free R factor                        =     0.2462
Average Fourier shell correlation    =     0.8965
AverageFree Fourier shell correlation=     0.8909
Average correlation coefficient      =     0.8657
Overall figure of merit              =     0.7649
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    162394.53       8567.0596       1011295.4       1011972.5    


     CGMAT cycle number =      4

 Weight matrix   0.35106808    
 Actual weight    6.1746435      is applied to the X-ray term


 function value    1011186.6    

-------------------------------------------------------------------------------
             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 =     0.0460, B  =   -0.0027
Partial structure    1: scale =     0.3917, B  =   38.0070
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2111
Free R factor                        =     0.2463
Average Fourier shell correlation    =     0.8972
AverageFree Fourier shell correlation=     0.8914
Average correlation coefficient      =     0.8663
Overall figure of merit              =     0.7660
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    162364.98       8640.6885       1011186.6       1011295.4    


     CGMAT cycle number =      5

 Weight matrix   0.35137427    
 Actual weight    6.1746435      is applied to the X-ray term


 function value    1011183.6    

-------------------------------------------------------------------------------
             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 =     0.0460, B  =   -0.0000
Partial structure    1: scale =     0.3918, B  =   37.9670
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2111
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.8974
AverageFree Fourier shell correlation=     0.8914
Average correlation coefficient      =     0.8665
Overall figure of merit              =     0.7663
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    162360.13       8667.7373       1011183.6       1011186.6    


     CGMAT cycle number =      6

 Weight matrix   0.35120207    
 Actual weight    6.1746435      is applied to the X-ray term


 function value    1011193.4    

-------------------------------------------------------------------------------
             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 =     0.0460, B  =   -0.0000
Partial structure    1: scale =     0.3918, B  =   37.9669
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2111
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.8974
AverageFree Fourier shell correlation=     0.8914
Average correlation coefficient      =     0.8666
Overall figure of merit              =     0.7663
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    162360.06       8674.3633       1011207.8       1011183.6    

 fvalues    162360.06       8674.3633       1011200.2       1011189.9    
 fvalues    162360.06       8674.3633       1011200.2       1011189.9    


     CGMAT cycle number =      7

 Weight matrix   0.35093591    
 Actual weight    6.1746435      is applied to the X-ray term


 function value    1011198.5    

-------------------------------------------------------------------------------
             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 =     0.0460, B  =   -0.0001
Partial structure    1: scale =     0.3918, B  =   37.9467
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2111
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.8974
AverageFree Fourier shell correlation=     0.8914
Average correlation coefficient      =     0.8666
Overall figure of merit              =     0.7664
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    162361.28       8673.4111       1011217.8       1011189.9    

 fvalues    162361.28       8673.4111       1011214.3       1011196.5    
 fvalues    162361.28       8673.4111       1011214.3       1011196.5    


     CGMAT cycle number =      8

 Weight matrix   0.35088605    
 Actual weight    6.1746435      is applied to the X-ray term


 function value    1011200.4    

-------------------------------------------------------------------------------
             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 =     0.0460, B  =   -0.0000
Partial structure    1: scale =     0.3918, B  =   37.9438
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2111
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.8974
AverageFree Fourier shell correlation=     0.8914
Average correlation coefficient      =     0.8666
Overall figure of merit              =     0.7664
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    162362.48       8671.7090       1011206.6       1011196.5    

 fvalues    162362.48       8671.7090       1011207.8       1011202.1    
 fvalues    162362.48       8671.7090       1011207.8       1011202.1    


     CGMAT cycle number =      9

 Weight matrix   0.35092810    
 Actual weight    6.1746435      is applied to the X-ray term


 function value    1011211.4    

-------------------------------------------------------------------------------
             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 =     0.0460, B  =   -0.0003
Partial structure    1: scale =     0.3918, B  =   37.9270
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2111
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.8974
AverageFree Fourier shell correlation=     0.8914
Average correlation coefficient      =     0.8666
Overall figure of merit              =     0.7665
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    162364.34       8671.6895       1011217.3       1011202.1    

 fvalues    162364.34       8671.6895       1011217.0       1011213.6    
 fvalues    162364.34       8671.6895       1011217.0       1011213.6    


     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  280
 Maximuum H,K,L                 :    40   40   84
 Minimum acceptable grid spacing:    88   88  187
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    40   40   84
 Minimum acceptable grid spacing:    88   88  187
 Weight matrix   0.35092503    
 Actual weight    6.1746435      is applied to the X-ray term
Norm of X_ray positional gradient                43.2
Norm of Geom. positional gradient                43.2
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  106.
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     -0.360E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.1003E+07 GEOM=      8672.     TOTAL=     0.1011E+07
 function value    1011212.9    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.844     1.644
Bond angles  : others                          3238     1.513     1.580
Torsion angles, period  1. refined              185     6.743     5.000
Torsion angles, period  2. refined               90    34.652    22.778
Torsion angles, period  3. refined              268    13.302    15.000
Torsion angles, period  4. refined                9    12.406    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                   306     0.244     0.200
VDW repulsions.others                          1361     0.195     0.200
VDW; torsion: refined_atoms                     726     0.174     0.200
VDW; torsion.others                             747     0.086     0.200
HBOND: refined_atoms                            207     0.199     0.200
HBOND.others                                      1     0.026     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 24     0.184     0.200
HBOND: symmetry: refined_atoms                   21     0.173     0.200
M. chain bond B values: refined atoms           746     1.817     1.650
M. chain bond B values: others                  746     1.811     1.650
M. chain angle B values: refined atoms          929     2.801     2.465
M. chain angle B values: others                 930     2.800     2.465
S. chain bond B values: refined atoms           811     3.256     2.066
S. chain bond B values: others                  810     3.251     2.066
S. chain angle B values: refined atoms         1177     4.950     2.927
S. chain angle B values: others                1178     4.948     2.927
Long range B values: refined atoms             1844     7.853    22.602
Long range B values: others                    1757     7.594    21.179
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0460, B  =   -0.0000
Partial structure    1: scale =     0.3918, B  =   37.9265
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.058    4597 100.00   397.6   407.2  0.17  0.18     214   392.3   398.2  0.21  0.21
 0.174    7833  99.98   219.4   198.1  0.18  0.16     439   230.8   208.0  0.22  0.20
 0.289    9951 100.00   111.8   104.4  0.21  0.19     555   112.2   105.5  0.25  0.22
 0.405   11763 100.00    45.5    56.7  0.43  0.39     596    45.7    57.1  0.44  0.41
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0583   3446   0.914   1151   0.813   4597   0.889  0.948  0.9623  0.9706  0.9030  0.9357
  0.1739   6670   0.880   1163   0.781   7833   0.866  1.071  0.9488  0.9585  0.8928  0.9339
  0.2894   8803   0.840   1148   0.758   9951   0.830  1.002  0.9398  0.9485  0.8944  0.9269
  0.4050  10595   0.605   1183   0.547  11778   0.599  0.561  0.7787  0.7851  0.7188  0.7436
 $$
Resolution limits                    =     41.964     1.470
Number of used reflections           =      34159
Percentage observed                  =    99.9917
Percentage of free reflections       =     5.0163
Overall R factor                     =     0.2111
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.8974
AverageFree Fourier shell correlation=     0.8914
Overall weighted R factor            =     0.1784
Free weighted R factor               =     0.2121
Overall weighted R2 factor           =     0.2075
Free weighted R2 factor              =     0.2482
Average correlation coefficient      =     0.8666
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9401
Cruickshanks DPI for coordinate error=     0.0826
DPI based on free R factor           =     0.0854
Overall figure of merit              =     0.7665
ML based su of positional parameters =     0.0642
ML based su of thermal parameters    =     1.8349
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    162364.22       8671.6777       1011212.9       1011213.6    

    ****                              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_1-47A.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     1.844     1.644
Bond angles  : others                          3238     1.513     1.580
Torsion angles, period  1. refined              185     6.742     5.000
Torsion angles, period  2. refined               90    34.652    22.778
Torsion angles, period  3. refined              268    13.302    15.000
Torsion angles, period  4. refined                9    12.407    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                   306     0.244     0.200
VDW repulsions.others                          1361     0.195     0.200
VDW; torsion: refined_atoms                     726     0.174     0.200
VDW; torsion.others                             747     0.086     0.200
HBOND: refined_atoms                            207     0.199     0.200
HBOND.others                                      1     0.026     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 24     0.184     0.200
HBOND: symmetry: refined_atoms                   21     0.173     0.200
M. chain bond B values: refined atoms           746     1.817     1.650
M. chain bond B values: others                  746     1.811     1.650
M. chain angle B values: refined atoms          929     2.801     2.465
M. chain angle B values: others                 930     2.800     2.465
S. chain bond B values: refined atoms           811     3.256     2.066
S. chain bond B values: others                  810     3.251     2.066
S. chain angle B values: refined atoms         1177     4.950     2.927
S. chain angle B values: others                1178     4.948     2.927
Long range B values: refined atoms             1844     7.853    22.602
Long range B values: others                    1757     7.594    21.179
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0460, B  =   -0.0001
Partial structure    1: scale =     0.3918, B  =   37.9264
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.058    4597 100.00   397.6   407.2  0.17  0.18     214   392.3   398.2  0.21  0.21
 0.174    7833  99.98   219.4   198.1  0.18  0.16     439   230.8   208.0  0.22  0.20
 0.289    9951 100.00   111.8   104.4  0.21  0.19     555   112.2   105.5  0.25  0.22
 0.405   11763 100.00    45.5    56.7  0.43  0.39     596    45.7    57.1  0.44  0.41
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0583   3446   0.914   1151   0.813   4597   0.889  0.948  0.9623  0.9706  0.9030  0.9357
  0.1739   6670   0.880   1163   0.781   7833   0.866  1.071  0.9488  0.9585  0.8928  0.9339
  0.2894   8803   0.840   1148   0.758   9951   0.830  1.002  0.9398  0.9485  0.8944  0.9269
  0.4050  10595   0.605   1183   0.546  11778   0.599  0.561  0.7786  0.7850  0.7188  0.7436
 $$
Resolution limits                    =     41.964     1.470
Number of used reflections           =      34159
Percentage observed                  =    99.9917
Percentage of free reflections       =     5.0163
Overall R factor                     =     0.2111
Free R factor                        =     0.2464
Average Fourier shell correlation    =     0.8974
AverageFree Fourier shell correlation=     0.8914
Overall weighted R factor            =     0.1784
Free weighted R factor               =     0.2121
Overall weighted R2 factor           =     0.2074
Free weighted R2 factor              =     0.2482
Average correlation coefficient      =     0.8666
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9401
Cruickshanks DPI for coordinate error=     0.0826
DPI based on free R factor           =     0.0854
Overall figure of merit              =     0.7664
ML based su of positional parameters =     0.0642
ML based su of thermal parameters    =     1.8349
-----------------------------------------------------------------------------
  Time in seconds: CPU =        30.22
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2113   0.2473   0.733      163657.    8827.8   0.0131  0.986   1.851  1.077   0.090
       1   0.2118   0.2459   0.760      162566.    8792.8   0.0119  0.895   1.778  1.034   0.087
       2   0.2112   0.2462   0.765      162395.    8788.9   0.0129  0.973   1.819  1.058   0.089
       3   0.2111   0.2463   0.766      162365.    8788.6   0.0130  0.979   1.834  1.067   0.090
       4   0.2111   0.2464   0.766      162360.    8788.7   0.0130  0.982   1.840  1.070   0.090
       5   0.2111   0.2464   0.766      162361.    8789.0   0.0130  0.983   1.843  1.072   0.090
       6   0.2111   0.2464   0.766      162362.    8789.1   0.0130  0.983   1.843  1.072   0.090
       7   0.2111   0.2464   0.766      162362.    8789.1   0.0130  0.983   1.844  1.072   0.090
       8   0.2111   0.2464   0.766      162364.    8789.2   0.0130  0.983   1.844  1.072   0.090
       9   0.2111   0.2464   0.766      162364.    8789.2   0.0130  0.983   1.844  1.072   0.090
      10   0.2111   0.2464   0.766      162365.    8789.2   0.0130  0.983   1.844  1.073   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2113   0.2111
             R free    0.2473   0.2464
     Rms BondLength    0.0131   0.0130
      Rms BondAngle    1.8507   1.8436
     Rms ChirVolume    0.0904   0.0904
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      61.7s System:    0.3s Elapsed:     1:03