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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 17:43:39 


 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 1.71     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_1-72A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-71A.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_1-71A.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       0.0855
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7100
  Estimated number of reflections :      29131
  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  1.7100

  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_1-72A.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=   2.044 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=   2.198 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=   1.835 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=   2.222 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=   2.419 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=   2.402 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       1188
Number of   all  reflections      23094
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23094

   Current auto weighting coefficient =    6.7746849    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.896 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   72
 Minimum acceptable grid spacing:    79   79  166
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   72
 Minimum acceptable grid spacing:    79   79  166
 Weight matrix   0.29006734    
 Actual weight    6.7746849      is applied to the X-ray term
Norm of X_ray positional gradient                36.2
Norm of Geom. positional gradient                80.7
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  119.
Product of X_ray and Geom posit. gradients     -0.133E+08
 Cosine of angle between them                      -0.470
Product of X_ray and Geom B-fact gradients     -0.399E+08
 Cosine of angle between them                      -0.931


Residuals: XRAY=     0.7732E+06 GEOM=     0.1350E+05 TOTAL=     0.7867E+06
 function value    786698.94    

-------------------------------------------------------------------------------
             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     1.817     1.644
Bond angles  : others                          3238     2.357     1.580
Torsion angles, period  1. refined              185     6.818     5.000
Torsion angles, period  2. refined               90    35.275    22.778
Torsion angles, period  3. refined              268    13.383    15.000
Torsion angles, period  4. refined                9    12.208    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   294     0.247     0.200
VDW repulsions.others                          1334     0.219     0.200
VDW; torsion: refined_atoms                     718     0.174     0.200
VDW; torsion.others                             726     0.080     0.200
HBOND: refined_atoms                            215     0.198     0.200
HBOND.others                                      1     0.081     0.200
VDW repulsions: symmetry: refined_atoms           8     0.210     0.200
VDW repulsions: symmetry: others                 23     0.194     0.200
HBOND: symmetry: refined_atoms                   23     0.178     0.200
M. chain bond B values: refined atoms           746     1.676     1.372
M. chain bond B values: others                  746     1.674     1.372
M. chain angle B values: refined atoms          929     2.636     2.046
M. chain angle B values: others                 930     2.634     2.046
S. chain bond B values: refined atoms           811     2.999     1.767
S. chain bond B values: others                  810     2.992     1.767
S. chain angle B values: refined atoms         1177     4.631     2.484
S. chain angle B values: others                1178     4.629     2.483
Long range B values: refined atoms             1836     7.073    19.025
Long range B values: others                    1747     6.781    17.626
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =    0.0575
Partial structure    1: scale =     0.3861, B  =   44.0107
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.043    2986 100.00   456.3   465.2  0.16  0.17     135   453.7   464.2  0.20  0.21
 0.129    5029 100.00   302.1   288.9  0.17  0.15     285   305.4   284.7  0.22  0.19
 0.214    6421  99.97   204.8   189.1  0.17  0.14     347   212.3   198.2  0.20  0.17
 0.299    7466 100.00   108.3   119.6  0.24  0.18     421   105.4   117.6  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0432   2140   0.912    846   0.817   2986   0.885  0.951  0.9615  0.9703  0.9003  0.9402
  0.1286   4170   0.873    859   0.762   5029   0.854  0.998  0.9468  0.9589  0.8981  0.9420
  0.2140   5552   0.885    869   0.781   6421   0.871  1.043  0.9555  0.9622  0.9100  0.9414
  0.2993   6625   0.769    843   0.698   7468   0.761  0.832  0.9110  0.9246  0.8591  0.9078
 $$
Resolution limits                    =     41.964     1.710
Number of used reflections           =      21904
Percentage observed                  =    99.9870
Percentage of free reflections       =     5.1446
Overall R factor                     =     0.1765
Free R factor                        =     0.2232
Average Fourier shell correlation    =     0.9497
AverageFree Fourier shell correlation=     0.9383
Overall weighted R factor            =     0.1581
Free weighted R factor               =     0.1974
Overall weighted R2 factor           =     0.1900
Free weighted R2 factor              =     0.2331
Average correlation coefficient      =     0.9299
Overall correlation coefficient      =     0.9578
Free correlation coefficient         =     0.9315
Cruickshanks DPI for coordinate error=     0.1091
DPI based on free R factor           =     0.1125
Overall figure of merit              =     0.8316
ML based su of positional parameters =     0.0741
ML based su of thermal parameters    =     2.3024
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    114130.13       13503.285       786698.94      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.33561388    
 Actual weight    6.7746849      is applied to the X-ray term


 function value    777706.00    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0716
Partial structure    1: scale =     0.3858, B  =   44.2524
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1767
Free R factor                        =     0.2226
Average Fourier shell correlation    =     0.9545
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9295
Overall figure of merit              =     0.8521
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    113510.13       8710.6191       777706.00       786698.94    


     CGMAT cycle number =      3

 Weight matrix   0.33927074    
 Actual weight    6.7746849      is applied to the X-ray term


 function value    777249.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0473
Partial structure    1: scale =     0.3858, B  =   44.0474
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1763
Free R factor                        =     0.2223
Average Fourier shell correlation    =     0.9550
AverageFree Fourier shell correlation=     0.9443
Average correlation coefficient      =     0.9301
Overall figure of merit              =     0.8535
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    113407.78       8947.9219       777249.94       777706.00    


     CGMAT cycle number =      4

 Weight matrix   0.33976704    
 Actual weight    6.7746849      is applied to the X-ray term


 function value    777140.06    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0304
Partial structure    1: scale =     0.3859, B  =   44.0056
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1763
Free R factor                        =     0.2224
Average Fourier shell correlation    =     0.9550
AverageFree Fourier shell correlation=     0.9443
Average correlation coefficient      =     0.9303
Overall figure of merit              =     0.8536
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    113380.54       9022.6514       777140.06       777249.94    


     CGMAT cycle number =      5

 Weight matrix   0.33986694    
 Actual weight    6.7746849      is applied to the X-ray term


 function value    777100.06    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0325
Partial structure    1: scale =     0.3860, B  =   43.9629
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1763
Free R factor                        =     0.2223
Average Fourier shell correlation    =     0.9551
AverageFree Fourier shell correlation=     0.9444
Average correlation coefficient      =     0.9303
Overall figure of merit              =     0.8537
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    113371.69       9042.6201       777100.06       777140.06    


     CGMAT cycle number =      6

 Weight matrix   0.33964115    
 Actual weight    6.7746849      is applied to the X-ray term


 function value    777095.69    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0305
Partial structure    1: scale =     0.3860, B  =   43.9819
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1763
Free R factor                        =     0.2223
Average Fourier shell correlation    =     0.9551
AverageFree Fourier shell correlation=     0.9444
Average correlation coefficient      =     0.9304
Overall figure of merit              =     0.8537
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    113369.95       9049.9834       777095.69       777100.06    


     CGMAT cycle number =      7

 Weight matrix   0.33942538    
 Actual weight    6.7746849      is applied to the X-ray term


 function value    777096.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0295
Partial structure    1: scale =     0.3859, B  =   43.9117
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1763
Free R factor                        =     0.2222
Average Fourier shell correlation    =     0.9551
AverageFree Fourier shell correlation=     0.9444
Average correlation coefficient      =     0.9304
Overall figure of merit              =     0.8537
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    113370.28       9047.9180       777110.81       777095.69    

 fvalues    113370.28       9047.9180       777080.50       777095.88    
 fvalues    113370.28       9047.9180       777080.50       777095.88    


     CGMAT cycle number =      8

 Weight matrix   0.33879429    
 Actual weight    6.7746849      is applied to the X-ray term


 function value    777111.50    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0212
Partial structure    1: scale =     0.3860, B  =   43.8630
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1764
Free R factor                        =     0.2221
Average Fourier shell correlation    =     0.9550
AverageFree Fourier shell correlation=     0.9443
Average correlation coefficient      =     0.9303
Overall figure of merit              =     0.8536
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02

 fvalues    113370.54       9043.2217       777092.94       777095.88    


     CGMAT cycle number =      9

 Weight matrix   0.33907276    
 Actual weight    6.7746849      is applied to the X-ray term


 function value    777107.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0266
Partial structure    1: scale =     0.3861, B  =   43.8109
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1764
Free R factor                        =     0.2221
Average Fourier shell correlation    =     0.9550
AverageFree Fourier shell correlation=     0.9443
Average correlation coefficient      =     0.9303
Overall figure of merit              =     0.8536
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    113372.98       9040.2871       777081.88       777092.94    
 fvalues    113372.98       9040.2871       777081.88       777106.56    


     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.= 0.906 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   72
 Minimum acceptable grid spacing:    79   79  166
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   72
 Minimum acceptable grid spacing:    79   79  166
 Weight matrix   0.33929777    
 Actual weight    6.7746849      is applied to the X-ray term
Norm of X_ray positional gradient                40.6
Norm of Geom. positional gradient                40.6
Norm of X_ray B-factor gradient                  124.
Norm of Geom. B-factor gradient                  125.
Product of X_ray and Geom posit. gradients     -0.160E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.499E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.7680E+06 GEOM=      9040.     TOTAL=     0.7771E+06
 function value    777075.56    

-------------------------------------------------------------------------------
             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     1.817     1.644
Bond angles  : others                          3238     1.504     1.580
Torsion angles, period  1. refined              185     6.844     5.000
Torsion angles, period  2. refined               90    35.286    22.778
Torsion angles, period  3. refined              268    13.401    15.000
Torsion angles, period  4. refined                9    12.088    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   292     0.248     0.200
VDW repulsions.others                          1363     0.192     0.200
VDW; torsion: refined_atoms                     719     0.174     0.200
VDW; torsion.others                             777     0.084     0.200
HBOND: refined_atoms                            212     0.200     0.200
HBOND.others                                      1     0.036     0.200
VDW repulsions: symmetry: refined_atoms           8     0.209     0.200
VDW repulsions: symmetry: others                 24     0.175     0.200
HBOND: symmetry: refined_atoms                   24     0.173     0.200
M. chain bond B values: refined atoms           746     1.682     1.383
M. chain bond B values: others                  746     1.679     1.383
M. chain angle B values: refined atoms          929     2.643     2.062
M. chain angle B values: others                 930     2.642     2.062
S. chain bond B values: refined atoms           811     3.031     1.781
S. chain bond B values: others                  810     3.024     1.781
S. chain angle B values: refined atoms         1177     4.668     2.504
S. chain angle B values: others                1178     4.666     2.504
Long range B values: refined atoms             1829     7.079    19.093
Long range B values: others                    1739     6.765    17.668
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0295
Partial structure    1: scale =     0.3862, B  =   43.8194
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.043    2986 100.00   456.4   465.6  0.16  0.17     135   453.7   465.0  0.20  0.21
 0.129    5029 100.00   302.1   288.8  0.16  0.15     285   305.4   284.5  0.21  0.19
 0.214    6421  99.97   204.9   189.2  0.17  0.14     347   212.3   197.9  0.20  0.17
 0.299    7466 100.00   108.3   119.5  0.24  0.18     421   105.5   117.6  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0432   2140   0.926    846   0.835   2986   0.900  0.953  0.9649  0.9731  0.9009  0.9401
  0.1286   4170   0.875    859   0.763   5029   0.856  0.998  0.9477  0.9597  0.8992  0.9423
  0.2140   5552   0.889    869   0.786   6421   0.875  1.043  0.9567  0.9636  0.9103  0.9421
  0.2993   6625   0.823    843   0.748   7468   0.815  0.848  0.9254  0.9374  0.8615  0.9082
 $$
Resolution limits                    =     41.964     1.710
Number of used reflections           =      21904
Percentage observed                  =    99.9870
Percentage of free reflections       =     5.1446
Overall R factor                     =     0.1764
Free R factor                        =     0.2221
Average Fourier shell correlation    =     0.9551
AverageFree Fourier shell correlation=     0.9444
Overall weighted R factor            =     0.1581
Free weighted R factor               =     0.1968
Overall weighted R2 factor           =     0.1901
Free weighted R2 factor              =     0.2326
Average correlation coefficient      =     0.9303
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9319
Cruickshanks DPI for coordinate error=     0.1090
DPI based on free R factor           =     0.1119
Overall figure of merit              =     0.8537
ML based su of positional parameters =     0.0684
ML based su of thermal parameters    =     2.0892
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    113368.39       9040.4111       777075.56       777106.56    

    ****                              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.= 0.906 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_1-71A.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     1.818     1.644
Bond angles  : others                          3238     1.504     1.580
Torsion angles, period  1. refined              185     6.843     5.000
Torsion angles, period  2. refined               90    35.284    22.778
Torsion angles, period  3. refined              268    13.409    15.000
Torsion angles, period  4. refined                9    12.096    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   292     0.248     0.200
VDW repulsions.others                          1362     0.192     0.200
VDW; torsion: refined_atoms                     719     0.174     0.200
VDW; torsion.others                             778     0.084     0.200
HBOND: refined_atoms                            212     0.200     0.200
HBOND.others                                      1     0.037     0.200
VDW repulsions: symmetry: refined_atoms           8     0.209     0.200
VDW repulsions: symmetry: others                 26     0.169     0.200
HBOND: symmetry: refined_atoms                   24     0.173     0.200
M. chain bond B values: refined atoms           746     1.682     1.383
M. chain bond B values: others                  746     1.679     1.383
M. chain angle B values: refined atoms          929     2.644     2.062
M. chain angle B values: others                 930     2.642     2.062
S. chain bond B values: refined atoms           811     3.032     1.782
S. chain bond B values: others                  810     3.025     1.781
S. chain angle B values: refined atoms         1177     4.670     2.505
S. chain angle B values: others                1178     4.668     2.504
Long range B values: refined atoms             1829     7.082    19.095
Long range B values: others                    1739     6.767    17.671
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0300
Partial structure    1: scale =     0.3862, B  =   43.8328
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.043    2986 100.00   456.4   465.6  0.16  0.17     135   453.7   464.9  0.20  0.21
 0.129    5029 100.00   302.1   288.8  0.16  0.15     285   305.4   284.5  0.21  0.19
 0.214    6421  99.97   204.9   189.2  0.17  0.14     347   212.3   197.9  0.20  0.17
 0.299    7466 100.00   108.3   119.5  0.24  0.18     421   105.5   117.6  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0432   2140   0.926    846   0.835   2986   0.900  0.953  0.9649  0.9730  0.9008  0.9401
  0.1286   4170   0.875    859   0.763   5029   0.856  0.998  0.9476  0.9596  0.8991  0.9423
  0.2140   5552   0.889    869   0.786   6421   0.875  1.043  0.9567  0.9636  0.9104  0.9421
  0.2993   6625   0.823    843   0.748   7468   0.815  0.848  0.9254  0.9374  0.8616  0.9082
 $$
Resolution limits                    =     41.964     1.710
Number of used reflections           =      21904
Percentage observed                  =    99.9870
Percentage of free reflections       =     5.1446
Overall R factor                     =     0.1764
Free R factor                        =     0.2221
Average Fourier shell correlation    =     0.9550
AverageFree Fourier shell correlation=     0.9444
Overall weighted R factor            =     0.1582
Free weighted R factor               =     0.1969
Overall weighted R2 factor           =     0.1901
Free weighted R2 factor              =     0.2327
Average correlation coefficient      =     0.9303
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9319
Cruickshanks DPI for coordinate error=     0.1090
DPI based on free R factor           =     0.1119
Overall figure of merit              =     0.8537
ML based su of positional parameters =     0.0684
ML based su of thermal parameters    =     2.0892
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.47
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1765   0.2232   0.832      114130.    6354.5   0.0128  0.955   1.817  1.054   0.089
       1   0.1767   0.2226   0.852      113510.    6336.6   0.0120  0.900   1.775  1.029   0.087
       2   0.1763   0.2223   0.853      113408.    6333.8   0.0127  0.949   1.801  1.045   0.089
       3   0.1763   0.2224   0.854      113381.    6333.0   0.0128  0.955   1.810  1.051   0.090
       4   0.1763   0.2223   0.854      113372.    6332.6   0.0128  0.957   1.814  1.053   0.090
       5   0.1763   0.2223   0.854      113370.    6332.6   0.0128  0.957   1.815  1.054   0.090
       6   0.1763   0.2222   0.854      113370.    6332.8   0.0128  0.957   1.816  1.054   0.090
       7   0.1764   0.2221   0.854      113373.    6332.8   0.0128  0.957   1.817  1.055   0.090
       8   0.1764   0.2221   0.854      113373.    6332.7   0.0128  0.957   1.817  1.055   0.090
       9   0.1764   0.2221   0.854      113368.    6332.5   0.0128  0.957   1.817  1.055   0.090
      10   0.1764   0.2221   0.854      113369.    6332.6   0.0128  0.958   1.818  1.055   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1765   0.1764
             R free    0.2232   0.2221
     Rms BondLength    0.0128   0.0128
      Rms BondAngle    1.8171   1.8175
     Rms ChirVolume    0.0889   0.0899
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      49.6s System:    0.1s Elapsed:     0:50