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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: 23:42:58 


 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 1.55     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_1-56A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-55A.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_1-55A.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       0.1041
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5500
  Estimated number of reflections :      39926
  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  1.5500

  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_1-56A.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=   2.191 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=   1.824 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=   2.215 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=   2.410 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=   2.390 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=   2.121 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       1548
Number of   all  reflections      30797
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          30797

   Current auto weighting coefficient =    6.3746147    

 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.= 0.889 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        :   128  128  280
 Maximuum H,K,L                 :    38   38   80
 Minimum acceptable grid spacing:    85   85  179
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  280
 Maximuum H,K,L                 :    38   38   80
 Minimum acceptable grid spacing:    85   85  179
 Weight matrix   0.28139669    
 Actual weight    6.3746147      is applied to the X-ray term
Norm of X_ray positional gradient                36.4
Norm of Geom. positional gradient                82.9
Norm of X_ray B-factor gradient                  102.
Norm of Geom. B-factor gradient                  111.
Product of X_ray and Geom posit. gradients     -0.145E+08
 Cosine of angle between them                      -0.497
Product of X_ray and Geom B-fact gradients     -0.313E+08
 Cosine of angle between them                      -0.862


Residuals: XRAY=     0.9246E+06 GEOM=     0.1351E+05 TOTAL=     0.9381E+06
 function value    938110.63    

-------------------------------------------------------------------------------
             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     1.873     1.644
Bond angles  : others                          3238     2.368     1.580
Torsion angles, period  1. refined              185     6.760     5.000
Torsion angles, period  2. refined               90    34.709    22.778
Torsion angles, period  3. refined              268    13.306    15.000
Torsion angles, period  4. refined                9    12.567    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                   304     0.246     0.200
VDW repulsions.others                          1339     0.220     0.200
VDW; torsion: refined_atoms                     731     0.174     0.200
VDW; torsion.others                             729     0.082     0.200
HBOND: refined_atoms                            212     0.199     0.200
HBOND.others                                      1     0.064     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 22     0.208     0.200
HBOND: symmetry: refined_atoms                   21     0.217     0.200
M. chain bond B values: refined atoms           746     1.776     1.550
M. chain bond B values: others                  746     1.770     1.550
M. chain angle B values: refined atoms          929     2.756     2.316
M. chain angle B values: others                 930     2.756     2.315
S. chain bond B values: refined atoms           811     3.211     1.958
S. chain bond B values: others                  810     3.207     1.958
S. chain angle B values: refined atoms         1177     4.871     2.768
S. chain angle B values: others                1178     4.869     2.768
Long range B values: refined atoms             1850     7.505    21.460
Long range B values: others                    1763     7.192    20.056
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0449, B  =    0.1158
Partial structure    1: scale =     0.3880, B  =   40.5184
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.053    3961 100.00   421.4   430.7  0.17  0.17     186   416.6   422.5  0.21  0.21
 0.156    6690  99.97   242.2   224.8  0.18  0.16     378   254.0   233.1  0.22  0.20
 0.260    8558 100.00   145.4   132.3  0.20  0.17     456   146.5   134.2  0.23  0.21
 0.364   10031 100.00    59.5    73.0  0.36  0.30     527    59.5    73.5  0.40  0.34
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0525   2918   0.907   1043   0.799   3961   0.879  0.948  0.9601  0.9686  0.9032  0.9365
  0.1564   5655   0.865   1035   0.770   6690   0.850  1.036  0.9442  0.9538  0.8847  0.9339
  0.2604   7509   0.849   1049   0.752   8558   0.837  1.042  0.9408  0.9519  0.8884  0.9357
  0.3643   8987   0.603   1051   0.527  10038   0.595  0.633  0.8104  0.8260  0.7681  0.8339
 $$
Resolution limits                    =     41.964     1.550
Number of used reflections           =      29247
Percentage observed                  =    99.9903
Percentage of free reflections       =     5.0268
Overall R factor                     =     0.1994
Free R factor                        =     0.2395
Average Fourier shell correlation    =     0.9114
AverageFree Fourier shell correlation=     0.8995
Overall weighted R factor            =     0.1718
Free weighted R factor               =     0.2097
Overall weighted R2 factor           =     0.2021
Free weighted R2 factor              =     0.2466
Average correlation coefficient      =     0.9005
Overall correlation coefficient      =     0.9588
Free correlation coefficient         =     0.9364
Cruickshanks DPI for coordinate error=     0.0911
DPI based on free R factor           =     0.0946
Overall figure of merit              =     0.7627
ML based su of positional parameters =     0.0730
ML based su of thermal parameters    =     2.1561
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    145043.88       13511.813       938110.63      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36181727    
 Actual weight    6.3746147      is applied to the X-ray term


 function value    925175.94    

-------------------------------------------------------------------------------
             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 =     0.0449, B  =   -0.0617
Partial structure    1: scale =     0.3876, B  =   40.5007
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1998
Free R factor                        =     0.2385
Average Fourier shell correlation    =     0.9273
AverageFree Fourier shell correlation=     0.9169
Average correlation coefficient      =     0.8990
Overall figure of merit              =     0.8035
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    143816.05       8404.0859       925175.94       938110.63    


     CGMAT cycle number =      3

 Weight matrix   0.37667444    
 Actual weight    6.3746147      is applied to the X-ray term


 function value    923816.50    

-------------------------------------------------------------------------------
             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 =     0.0448, B  =   -0.0106
Partial structure    1: scale =     0.3877, B  =   40.6133
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1993
Free R factor                        =     0.2385
Average Fourier shell correlation    =     0.9314
AverageFree Fourier shell correlation=     0.9207
Average correlation coefficient      =     0.9001
Overall figure of merit              =     0.8153
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    143546.94       8760.0664       923816.50       925175.94    


     CGMAT cycle number =      4

 Weight matrix   0.38178003    
 Actual weight    6.3746147      is applied to the X-ray term


 function value    923423.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0448, B  =   -0.0042
Partial structure    1: scale =     0.3877, B  =   40.6772
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1992
Free R factor                        =     0.2386
Average Fourier shell correlation    =     0.9328
AverageFree Fourier shell correlation=     0.9219
Average correlation coefficient      =     0.9006
Overall figure of merit              =     0.8196
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    143470.00       8857.4600       923423.44       923816.50    


     CGMAT cycle number =      5

 Weight matrix   0.38302043    
 Actual weight    6.3746147      is applied to the X-ray term


 function value    923297.06    

-------------------------------------------------------------------------------
             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 =     0.0448, B  =    0.0009
Partial structure    1: scale =     0.3877, B  =   40.7070
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1993
Free R factor                        =     0.2388
Average Fourier shell correlation    =     0.9332
AverageFree Fourier shell correlation=     0.9222
Average correlation coefficient      =     0.9009
Overall figure of merit              =     0.8209
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    143442.95       8903.4990       923297.06       923423.44    


     CGMAT cycle number =      6

 Weight matrix   0.38358733    
 Actual weight    6.3746147      is applied to the X-ray term


 function value    923262.94    

-------------------------------------------------------------------------------
             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 =     0.0448, B  =    0.0000
Partial structure    1: scale =     0.3877, B  =   40.7069
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1993
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9333
AverageFree Fourier shell correlation=     0.9222
Average correlation coefficient      =     0.9011
Overall figure of merit              =     0.8211
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    143434.30       8924.5469       923262.94       923297.06    


     CGMAT cycle number =      7

 Weight matrix   0.38276380    
 Actual weight    6.3746147      is applied to the X-ray term


 function value    923256.75    

-------------------------------------------------------------------------------
             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 =     0.0448, B  =    0.0122
Partial structure    1: scale =     0.3880, B  =   40.6366
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1993
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9332
AverageFree Fourier shell correlation=     0.9221
Average correlation coefficient      =     0.9011
Overall figure of merit              =     0.8209
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    143432.53       8929.6436       923256.75       923262.94    


     CGMAT cycle number =      8

 Weight matrix   0.38305938    
 Actual weight    6.3746147      is applied to the X-ray term


 function value    923275.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0448, B  =    0.0000
Partial structure    1: scale =     0.3880, B  =   40.6366
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1993
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9333
AverageFree Fourier shell correlation=     0.9222
Average correlation coefficient      =     0.9010
Overall figure of merit              =     0.8210
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    143435.94       8926.8281       923269.56       923256.75    
 fvalues    143435.94       8926.8281       923269.56       923275.63    


     CGMAT cycle number =      9

 Weight matrix   0.38245776    
 Actual weight    6.3746147      is applied to the X-ray term


 function value    923271.25    

-------------------------------------------------------------------------------
             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 =     0.0449, B  =    0.0092
Partial structure    1: scale =     0.3881, B  =   40.6391
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1993
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9332
AverageFree Fourier shell correlation=     0.9221
Average correlation coefficient      =     0.9011
Overall figure of merit              =     0.8209
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    143435.98       8922.1055       923271.25       923275.63    


     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.= 0.908 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        :   128  128  280
 Maximuum H,K,L                 :    38   38   80
 Minimum acceptable grid spacing:    85   85  179
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  280
 Maximuum H,K,L                 :    38   38   80
 Minimum acceptable grid spacing:    85   85  179
 Weight matrix   0.38234457    
 Actual weight    6.3746147      is applied to the X-ray term
Norm of X_ray positional gradient                43.7
Norm of Geom. positional gradient                43.7
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  114.
Product of X_ray and Geom posit. gradients     -0.185E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.422E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.9143E+06 GEOM=      8921.     TOTAL=     0.9233E+06
 function value    923253.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.864     1.644
Bond angles  : others                          3238     1.519     1.580
Torsion angles, period  1. refined              185     6.750     5.000
Torsion angles, period  2. refined               90    34.697    22.778
Torsion angles, period  3. refined              268    13.293    15.000
Torsion angles, period  4. refined                9    12.500    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   306     0.245     0.200
VDW repulsions.others                          1372     0.193     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             801     0.084     0.200
HBOND: refined_atoms                            213     0.199     0.200
HBOND.others                                      1     0.020     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 24     0.184     0.200
HBOND: symmetry: refined_atoms                   22     0.178     0.200
M. chain bond B values: refined atoms           746     1.778     1.562
M. chain bond B values: others                  746     1.774     1.562
M. chain angle B values: refined atoms          929     2.758     2.333
M. chain angle B values: others                 930     2.757     2.333
S. chain bond B values: refined atoms           811     3.213     1.970
S. chain bond B values: others                  810     3.208     1.970
S. chain angle B values: refined atoms         1177     4.875     2.787
S. chain angle B values: others                1178     4.873     2.786
Long range B values: refined atoms             1851     7.735    21.614
Long range B values: others                    1763     7.440    20.205
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0449, B  =    0.0092
Partial structure    1: scale =     0.3881, B  =   40.6256
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.053    3961 100.00   421.8   431.1  0.17  0.17     186   416.9   423.4  0.21  0.21
 0.156    6690  99.97   242.4   225.0  0.18  0.16     378   254.2   233.3  0.22  0.20
 0.260    8558 100.00   145.5   132.5  0.20  0.17     456   146.7   134.2  0.23  0.21
 0.364   10031 100.00    59.6    73.0  0.36  0.30     527    59.5    73.6  0.40  0.34
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0525   2918   0.922   1043   0.822   3961   0.896  0.950  0.9640  0.9721  0.9036  0.9366
  0.1564   5655   0.873   1035   0.778   6690   0.858  1.036  0.9464  0.9558  0.8868  0.9342
  0.2604   7509   0.863   1049   0.767   8558   0.851  1.042  0.9456  0.9563  0.8892  0.9353
  0.3643   8987   0.749   1051   0.671  10038   0.741  0.703  0.8698  0.8832  0.7692  0.8358
 $$
Resolution limits                    =     41.964     1.550
Number of used reflections           =      29247
Percentage observed                  =    99.9903
Percentage of free reflections       =     5.0268
Overall R factor                     =     0.1993
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9332
AverageFree Fourier shell correlation=     0.9221
Overall weighted R factor            =     0.1716
Free weighted R factor               =     0.2089
Overall weighted R2 factor           =     0.2019
Free weighted R2 factor              =     0.2455
Average correlation coefficient      =     0.9011
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9369
Cruickshanks DPI for coordinate error=     0.0910
DPI based on free R factor           =     0.0943
Overall figure of merit              =     0.8209
ML based su of positional parameters =     0.0625
ML based su of thermal parameters    =     1.8000
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    143433.39       8920.8232       923253.44       923271.25    

    ****                              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.= 0.908 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_1-55A.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     1.865     1.644
Bond angles  : others                          3238     1.519     1.580
Torsion angles, period  1. refined              185     6.748     5.000
Torsion angles, period  2. refined               90    34.693    22.778
Torsion angles, period  3. refined              268    13.294    15.000
Torsion angles, period  4. refined                9    12.499    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   306     0.245     0.200
VDW repulsions.others                          1370     0.193     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             806     0.084     0.200
HBOND: refined_atoms                            212     0.200     0.200
HBOND.others                                      1     0.022     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 26     0.177     0.200
HBOND: symmetry: refined_atoms                   22     0.177     0.200
M. chain bond B values: refined atoms           746     1.778     1.562
M. chain bond B values: others                  746     1.774     1.562
M. chain angle B values: refined atoms          929     2.758     2.333
M. chain angle B values: others                 930     2.756     2.333
S. chain bond B values: refined atoms           811     3.214     1.971
S. chain bond B values: others                  810     3.209     1.970
S. chain angle B values: refined atoms         1177     4.877     2.787
S. chain angle B values: others                1178     4.874     2.787
Long range B values: refined atoms             1850     7.730    21.596
Long range B values: others                    1762     7.435    20.185
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0449, B  =    0.0022
Partial structure    1: scale =     0.3881, B  =   40.6249
Overall anisotropic scale factors
   B11 =  -0.19 B22 =  -0.19 B33 =   0.39 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.053    3961 100.00   421.8   431.1  0.17  0.17     186   416.9   423.4  0.21  0.21
 0.156    6690  99.97   242.4   225.0  0.18  0.16     378   254.2   233.3  0.22  0.20
 0.260    8558 100.00   145.5   132.5  0.20  0.17     456   146.7   134.2  0.23  0.21
 0.364   10031 100.00    59.6    73.0  0.36  0.30     527    59.5    73.6  0.40  0.34
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0525   2918   0.922   1043   0.822   3961   0.896  0.950  0.9640  0.9721  0.9035  0.9366
  0.1564   5655   0.873   1035   0.778   6690   0.858  1.036  0.9464  0.9558  0.8868  0.9342
  0.2604   7509   0.863   1049   0.767   8558   0.851  1.042  0.9456  0.9563  0.8891  0.9353
  0.3643   8987   0.749   1051   0.671  10038   0.741  0.703  0.8698  0.8833  0.7691  0.8358
 $$
Resolution limits                    =     41.964     1.550
Number of used reflections           =      29247
Percentage observed                  =    99.9903
Percentage of free reflections       =     5.0268
Overall R factor                     =     0.1993
Free R factor                        =     0.2387
Average Fourier shell correlation    =     0.9332
AverageFree Fourier shell correlation=     0.9221
Overall weighted R factor            =     0.1716
Free weighted R factor               =     0.2088
Overall weighted R2 factor           =     0.2018
Free weighted R2 factor              =     0.2455
Average correlation coefficient      =     0.9011
Overall correlation coefficient      =     0.9589
Free correlation coefficient         =     0.9369
Cruickshanks DPI for coordinate error=     0.0910
DPI based on free R factor           =     0.0943
Overall figure of merit              =     0.8210
ML based su of positional parameters =     0.0625
ML based su of thermal parameters    =     1.8000
-----------------------------------------------------------------------------
  Time in seconds: CPU =        19.05
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1994   0.2395   0.763      145044.    7856.9   0.0133  0.999   1.873  1.089   0.090
       1   0.1998   0.2385   0.804      143816.    7814.0   0.0120  0.902   1.795  1.042   0.087
       2   0.1993   0.2385   0.815      143547.    7804.4   0.0130  0.975   1.831  1.065   0.089
       3   0.1992   0.2386   0.820      143470.    7801.9   0.0131  0.986   1.846  1.074   0.090
       4   0.1993   0.2388   0.821      143443.    7801.1   0.0132  0.991   1.854  1.079   0.090
       5   0.1993   0.2387   0.821      143434.    7801.0   0.0132  0.993   1.859  1.081   0.091
       6   0.1993   0.2387   0.821      143433.    7801.0   0.0132  0.994   1.861  1.083   0.091
       7   0.1993   0.2387   0.821      143436.    7801.5   0.0132  0.993   1.863  1.084   0.091
       8   0.1993   0.2387   0.821      143436.    7801.3   0.0132  0.994   1.864  1.084   0.091
       9   0.1993   0.2387   0.821      143433.    7801.2   0.0132  0.993   1.864  1.084   0.091
      10   0.1993   0.2387   0.821      143431.    7801.3   0.0132  0.993   1.865  1.084   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1994   0.1993
             R free    0.2395   0.2387
     Rms BondLength    0.0133   0.0132
      Rms BondAngle    1.8728   1.8647
     Rms ChirVolume    0.0903   0.0909
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      51.0s System:    0.2s Elapsed:     0:52