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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: 14:38:04 


 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 1.84     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_1-85A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-84A.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_1-84A.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       0.0738
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8400
  Estimated number of reflections :      24012
  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  1.8400

  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_1-85A.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=   2.041 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=   2.223 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=   1.861 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=   2.223 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=   2.392 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=   2.427 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=   2.133 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        936
Number of   all  reflections      18657
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          18657

   Current auto weighting coefficient =    7.0996003    

 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.= 0.924 id.= 3.000 dev= -2.08 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        :   112  112  240
 Maximuum H,K,L                 :    32   32   67
 Minimum acceptable grid spacing:    74   74  157
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   67
 Minimum acceptable grid spacing:    74   74  157
 Weight matrix   0.24145429    
 Actual weight    7.0996003      is applied to the X-ray term
Norm of X_ray positional gradient                32.7
Norm of Geom. positional gradient                78.4
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  110.
Product of X_ray and Geom posit. gradients     -0.100E+08
 Cosine of angle between them                      -0.405
Product of X_ray and Geom B-fact gradients     -0.373E+08
 Cosine of angle between them                      -0.944


Residuals: XRAY=     0.6776E+06 GEOM=     0.1289E+05 TOTAL=     0.6904E+06
 function value    690445.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.750     1.644
Bond angles  : others                          3238     2.350     1.580
Torsion angles, period  1. refined              185     6.983     5.000
Torsion angles, period  2. refined               90    35.868    22.778
Torsion angles, period  3. refined              268    13.394    15.000
Torsion angles, period  4. refined                9    11.238    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   301     0.241     0.200
VDW repulsions.others                          1332     0.219     0.200
VDW; torsion: refined_atoms                     719     0.171     0.200
VDW; torsion.others                             720     0.079     0.200
HBOND: refined_atoms                            227     0.205     0.200
VDW repulsions: symmetry: refined_atoms           9     0.212     0.200
VDW repulsions: symmetry: others                 22     0.215     0.200
HBOND: symmetry: refined_atoms                   20     0.205     0.200
M. chain bond B values: refined atoms           746     1.570     1.256
M. chain bond B values: others                  746     1.569     1.256
M. chain angle B values: refined atoms          929     2.508     1.870
M. chain angle B values: others                 930     2.507     1.870
S. chain bond B values: refined atoms           811     2.609     1.606
S. chain bond B values: others                  810     2.607     1.606
S. chain angle B values: refined atoms         1177     4.098     2.258
S. chain angle B values: others                1178     4.096     2.257
Long range B values: refined atoms             1853     6.739    17.448
Long range B values: others                    1759     6.436    16.122
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0161
Partial structure    1: scale =     0.3766, B  =   46.7658
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.037    2427 100.00   474.9   481.4  0.16  0.17     110   469.2   478.6  0.21  0.22
 0.111    4082 100.00   359.7   344.3  0.16  0.15     216   360.8   335.2  0.22  0.20
 0.185    5148  99.96   235.4   226.9  0.16  0.13     292   249.3   236.2  0.21  0.18
 0.259    6059 100.00   163.8   167.6  0.18  0.14     317   167.0   171.7  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0374   1692   0.912    735   0.803   2427   0.879  0.956  0.9607  0.9690  0.9071  0.9406
  0.1111   3339   0.877    743   0.774   4082   0.858  0.993  0.9472  0.9616  0.8906  0.9451
  0.1848   4411   0.873    737   0.768   5148   0.858  0.998  0.9491  0.9591  0.8938  0.9398
  0.2585   5314   0.840    748   0.737   6062   0.827  0.923  0.9364  0.9496  0.8698  0.9298
 $$
Resolution limits                    =     41.964     1.840
Number of used reflections           =      17719
Percentage observed                  =    99.9839
Percentage of free reflections       =     5.0174
Overall R factor                     =     0.1644
Free R factor                        =     0.2166
Average Fourier shell correlation    =     0.9578
AverageFree Fourier shell correlation=     0.9457
Overall weighted R factor            =     0.1516
Free weighted R factor               =     0.1994
Overall weighted R2 factor           =     0.1843
Free weighted R2 factor              =     0.2393
Average correlation coefficient      =     0.9377
Overall correlation coefficient      =     0.9560
Free correlation coefficient         =     0.9188
Cruickshanks DPI for coordinate error=     0.1295
DPI based on free R factor           =     0.1305
Overall figure of merit              =     0.8505
ML based su of positional parameters =     0.0831
ML based su of thermal parameters    =     2.7056
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    95435.570       12891.287       690445.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25789410    
 Actual weight    7.0996003      is applied to the X-ray term


 function value    683916.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0938
Partial structure    1: scale =     0.3770, B  =   47.0932
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1644
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9596
AverageFree Fourier shell correlation=     0.9476
Average correlation coefficient      =     0.9381
Overall figure of merit              =     0.8582
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    95156.242       8345.1777       683916.50       690445.69    


     CGMAT cycle number =      3

 Weight matrix   0.25856400    
 Actual weight    7.0996003      is applied to the X-ray term


 function value    683788.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0954
Partial structure    1: scale =     0.3771, B  =   46.9006
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1640
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9384
Overall figure of merit              =     0.8585
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    95121.914       8460.5088       683788.06       683916.50    


     CGMAT cycle number =      4

 Weight matrix   0.25877258    
 Actual weight    7.0996003      is applied to the X-ray term


 function value    683752.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0849
Partial structure    1: scale =     0.3772, B  =   46.7975
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1640
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    95111.953       8495.2813       683752.13       683788.06    


     CGMAT cycle number =      5

 Weight matrix   0.25890094    
 Actual weight    7.0996003      is applied to the X-ray term


 function value    683716.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0856
Partial structure    1: scale =     0.3772, B  =   46.7502
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1640
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8587
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    95105.852       8503.0342       683716.63       683752.13    


     CGMAT cycle number =      6

 Weight matrix   0.25882068    
 Actual weight    7.0996003      is applied to the X-ray term


 function value    683727.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0866
Partial structure    1: scale =     0.3771, B  =   46.7931
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1640
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9478
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    95108.875       8505.4355       683717.13       683716.63    
 fvalues    95108.875       8505.4355       683717.13       683740.44    


     CGMAT cycle number =      7

 Weight matrix   0.25860453    
 Actual weight    7.0996003      is applied to the X-ray term


 function value    683754.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0876
Partial structure    1: scale =     0.3771, B  =   46.8954
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1640
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    95111.703       8500.0586       683763.44       683740.44    

 fvalues    95111.703       8500.0586       683768.88       683755.13    
 fvalues    95111.703       8500.0586       683768.88       683755.13    


     CGMAT cycle number =      8

 Weight matrix   0.25846896    
 Actual weight    7.0996003      is applied to the X-ray term


 function value    683762.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0861
Partial structure    1: scale =     0.3771, B  =   46.8585
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1640
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8585
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    95113.453       8496.4014       683755.25       683755.13    
 fvalues    95113.453       8496.4014       683755.25       683763.88    


     CGMAT cycle number =      9

 Weight matrix   0.25872761    
 Actual weight    7.0996003      is applied to the X-ray term


 function value    683733.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0853
Partial structure    1: scale =     0.3771, B  =   46.8946
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1640
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    95109.172       8496.4063       683733.50       683763.88    


     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.= 0.930 id.= 3.000 dev= -2.07 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        :   112  112  240
 Maximuum H,K,L                 :    32   32   67
 Minimum acceptable grid spacing:    74   74  157
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    32   32   67
 Minimum acceptable grid spacing:    74   74  157
 Weight matrix   0.25846520    
 Actual weight    7.0996003      is applied to the X-ray term
Norm of X_ray positional gradient                34.1
Norm of Geom. positional gradient                34.1
Norm of X_ray B-factor gradient                  113.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.113E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.425E+08
 Cosine of angle between them                      -0.990


Residuals: XRAY=     0.6753E+06 GEOM=      8496.     TOTAL=     0.6838E+06
 function value    683767.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.764     1.644
Bond angles  : others                          3238     1.453     1.580
Torsion angles, period  1. refined              185     6.963     5.000
Torsion angles, period  2. refined               90    35.859    22.778
Torsion angles, period  3. refined              268    13.374    15.000
Torsion angles, period  4. refined                9    11.519    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   300     0.242     0.200
VDW repulsions.others                          1367     0.192     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             765     0.084     0.200
HBOND: refined_atoms                            229     0.204     0.200
VDW repulsions: symmetry: refined_atoms           8     0.225     0.200
VDW repulsions: symmetry: others                 22     0.197     0.200
HBOND: symmetry: refined_atoms                   20     0.204     0.200
M. chain bond B values: refined atoms           746     1.580     1.261
M. chain bond B values: others                  746     1.579     1.261
M. chain angle B values: refined atoms          929     2.509     1.877
M. chain angle B values: others                 930     2.508     1.877
S. chain bond B values: refined atoms           811     2.646     1.613
S. chain bond B values: others                  810     2.643     1.613
S. chain angle B values: refined atoms         1177     4.146     2.268
S. chain angle B values: others                1178     4.145     2.267
Long range B values: refined atoms             1858     6.746    17.543
Long range B values: others                    1763     6.428    16.146
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0829
Partial structure    1: scale =     0.3770, B  =   46.8695
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.037    2427 100.00   475.7   482.1  0.16  0.17     110   470.0   479.6  0.21  0.22
 0.111    4082 100.00   360.3   344.4  0.16  0.15     216   361.4   335.1  0.22  0.20
 0.185    5148  99.96   235.8   227.0  0.16  0.13     292   249.7   236.6  0.21  0.18
 0.259    6059 100.00   164.0   167.8  0.18  0.14     317   167.3   172.3  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0374   1692   0.924    735   0.817   2427   0.891  0.956  0.9637  0.9715  0.9082  0.9407
  0.1111   3339   0.879    743   0.777   4082   0.861  0.993  0.9484  0.9624  0.8920  0.9449
  0.1848   4411   0.875    737   0.770   5148   0.860  0.998  0.9501  0.9596  0.8963  0.9403
  0.2585   5314   0.855    748   0.754   6062   0.843  0.927  0.9396  0.9534  0.8710  0.9320
 $$
Resolution limits                    =     41.964     1.840
Number of used reflections           =      17719
Percentage observed                  =    99.9839
Percentage of free reflections       =     5.0174
Overall R factor                     =     0.1640
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9477
Overall weighted R factor            =     0.1516
Free weighted R factor               =     0.1987
Overall weighted R2 factor           =     0.1845
Free weighted R2 factor              =     0.2375
Average correlation coefficient      =     0.9385
Overall correlation coefficient      =     0.9561
Free correlation coefficient         =     0.9198
Cruickshanks DPI for coordinate error=     0.1291
DPI based on free R factor           =     0.1300
Overall figure of merit              =     0.8585
ML based su of positional parameters =     0.0802
ML based su of thermal parameters    =     2.6004
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    95114.469       8496.2568       683774.50       683733.50    

 fvalues    95114.469       8496.2568       683744.63       683770.94    
 fvalues    95114.469       8496.2568       683744.63       683770.94    

    ****                              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.= 0.930 id.= 3.000 dev= -2.07 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_1-84A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.764     1.644
Bond angles  : others                          3238     1.453     1.580
Torsion angles, period  1. refined              185     6.962     5.000
Torsion angles, period  2. refined               90    35.858    22.778
Torsion angles, period  3. refined              268    13.374    15.000
Torsion angles, period  4. refined                9    11.521    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   300     0.242     0.200
VDW repulsions.others                          1368     0.192     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             766     0.084     0.200
HBOND: refined_atoms                            229     0.204     0.200
VDW repulsions: symmetry: refined_atoms           8     0.225     0.200
VDW repulsions: symmetry: others                 22     0.197     0.200
HBOND: symmetry: refined_atoms                   21     0.199     0.200
M. chain bond B values: refined atoms           746     1.580     1.260
M. chain bond B values: others                  746     1.579     1.261
M. chain angle B values: refined atoms          929     2.509     1.877
M. chain angle B values: others                 930     2.508     1.877
S. chain bond B values: refined atoms           811     2.645     1.613
S. chain bond B values: others                  810     2.643     1.613
S. chain angle B values: refined atoms         1177     4.146     2.268
S. chain angle B values: others                1178     4.144     2.267
Long range B values: refined atoms             1858     6.746    17.542
Long range B values: others                    1763     6.428    16.145
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0408, B  =   -0.0859
Partial structure    1: scale =     0.3770, B  =   46.8254
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.52 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.037    2427 100.00   475.7   482.1  0.16  0.17     110   470.0   479.7  0.21  0.22
 0.111    4082 100.00   360.2   344.5  0.16  0.15     216   361.3   335.2  0.22  0.20
 0.185    5148  99.96   235.8   227.1  0.16  0.13     292   249.7   236.6  0.21  0.18
 0.259    6059 100.00   164.0   167.9  0.18  0.14     317   167.2   172.4  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0374   1692   0.924    735   0.817   2427   0.891  0.956  0.9638  0.9715  0.9082  0.9407
  0.1111   3339   0.879    743   0.777   4082   0.861  0.993  0.9484  0.9624  0.8920  0.9448
  0.1848   4411   0.875    737   0.770   5148   0.860  0.998  0.9501  0.9596  0.8963  0.9403
  0.2585   5314   0.855    748   0.754   6062   0.843  0.927  0.9396  0.9534  0.8709  0.9320
 $$
Resolution limits                    =     41.964     1.840
Number of used reflections           =      17719
Percentage observed                  =    99.9839
Percentage of free reflections       =     5.0174
Overall R factor                     =     0.1640
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9477
Overall weighted R factor            =     0.1516
Free weighted R factor               =     0.1987
Overall weighted R2 factor           =     0.1846
Free weighted R2 factor              =     0.2375
Average correlation coefficient      =     0.9385
Overall correlation coefficient      =     0.9561
Free correlation coefficient         =     0.9198
Cruickshanks DPI for coordinate error=     0.1291
DPI based on free R factor           =     0.1300
Overall figure of merit              =     0.8586
ML based su of positional parameters =     0.0802
ML based su of thermal parameters    =     2.6004
-----------------------------------------------------------------------------
  Time in seconds: CPU =        18.11
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1644   0.2166   0.850       95436.    5216.4   0.0117  0.870   1.750  1.014   0.085
       1   0.1644   0.2158   0.858       95156.    5211.3   0.0113  0.841   1.731  1.003   0.085
       2   0.1640   0.2156   0.859       95122.    5210.8   0.0117  0.871   1.751  1.015   0.086
       3   0.1640   0.2156   0.859       95112.    5210.5   0.0117  0.874   1.757  1.018   0.086
       4   0.1640   0.2156   0.859       95106.    5210.2   0.0118  0.875   1.760  1.020   0.086
       5   0.1640   0.2156   0.859       95107.    5210.5   0.0118  0.876   1.762  1.020   0.086
       6   0.1640   0.2158   0.859       95112.    5210.9   0.0118  0.876   1.763  1.021   0.086
       7   0.1640   0.2158   0.859       95113.    5211.0   0.0118  0.876   1.763  1.021   0.086
       8   0.1640   0.2158   0.859       95109.    5210.8   0.0118  0.876   1.763  1.021   0.086
       9   0.1640   0.2158   0.859       95114.    5211.0   0.0118  0.876   1.764  1.021   0.086
      10   0.1640   0.2158   0.859       95111.    5210.9   0.0118  0.876   1.764  1.021   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1644   0.1640
             R free    0.2166   0.2158
     Rms BondLength    0.0117   0.0118
      Rms BondAngle    1.7500   1.7637
     Rms ChirVolume    0.0855   0.0862
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      50.2s System:    0.1s Elapsed:     0:50