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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 27/ 5/2020 Run time: 02:34:01 


 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 1.49     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_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-49A.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_1-49A.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       0.1126
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4900
  Estimated number of reflections :      44185
  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  1.4900

  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_1-50A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.056 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.194 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=   1.829 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=   2.220 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=   2.409 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=   2.388 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=   2.109 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       1727
Number of   all  reflections      34578
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          34578

   Current auto weighting coefficient =    6.2246284    

 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.= 0.894 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   83
 Minimum acceptable grid spacing:    87   87  185
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   83
 Minimum acceptable grid spacing:    87   87  185
 Weight matrix   0.27587610    
 Actual weight    6.2246284      is applied to the X-ray term
Norm of X_ray positional gradient                36.7
Norm of Geom. positional gradient                82.9
Norm of X_ray B-factor gradient                  94.7
Norm of Geom. B-factor gradient                  104.
Product of X_ray and Geom posit. gradients     -0.148E+08
 Cosine of angle between them                      -0.504
Product of X_ray and Geom B-fact gradients     -0.286E+08
 Cosine of angle between them                      -0.900


Residuals: XRAY=     0.9889E+06 GEOM=     0.1332E+05 TOTAL=     0.1002E+07
 function value    1002188.9    

-------------------------------------------------------------------------------
             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     1.857     1.644
Bond angles  : others                          3238     2.368     1.580
Torsion angles, period  1. refined              185     6.758     5.000
Torsion angles, period  2. refined               90    34.691    22.778
Torsion angles, period  3. refined              268    13.312    15.000
Torsion angles, period  4. refined                9    12.432    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   303     0.245     0.200
VDW repulsions.others                          1337     0.220     0.200
VDW; torsion: refined_atoms                     729     0.174     0.200
VDW; torsion.others                             722     0.082     0.200
HBOND: refined_atoms                            207     0.200     0.200
HBOND.others                                      1     0.069     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 23     0.200     0.200
HBOND: symmetry: refined_atoms                   22     0.165     0.200
M. chain bond B values: refined atoms           746     1.816     1.618
M. chain bond B values: others                  746     1.811     1.618
M. chain angle B values: refined atoms          929     2.802     2.418
M. chain angle B values: others                 930     2.802     2.418
S. chain bond B values: refined atoms           811     3.246     2.034
S. chain bond B values: others                  810     3.241     2.033
S. chain angle B values: refined atoms         1177     4.942     2.879
S. chain angle B values: others                1178     4.939     2.878
Long range B values: refined atoms             1842     7.858    22.210
Long range B values: others                    1757     7.597    20.836
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =    0.1046
Partial structure    1: scale =     0.3921, B  =   38.2022
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.057    4428 100.00   403.6   413.2  0.17  0.18     209   396.8   402.8  0.21  0.21
 0.169    7541  99.97   224.3   204.2  0.18  0.16     420   236.6   213.2  0.22  0.20
 0.282    9573 100.00   119.8   110.7  0.21  0.19     527   120.1   112.1  0.25  0.22
 0.394   11301 100.00    48.5    60.4  0.41  0.37     570    48.5    61.4  0.44  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0568   3300   0.901   1128   0.794   4428   0.874  0.946  0.9587  0.9674  0.9036  0.9360
  0.1693   6412   0.866   1129   0.764   7541   0.851  1.062  0.9451  0.9543  0.8885  0.9330
  0.2817   8445   0.830   1128   0.746   9573   0.820  1.013  0.9358  0.9452  0.8974  0.9306
  0.3942  10169   0.550   1138   0.483  11307   0.543  0.550  0.7520  0.7612  0.7283  0.7708
 $$
Resolution limits                    =     41.964     1.490
Number of used reflections           =      32849
Percentage observed                  =    99.9913
Percentage of free reflections       =     4.9948
Overall R factor                     =     0.2083
Free R factor                        =     0.2457
Average Fourier shell correlation    =     0.8870
AverageFree Fourier shell correlation=     0.8801
Overall weighted R factor            =     0.1766
Free weighted R factor               =     0.2118
Overall weighted R2 factor           =     0.2058
Free weighted R2 factor              =     0.2474
Average correlation coefficient      =     0.8769
Overall correlation coefficient      =     0.9594
Free correlation coefficient         =     0.9390
Cruickshanks DPI for coordinate error=     0.0847
DPI based on free R factor           =     0.0881
Overall figure of merit              =     0.7389
ML based su of positional parameters =     0.0728
ML based su of thermal parameters    =     2.1095
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    158863.14       13324.918       1002188.9      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.34991059    
 Actual weight    6.2246284      is applied to the X-ray term


 function value    990146.13    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0607
Partial structure    1: scale =     0.3917, B  =   38.2997
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2087
Free R factor                        =     0.2447
Average Fourier shell correlation    =     0.9009
AverageFree Fourier shell correlation=     0.8951
Average correlation coefficient      =     0.8752
Overall figure of merit              =     0.7652
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    157742.00       8260.8223       990146.13       1002188.9    


     CGMAT cycle number =      3

 Weight matrix   0.35810459    
 Actual weight    6.2246284      is applied to the X-ray term


 function value    989443.06    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0165
Partial structure    1: scale =     0.3917, B  =   38.1088
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2082
Free R factor                        =     0.2446
Average Fourier shell correlation    =     0.9040
AverageFree Fourier shell correlation=     0.8979
Average correlation coefficient      =     0.8763
Overall figure of merit              =     0.7700
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    157564.63       8661.7871       989443.06       990146.13    


     CGMAT cycle number =      4

 Weight matrix   0.35888726    
 Actual weight    6.2246284      is applied to the X-ray term


 function value    989268.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0025
Partial structure    1: scale =     0.3919, B  =   38.1506
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2080
Free R factor                        =     0.2449
Average Fourier shell correlation    =     0.9046
AverageFree Fourier shell correlation=     0.8984
Average correlation coefficient      =     0.8768
Overall figure of merit              =     0.7711
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    157522.78       8747.5586       989268.38       989443.06    


     CGMAT cycle number =      5

 Weight matrix   0.35893157    
 Actual weight    6.2246284      is applied to the X-ray term


 function value    989265.50    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =    0.0002
Partial structure    1: scale =     0.3919, B  =   38.1509
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2080
Free R factor                        =     0.2450
Average Fourier shell correlation    =     0.9047
AverageFree Fourier shell correlation=     0.8983
Average correlation coefficient      =     0.8769
Overall figure of merit              =     0.7712
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    157516.77       8782.1895       989265.50       989268.38    


     CGMAT cycle number =      6

 Weight matrix   0.35869569    
 Actual weight    6.2246284      is applied to the X-ray term


 function value    989254.00    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =    0.0003
Partial structure    1: scale =     0.3920, B  =   38.1523
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2080
Free R factor                        =     0.2450
Average Fourier shell correlation    =     0.9047
AverageFree Fourier shell correlation=     0.8983
Average correlation coefficient      =     0.8770
Overall figure of merit              =     0.7712
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    157513.67       8789.9346       989254.00       989265.50    


     CGMAT cycle number =      7

 Weight matrix   0.35849997    
 Actual weight    6.2246284      is applied to the X-ray term


 function value    989253.81    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0003
Partial structure    1: scale =     0.3921, B  =   38.1631
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2080
Free R factor                        =     0.2449
Average Fourier shell correlation    =     0.9047
AverageFree Fourier shell correlation=     0.8982
Average correlation coefficient      =     0.8770
Overall figure of merit              =     0.7711
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    157513.94       8788.0332       989253.81       989254.00    


     CGMAT cycle number =      8

 Weight matrix   0.35811514    
 Actual weight    6.2246284      is applied to the X-ray term


 function value    989289.56    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0005
Partial structure    1: scale =     0.3921, B  =   38.2003
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2080
Free R factor                        =     0.2450
Average Fourier shell correlation    =     0.9046
AverageFree Fourier shell correlation=     0.8982
Average correlation coefficient      =     0.8769
Overall figure of merit              =     0.7711
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    157519.72       8787.2324       989287.75       989253.81    
 fvalues    157519.72       8787.2324       989287.75       989289.00    


     CGMAT cycle number =      9

 Weight matrix   0.35794529    
 Actual weight    6.2246284      is applied to the X-ray term


 function value    989290.25    

-------------------------------------------------------------------------------
             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 =     0.0457, B  =   -0.0012
Partial structure    1: scale =     0.3921, B  =   38.2348
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2080
Free R factor                        =     0.2450
Average Fourier shell correlation    =     0.9046
AverageFree Fourier shell correlation=     0.8982
Average correlation coefficient      =     0.8769
Overall figure of merit              =     0.7710
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    157521.81       8777.4102       989291.69       989289.00    
 fvalues    157521.81       8777.4102       989291.69       989292.19    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   83
 Minimum acceptable grid spacing:    87   87  185
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   83
 Minimum acceptable grid spacing:    87   87  185
 Weight matrix   0.35791859    
 Actual weight    6.2246284      is applied to the X-ray term
Norm of X_ray positional gradient                43.8
Norm of Geom. positional gradient                43.8
Norm of X_ray B-factor gradient                  108.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.186E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.378E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.9805E+06 GEOM=      8778.     TOTAL=     0.9893E+06
 function value    989296.44    

-------------------------------------------------------------------------------
             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     1.857     1.644
Bond angles  : others                          3238     1.516     1.580
Torsion angles, period  1. refined              185     6.760     5.000
Torsion angles, period  2. refined               90    34.700    22.778
Torsion angles, period  3. refined              268    13.341    15.000
Torsion angles, period  4. refined                9    12.346    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                   302     0.246     0.200
VDW repulsions.others                          1369     0.192     0.200
VDW; torsion: refined_atoms                     728     0.174     0.200
VDW; torsion.others                             788     0.085     0.200
HBOND: refined_atoms                            206     0.202     0.200
HBOND.others                                      1     0.012     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 24     0.184     0.200
HBOND: symmetry: refined_atoms                   22     0.164     0.200
M. chain bond B values: refined atoms           746     1.824     1.629
M. chain bond B values: others                  746     1.818     1.629
M. chain angle B values: refined atoms          929     2.808     2.435
M. chain angle B values: others                 930     2.807     2.434
S. chain bond B values: refined atoms           811     3.258     2.045
S. chain bond B values: others                  810     3.254     2.044
S. chain angle B values: refined atoms         1177     4.956     2.895
S. chain angle B values: others                1178     4.954     2.894
Long range B values: refined atoms             1840     7.739    22.311
Long range B values: others                    1755     7.456    20.916
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0024
Partial structure    1: scale =     0.3921, B  =   38.2805
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.057    4428 100.00   404.1   413.6  0.17  0.18     209   397.2   403.1  0.21  0.21
 0.169    7541  99.97   224.6   204.3  0.18  0.16     420   236.9   213.3  0.22  0.20
 0.282    9573 100.00   120.0   110.9  0.21  0.18     527   120.3   112.3  0.25  0.22
 0.394   11301 100.00    48.5    60.4  0.41  0.37     570    48.6    61.5  0.44  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0568   3300   0.917   1128   0.820   4428   0.892  0.948  0.9632  0.9714  0.9039  0.9362
  0.1693   6412   0.879   1129   0.777   7541   0.864  1.064  0.9481  0.9574  0.8899  0.9332
  0.2817   8445   0.850   1128   0.767   9573   0.840  1.017  0.9427  0.9521  0.8976  0.9309
  0.3942  10169   0.610   1138   0.547  11307   0.604  0.579  0.7965  0.8031  0.7273  0.7705
 $$
Resolution limits                    =     41.964     1.490
Number of used reflections           =      32849
Percentage observed                  =    99.9913
Percentage of free reflections       =     4.9948
Overall R factor                     =     0.2080
Free R factor                        =     0.2451
Average Fourier shell correlation    =     0.9046
AverageFree Fourier shell correlation=     0.8982
Overall weighted R factor            =     0.1764
Free weighted R factor               =     0.2112
Overall weighted R2 factor           =     0.2055
Free weighted R2 factor              =     0.2464
Average correlation coefficient      =     0.8769
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9393
Cruickshanks DPI for coordinate error=     0.0846
DPI based on free R factor           =     0.0878
Overall figure of merit              =     0.7711
ML based su of positional parameters =     0.0638
ML based su of thermal parameters    =     1.8312
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    157522.88       8777.6992       989307.38       989292.19    

 fvalues    157522.88       8777.6992       989305.75       989299.06    
 fvalues    157522.88       8777.6992       989305.75       989299.06    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 LABOUT FreeR_flag=FreeR_flag FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-49A.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     1.857     1.644
Bond angles  : others                          3238     1.516     1.580
Torsion angles, period  1. refined              185     6.760     5.000
Torsion angles, period  2. refined               90    34.700    22.778
Torsion angles, period  3. refined              268    13.341    15.000
Torsion angles, period  4. refined                9    12.343    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                   302     0.246     0.200
VDW repulsions.others                          1368     0.192     0.200
VDW; torsion: refined_atoms                     728     0.174     0.200
VDW; torsion.others                             788     0.085     0.200
HBOND: refined_atoms                            206     0.202     0.200
HBOND.others                                      1     0.012     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 24     0.184     0.200
HBOND: symmetry: refined_atoms                   22     0.164     0.200
M. chain bond B values: refined atoms           746     1.824     1.629
M. chain bond B values: others                  746     1.818     1.629
M. chain angle B values: refined atoms          929     2.808     2.435
M. chain angle B values: others                 930     2.807     2.434
S. chain bond B values: refined atoms           811     3.259     2.045
S. chain bond B values: others                  810     3.254     2.044
S. chain angle B values: refined atoms         1177     4.956     2.895
S. chain angle B values: others                1178     4.954     2.894
Long range B values: refined atoms             1840     7.741    22.311
Long range B values: others                    1755     7.457    20.916
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =   -0.0016
Partial structure    1: scale =     0.3921, B  =   38.2826
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.057    4428 100.00   404.1   413.6  0.17  0.18     209   397.2   403.1  0.21  0.21
 0.169    7541  99.97   224.6   204.3  0.18  0.16     420   236.9   213.3  0.22  0.20
 0.282    9573 100.00   120.0   110.9  0.21  0.18     527   120.3   112.3  0.25  0.22
 0.394   11301 100.00    48.5    60.4  0.41  0.37     570    48.6    61.5  0.44  0.40
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0568   3300   0.917   1128   0.820   4428   0.893  0.948  0.9632  0.9714  0.9039  0.9362
  0.1693   6412   0.879   1129   0.777   7541   0.864  1.064  0.9481  0.9574  0.8899  0.9332
  0.2817   8445   0.850   1128   0.767   9573   0.840  1.017  0.9427  0.9521  0.8976  0.9309
  0.3942  10169   0.610   1138   0.547  11307   0.603  0.579  0.7965  0.8031  0.7273  0.7705
 $$
Resolution limits                    =     41.964     1.490
Number of used reflections           =      32849
Percentage observed                  =    99.9913
Percentage of free reflections       =     4.9948
Overall R factor                     =     0.2080
Free R factor                        =     0.2451
Average Fourier shell correlation    =     0.9046
AverageFree Fourier shell correlation=     0.8982
Overall weighted R factor            =     0.1764
Free weighted R factor               =     0.2112
Overall weighted R2 factor           =     0.2055
Free weighted R2 factor              =     0.2464
Average correlation coefficient      =     0.8769
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9393
Cruickshanks DPI for coordinate error=     0.0846
DPI based on free R factor           =     0.0878
Overall figure of merit              =     0.7710
ML based su of positional parameters =     0.0638
ML based su of thermal parameters    =     1.8312
-----------------------------------------------------------------------------
  Time in seconds: CPU =        25.00
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2083   0.2457   0.739      158863.    8537.6   0.0132  0.993   1.857  1.081   0.091
       1   0.2087   0.2447   0.765      157742.    8504.0   0.0120  0.901   1.784  1.038   0.087
       2   0.2082   0.2446   0.770      157565.    8500.4   0.0131  0.982   1.827  1.064   0.090
       3   0.2080   0.2449   0.771      157523.    8499.3   0.0131  0.990   1.842  1.073   0.091
       4   0.2080   0.2450   0.771      157517.    8499.8   0.0132  0.992   1.849  1.077   0.091
       5   0.2080   0.2450   0.771      157514.    8500.0   0.0132  0.993   1.853  1.079   0.091
       6   0.2080   0.2449   0.771      157514.    8500.2   0.0132  0.994   1.855  1.080   0.091
       7   0.2080   0.2450   0.771      157520.    8500.6   0.0132  0.993   1.856  1.080   0.091
       8   0.2080   0.2450   0.771      157522.    8500.8   0.0132  0.993   1.856  1.081   0.091
       9   0.2080   0.2451   0.771      157522.    8500.9   0.0132  0.993   1.857  1.081   0.091
      10   0.2080   0.2451   0.771      157523.    8500.9   0.0132  0.993   1.857  1.081   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2083   0.2080
             R free    0.2457   0.2451
     Rms BondLength    0.0132   0.0132
      Rms BondAngle    1.8570   1.8568
     Rms ChirVolume    0.0913   0.0910
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      57.0s System:    0.2s Elapsed:     0:57