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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: 16:21:08 


 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 1.76     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_1-77A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-76A.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_1-76A.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       0.0807
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7600
  Estimated number of reflections :      26680
  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  1.7600

  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_1-77A.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=   2.055 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=   2.206 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=   1.843 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=   2.208 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=   2.413 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=   2.408 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       1079
Number of   all  reflections      21235
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          21235

   Current auto weighting coefficient =    6.8997955    

 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.= 0.903 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   70
 Minimum acceptable grid spacing:    77   77  163
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   70
 Minimum acceptable grid spacing:    77   77  163
 Weight matrix   0.27410659    
 Actual weight    6.8997955      is applied to the X-ray term
Norm of X_ray positional gradient                35.3
Norm of Geom. positional gradient                79.8
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.122E+08
 Cosine of angle between them                      -0.446
Product of X_ray and Geom B-fact gradients     -0.396E+08
 Cosine of angle between them                      -0.916


Residuals: XRAY=     0.7347E+06 GEOM=     0.1331E+05 TOTAL=     0.7481E+06
 function value    748053.94    

-------------------------------------------------------------------------------
             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     1.810     1.644
Bond angles  : others                          3238     2.356     1.580
Torsion angles, period  1. refined              185     6.853     5.000
Torsion angles, period  2. refined               90    35.703    22.778
Torsion angles, period  3. refined              268    13.230    15.000
Torsion angles, period  4. refined                9    12.261    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   297     0.245     0.200
VDW repulsions.others                          1334     0.219     0.200
VDW; torsion: refined_atoms                     721     0.172     0.200
VDW; torsion.others                             726     0.080     0.200
HBOND: refined_atoms                            213     0.202     0.200
HBOND.others                                      1     0.053     0.200
VDW repulsions: symmetry: refined_atoms           8     0.218     0.200
VDW repulsions: symmetry: others                 21     0.200     0.200
HBOND: symmetry: refined_atoms                   23     0.185     0.200
M. chain bond B values: refined atoms           746     1.648     1.326
M. chain bond B values: others                  746     1.645     1.326
M. chain angle B values: refined atoms          929     2.591     1.975
M. chain angle B values: others                 930     2.590     1.975
S. chain bond B values: refined atoms           811     2.877     1.705
S. chain bond B values: others                  810     2.872     1.704
S. chain angle B values: refined atoms         1177     4.455     2.397
S. chain angle B values: others                1178     4.454     2.396
Long range B values: refined atoms             1839     6.876    18.299
Long range B values: others                    1749     6.569    16.907
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0419, B  =    0.0341
Partial structure    1: scale =     0.3845, B  =   44.7983
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.041    2761 100.00   465.9   474.0  0.16  0.17     126   457.2   468.8  0.20  0.21
 0.121    4613 100.00   323.1   309.4  0.17  0.15     263   322.9   298.5  0.22  0.20
 0.202    5905  99.97   216.3   203.2  0.16  0.14     313   225.9   214.8  0.20  0.17
 0.283    6869 100.00   129.9   138.3  0.21  0.16     377   132.0   139.9  0.26  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0409   1955   0.913    806   0.810   2761   0.883  0.952  0.9615  0.9698  0.9085  0.9404
  0.1214   3807   0.873    806   0.771   4613   0.856  0.994  0.9459  0.9597  0.8922  0.9421
  0.2020   5087   0.879    818   0.772   5905   0.864  1.026  0.9528  0.9606  0.9036  0.9416
  0.2825   6069   0.805    806   0.727   6875   0.796  0.877  0.9288  0.9394  0.8721  0.9184
 $$
Resolution limits                    =     41.964     1.760
Number of used reflections           =      20154
Percentage observed                  =    99.9859
Percentage of free reflections       =     5.0817
Overall R factor                     =     0.1714
Free R factor                        =     0.2202
Average Fourier shell correlation    =     0.9544
AverageFree Fourier shell correlation=     0.9437
Overall weighted R factor            =     0.1554
Free weighted R factor               =     0.1985
Overall weighted R2 factor           =     0.1876
Free weighted R2 factor              =     0.2356
Average correlation coefficient      =     0.9336
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9265
Cruickshanks DPI for coordinate error=     0.1162
DPI based on free R factor           =     0.1190
Overall figure of merit              =     0.8416
ML based su of positional parameters =     0.0769
ML based su of thermal parameters    =     2.4287
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    106487.10       13314.658       748053.94      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30391812    
 Actual weight    6.8997955      is applied to the X-ray term


 function value    740281.31    

-------------------------------------------------------------------------------
             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 =     0.0418, B  =   -0.0825
Partial structure    1: scale =     0.3843, B  =   44.8947
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1714
Free R factor                        =     0.2197
Average Fourier shell correlation    =     0.9575
AverageFree Fourier shell correlation=     0.9469
Average correlation coefficient      =     0.9337
Overall figure of merit              =     0.8550
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    106043.71       8601.3564       740281.31       748053.94    


     CGMAT cycle number =      3

 Weight matrix   0.30603838    
 Actual weight    6.8997955      is applied to the X-ray term


 function value    740019.25    

-------------------------------------------------------------------------------
             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 =     0.0418, B  =   -0.0579
Partial structure    1: scale =     0.3843, B  =   44.7277
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1710
Free R factor                        =     0.2194
Average Fourier shell correlation    =     0.9578
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9342
Overall figure of merit              =     0.8558
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    105980.01       8778.8750       740019.25       740281.31    


     CGMAT cycle number =      4

 Weight matrix   0.30640370    
 Actual weight    6.8997955      is applied to the X-ray term


 function value    739949.63    

-------------------------------------------------------------------------------
             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 =     0.0418, B  =   -0.0474
Partial structure    1: scale =     0.3842, B  =   44.5454
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1709
Free R factor                        =     0.2191
Average Fourier shell correlation    =     0.9579
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9343
Overall figure of merit              =     0.8560
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    105962.99       8826.6064       739949.63       740019.25    


     CGMAT cycle number =      5

 Weight matrix   0.30614838    
 Actual weight    6.8997955      is applied to the X-ray term


 function value    739936.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0418, B  =   -0.0421
Partial structure    1: scale =     0.3842, B  =   44.5087
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1709
Free R factor                        =     0.2190
Average Fourier shell correlation    =     0.9579
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9343
Overall figure of merit              =     0.8560
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    105958.88       8841.8359       739936.38       739949.63    


     CGMAT cycle number =      6

 Weight matrix   0.30643585    
 Actual weight    6.8997955      is applied to the X-ray term


 function value    739903.94    

-------------------------------------------------------------------------------
             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 =     0.0418, B  =   -0.0462
Partial structure    1: scale =     0.3843, B  =   44.4813
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1709
Free R factor                        =     0.2190
Average Fourier shell correlation    =     0.9579
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9343
Overall figure of merit              =     0.8561
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    105954.01       8842.9141       739903.94       739936.38    


     CGMAT cycle number =      7

 Weight matrix   0.30650949    
 Actual weight    6.8997955      is applied to the X-ray term


 function value    739868.06    

-------------------------------------------------------------------------------
             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 =     0.0418, B  =   -0.0484
Partial structure    1: scale =     0.3843, B  =   44.3945
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1709
Free R factor                        =     0.2188
Average Fourier shell correlation    =     0.9579
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9343
Overall figure of merit              =     0.8561
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    105949.05       8841.2314       739868.06       739903.94    


     CGMAT cycle number =      8

 Weight matrix   0.30610174    
 Actual weight    6.8997955      is applied to the X-ray term


 function value    739893.44    

-------------------------------------------------------------------------------
             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 =     0.0418, B  =   -0.0489
Partial structure    1: scale =     0.3843, B  =   44.3870
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1709
Free R factor                        =     0.2188
Average Fourier shell correlation    =     0.9579
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9342
Overall figure of merit              =     0.8560
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    105954.69       8841.3594       739868.81       739868.06    
 fvalues    105954.69       8841.3594       739868.81       739907.06    


     CGMAT cycle number =      9

 Weight matrix   0.30600774    
 Actual weight    6.8997955      is applied to the X-ray term


 function value    739891.06    

-------------------------------------------------------------------------------
             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 =     0.0418, B  =   -0.0476
Partial structure    1: scale =     0.3844, B  =   44.3752
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1709
Free R factor                        =     0.2188
Average Fourier shell correlation    =     0.9579
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9342
Overall figure of merit              =     0.8560
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    105953.77       8831.6680       739891.06       739907.06    


     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        :   120  120  256
 Maximuum H,K,L                 :    33   33   70
 Minimum acceptable grid spacing:    77   77  163
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   70
 Minimum acceptable grid spacing:    77   77  163
 Weight matrix   0.30577928    
 Actual weight    6.8997955      is applied to the X-ray term
Norm of X_ray positional gradient                38.1
Norm of Geom. positional gradient                38.1
Norm of X_ray B-factor gradient                  120.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.140E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.471E+08
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.7311E+06 GEOM=      8833.     TOTAL=     0.7399E+06
 function value    739901.50    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.808     1.644
Bond angles  : others                          3238     1.484     1.580
Torsion angles, period  1. refined              185     6.857     5.000
Torsion angles, period  2. refined               90    35.667    22.778
Torsion angles, period  3. refined              268    13.281    15.000
Torsion angles, period  4. refined                9    12.297    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   292     0.247     0.200
VDW repulsions.others                          1362     0.190     0.200
VDW; torsion: refined_atoms                     718     0.172     0.200
VDW; torsion.others                             785     0.084     0.200
HBOND: refined_atoms                            210     0.204     0.200
VDW repulsions: symmetry: refined_atoms           8     0.219     0.200
VDW repulsions: symmetry: others                 22     0.182     0.200
HBOND: symmetry: refined_atoms                   22     0.189     0.200
M. chain bond B values: refined atoms           746     1.650     1.334
M. chain bond B values: others                  746     1.648     1.334
M. chain angle B values: refined atoms          929     2.604     1.988
M. chain angle B values: others                 930     2.603     1.987
S. chain bond B values: refined atoms           811     2.894     1.716
S. chain bond B values: others                  810     2.888     1.716
S. chain angle B values: refined atoms         1177     4.485     2.413
S. chain angle B values: others                1178     4.484     2.413
Long range B values: refined atoms             1827     6.879    18.384
Long range B values: others                    1738     6.549    16.988
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0418, B  =   -0.0432
Partial structure    1: scale =     0.3843, B  =   44.3637
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.041    2761 100.00   466.3   474.4  0.16  0.17     126   457.6   469.3  0.20  0.21
 0.121    4613 100.00   323.4   309.3  0.17  0.15     263   323.2   299.2  0.22  0.20
 0.202    5905  99.97   216.5   203.3  0.16  0.14     313   226.1   214.5  0.20  0.17
 0.283    6869 100.00   130.0   138.4  0.21  0.16     377   132.1   139.8  0.26  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0409   1955   0.928    806   0.829   2761   0.899  0.954  0.9652  0.9728  0.9097  0.9409
  0.1214   3807   0.876    806   0.773   4613   0.858  0.994  0.9472  0.9605  0.8942  0.9424
  0.2020   5087   0.882    818   0.775   5905   0.867  1.026  0.9537  0.9615  0.9035  0.9415
  0.2825   6069   0.837    806   0.759   6875   0.828  0.884  0.9359  0.9469  0.8735  0.9199
 $$
Resolution limits                    =     41.964     1.760
Number of used reflections           =      20154
Percentage observed                  =    99.9859
Percentage of free reflections       =     5.0817
Overall R factor                     =     0.1709
Free R factor                        =     0.2188
Average Fourier shell correlation    =     0.9578
AverageFree Fourier shell correlation=     0.9472
Overall weighted R factor            =     0.1550
Free weighted R factor               =     0.1971
Overall weighted R2 factor           =     0.1870
Free weighted R2 factor              =     0.2334
Average correlation coefficient      =     0.9342
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9275
Cruickshanks DPI for coordinate error=     0.1159
DPI based on free R factor           =     0.1183
Overall figure of merit              =     0.8560
ML based su of positional parameters =     0.0727
ML based su of thermal parameters    =     2.2756
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    105954.62       8832.6631       739875.13       739891.06    
 fvalues    105954.62       8832.6631       739875.13       739897.88    

    ****                              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_1-76A.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     1.808     1.644
Bond angles  : others                          3238     1.485     1.580
Torsion angles, period  1. refined              185     6.854     5.000
Torsion angles, period  2. refined               90    35.663    22.778
Torsion angles, period  3. refined              268    13.287    15.000
Torsion angles, period  4. refined                9    12.291    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   292     0.247     0.200
VDW repulsions.others                          1360     0.190     0.200
VDW; torsion: refined_atoms                     718     0.172     0.200
VDW; torsion.others                             791     0.083     0.200
HBOND: refined_atoms                            211     0.204     0.200
VDW repulsions: symmetry: refined_atoms           8     0.219     0.200
VDW repulsions: symmetry: others                 22     0.182     0.200
HBOND: symmetry: refined_atoms                   22     0.189     0.200
M. chain bond B values: refined atoms           746     1.650     1.334
M. chain bond B values: others                  746     1.648     1.334
M. chain angle B values: refined atoms          929     2.604     1.987
M. chain angle B values: others                 930     2.602     1.987
S. chain bond B values: refined atoms           811     2.894     1.716
S. chain bond B values: others                  810     2.888     1.716
S. chain angle B values: refined atoms         1177     4.486     2.413
S. chain angle B values: others                1178     4.484     2.413
Long range B values: refined atoms             1828     6.879    18.384
Long range B values: others                    1739     6.548    16.989
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0418, B  =   -0.0470
Partial structure    1: scale =     0.3843, B  =   44.3639
Overall anisotropic scale factors
   B11 =  -0.24 B22 =  -0.24 B33 =   0.48 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.041    2761 100.00   466.2   474.5  0.16  0.17     126   457.5   469.4  0.20  0.21
 0.121    4613 100.00   323.4   309.4  0.17  0.15     263   323.2   299.2  0.22  0.20
 0.202    5905  99.97   216.4   203.3  0.16  0.14     313   226.0   214.5  0.20  0.17
 0.283    6869 100.00   130.0   138.5  0.21  0.16     377   132.1   139.9  0.26  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0409   1955   0.928    806   0.829   2761   0.899  0.954  0.9652  0.9728  0.9096  0.9409
  0.1214   3807   0.876    806   0.773   4613   0.858  0.994  0.9472  0.9606  0.8942  0.9424
  0.2020   5087   0.882    818   0.775   5905   0.867  1.026  0.9537  0.9615  0.9035  0.9414
  0.2825   6069   0.837    806   0.759   6875   0.828  0.884  0.9360  0.9469  0.8736  0.9199
 $$
Resolution limits                    =     41.964     1.760
Number of used reflections           =      20154
Percentage observed                  =    99.9859
Percentage of free reflections       =     5.0817
Overall R factor                     =     0.1709
Free R factor                        =     0.2188
Average Fourier shell correlation    =     0.9579
AverageFree Fourier shell correlation=     0.9473
Overall weighted R factor            =     0.1550
Free weighted R factor               =     0.1971
Overall weighted R2 factor           =     0.1870
Free weighted R2 factor              =     0.2334
Average correlation coefficient      =     0.9342
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9275
Cruickshanks DPI for coordinate error=     0.1159
DPI based on free R factor           =     0.1183
Overall figure of merit              =     0.8560
ML based su of positional parameters =     0.0727
ML based su of thermal parameters    =     2.2756
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.83
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1714   0.2202   0.842      106487.    5874.0   0.0123  0.917   1.810  1.046   0.086
       1   0.1714   0.2197   0.855      106044.    5866.1   0.0117  0.873   1.770  1.023   0.085
       2   0.1710   0.2194   0.856      105980.    5865.1   0.0122  0.913   1.793  1.037   0.086
       3   0.1709   0.2191   0.856      105963.    5864.3   0.0123  0.918   1.800  1.041   0.087
       4   0.1709   0.2190   0.856      105959.    5864.2   0.0123  0.920   1.804  1.043   0.087
       5   0.1709   0.2190   0.856      105954.    5864.0   0.0123  0.921   1.805  1.044   0.087
       6   0.1709   0.2188   0.856      105949.    5863.7   0.0124  0.922   1.806  1.045   0.087
       7   0.1709   0.2188   0.856      105953.    5863.8   0.0124  0.922   1.807  1.045   0.087
       8   0.1709   0.2188   0.856      105954.    5863.8   0.0124  0.922   1.807  1.045   0.087
       9   0.1709   0.2188   0.856      105955.    5863.8   0.0124  0.922   1.808  1.046   0.087
      10   0.1709   0.2188   0.856      105951.    5863.7   0.0124  0.922   1.808  1.046   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1714   0.1709
             R free    0.2202   0.2188
     Rms BondLength    0.0123   0.0124
      Rms BondAngle    1.8096   1.8080
     Rms ChirVolume    0.0858   0.0867
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      48.7s System:    0.2s Elapsed:     0:49