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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: 05:12:49 


 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 1.44     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_1-45A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-44A.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_1-44A.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       0.1206
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4400
  Estimated number of reflections :      50009
  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  1.4400

  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_1-45A.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=   2.191 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.832 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=   2.218 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=   2.386 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=   2.111 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       1911
Number of   all  reflections      38211
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          38211

   Current auto weighting coefficient =    6.0996604    

 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.= 0.897 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        :   144  144  288
 Maximuum H,K,L                 :    41   41   86
 Minimum acceptable grid spacing:    90   90  190
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   86
 Minimum acceptable grid spacing:    90   90  190
 Weight matrix   0.24735659    
 Actual weight    6.0996604      is applied to the X-ray term
Norm of X_ray positional gradient                36.0
Norm of Geom. positional gradient                82.9
Norm of X_ray B-factor gradient                  89.9
Norm of Geom. B-factor gradient                  101.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.498
Product of X_ray and Geom B-fact gradients     -0.261E+08
 Cosine of angle between them                      -0.893


Residuals: XRAY=     0.1048E+07 GEOM=     0.1318E+05 TOTAL=     0.1061E+07
 function value    1060791.9    

-------------------------------------------------------------------------------
             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     1.847     1.644
Bond angles  : others                          3238     2.365     1.580
Torsion angles, period  1. refined              185     6.740     5.000
Torsion angles, period  2. refined               90    34.681    22.778
Torsion angles, period  3. refined              268    13.333    15.000
Torsion angles, period  4. refined                9    12.348    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.017     0.020
VDW repulsions: refined_atoms                   301     0.245     0.200
VDW repulsions.others                          1339     0.219     0.200
VDW; torsion: refined_atoms                     727     0.174     0.200
VDW; torsion.others                             717     0.082     0.200
HBOND: refined_atoms                            203     0.201     0.200
HBOND.others                                      1     0.071     0.200
VDW repulsions: symmetry: refined_atoms           9     0.185     0.200
VDW repulsions: symmetry: others                 23     0.204     0.200
HBOND: symmetry: refined_atoms                   20     0.167     0.200
M. chain bond B values: refined atoms           746     1.840     1.667
M. chain bond B values: others                  746     1.834     1.667
M. chain angle B values: refined atoms          929     2.822     2.491
M. chain angle B values: others                 930     2.821     2.491
S. chain bond B values: refined atoms           811     3.270     2.083
S. chain bond B values: others                  810     3.265     2.083
S. chain angle B values: refined atoms         1177     4.972     2.952
S. chain angle B values: others                1178     4.970     2.951
Long range B values: refined atoms             1834     7.719    22.717
Long range B values: others                    1749     7.439    21.313
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0464, B  =    0.1023
Partial structure    1: scale =     0.3935, B  =   37.2713
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.061    4875 100.00   387.3   397.0  0.17  0.18     229   381.2   384.9  0.22  0.22
 0.181    8324  99.98   211.2   188.2  0.19  0.17     468   222.9   199.8  0.22  0.20
 0.302   10593 100.00    99.4    94.4  0.22  0.19     584    98.9    94.4  0.26  0.23
 0.422   12492 100.00    41.5    51.4  0.45  0.42     628    41.6    52.0  0.45  0.43
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0608   3669   0.894   1206   0.784   4875   0.867  0.945  0.9560  0.9656  0.9000  0.9356
  0.1812   7111   0.864   1213   0.766   8324   0.850  1.084  0.9472  0.9550  0.8951  0.9343
  0.3016   9389   0.809   1204   0.726  10593   0.800  0.971  0.9264  0.9370  0.8853  0.9216
  0.4220  11286   0.402   1220   0.356  12506   0.398  0.401  0.6525  0.6494  0.6992  0.6923
 $$
Resolution limits                    =     41.964     1.440
Number of used reflections           =      36298
Percentage observed                  =    99.9921
Percentage of free reflections       =     5.0014
Overall R factor                     =     0.2155
Free R factor                        =     0.2504
Average Fourier shell correlation    =     0.8459
AverageFree Fourier shell correlation=     0.8448
Overall weighted R factor            =     0.1809
Free weighted R factor               =     0.2158
Overall weighted R2 factor           =     0.2097
Free weighted R2 factor              =     0.2514
Average correlation coefficient      =     0.8474
Overall correlation coefficient      =     0.9598
Free correlation coefficient         =     0.9407
Cruickshanks DPI for coordinate error=     0.0795
DPI based on free R factor           =     0.0825
Overall figure of merit              =     0.6817
ML based su of positional parameters =     0.0761
ML based su of thermal parameters    =     2.1968
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    171749.30       13179.480       1060791.9      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31616053    
 Actual weight    6.0996604      is applied to the X-ray term


 function value    1048576.8    

-------------------------------------------------------------------------------
             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 =     0.0463, B  =   -0.0642
Partial structure    1: scale =     0.3933, B  =   37.2890
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2160
Free R factor                        =     0.2494
Average Fourier shell correlation    =     0.8639
AverageFree Fourier shell correlation=     0.8628
Average correlation coefficient      =     0.8456
Overall figure of merit              =     0.7115
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    170581.50       8087.4937       1048576.8       1060791.9    


     CGMAT cycle number =      3

 Weight matrix   0.32198295    
 Actual weight    6.0996604      is applied to the X-ray term


 function value    1047943.9    

-------------------------------------------------------------------------------
             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 =     0.0463, B  =   -0.0069
Partial structure    1: scale =     0.3936, B  =   37.3565
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2154
Free R factor                        =     0.2495
Average Fourier shell correlation    =     0.8670
AverageFree Fourier shell correlation=     0.8654
Average correlation coefficient      =     0.8467
Overall figure of merit              =     0.7150
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    170410.64       8496.8955       1047943.9       1048576.8    


     CGMAT cycle number =      4

 Weight matrix   0.32192799    
 Actual weight    6.0996604      is applied to the X-ray term


 function value    1047884.6    

-------------------------------------------------------------------------------
             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 =     0.0463, B  =   -0.0012
Partial structure    1: scale =     0.3937, B  =   37.4300
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2153
Free R factor                        =     0.2496
Average Fourier shell correlation    =     0.8675
AverageFree Fourier shell correlation=     0.8657
Average correlation coefficient      =     0.8471
Overall figure of merit              =     0.7154
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    170389.75       8565.0166       1047884.6       1047943.9    


     CGMAT cycle number =      5

 Weight matrix   0.32184559    
 Actual weight    6.0996604      is applied to the X-ray term


 function value    1047905.4    

-------------------------------------------------------------------------------
             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 =     0.0463, B  =    0.0003
Partial structure    1: scale =     0.3937, B  =   37.4277
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2154
Free R factor                        =     0.2497
Average Fourier shell correlation    =     0.8675
AverageFree Fourier shell correlation=     0.8657
Average correlation coefficient      =     0.8473
Overall figure of merit              =     0.7154
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    170389.27       8589.5605       1047924.1       1047884.6    

 fvalues    170389.27       8589.5605       1047926.9       1047906.2    
 fvalues    170389.27       8589.5605       1047926.9       1047906.2    


     CGMAT cycle number =      6

 Weight matrix   0.32177332    
 Actual weight    6.0996604      is applied to the X-ray term


 function value    1047908.3    

-------------------------------------------------------------------------------
             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 =     0.0463, B  =    0.0000
Partial structure    1: scale =     0.3937, B  =   37.4276
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2154
Free R factor                        =     0.2498
Average Fourier shell correlation    =     0.8675
AverageFree Fourier shell correlation=     0.8657
Average correlation coefficient      =     0.8473
Overall figure of merit              =     0.7153
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    170389.59       8590.0654       1047917.1       1047906.2    

 fvalues    170389.59       8590.0654       1047914.1       1047908.8    
 fvalues    170389.59       8590.0654       1047914.1       1047908.8    


     CGMAT cycle number =      7

 Weight matrix   0.32157335    
 Actual weight    6.0996604      is applied to the X-ray term


 function value    1047919.2    

-------------------------------------------------------------------------------
             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 =     0.0463, B  =    0.0022
Partial structure    1: scale =     0.3938, B  =   37.4026
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2154
Free R factor                        =     0.2498
Average Fourier shell correlation    =     0.8675
AverageFree Fourier shell correlation=     0.8656
Average correlation coefficient      =     0.8473
Overall figure of merit              =     0.7152
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    170392.66       8589.7354       1047922.6       1047908.8    
 fvalues    170392.66       8589.7354       1047922.6       1047927.1    


     CGMAT cycle number =      8

 Weight matrix   0.32158053    
 Actual weight    6.0996604      is applied to the X-ray term


 function value    1047928.6    

-------------------------------------------------------------------------------
             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 =     0.0463, B  =    0.0000
Partial structure    1: scale =     0.3938, B  =   37.3919
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2154
Free R factor                        =     0.2498
Average Fourier shell correlation    =     0.8675
AverageFree Fourier shell correlation=     0.8656
Average correlation coefficient      =     0.8473
Overall figure of merit              =     0.7152
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    170393.41       8586.5537       1047939.8       1047927.1    

 fvalues    170393.41       8586.5537       1047927.4       1047928.5    
 fvalues    170393.41       8586.5537       1047927.4       1047928.5    


     CGMAT cycle number =      9

 Weight matrix   0.32138214    
 Actual weight    6.0996604      is applied to the X-ray term


 function value    1047937.1    

-------------------------------------------------------------------------------
             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 =     0.0463, B  =    0.0025
Partial structure    1: scale =     0.3937, B  =   37.3442
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2154
Free R factor                        =     0.2498
Average Fourier shell correlation    =     0.8675
AverageFree Fourier shell correlation=     0.8656
Average correlation coefficient      =     0.8473
Overall figure of merit              =     0.7152
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    170394.45       8586.6973       1047934.1       1047928.5    
 fvalues    170394.45       8586.6973       1047934.1       1047935.0    


     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  288
 Maximuum H,K,L                 :    41   41   86
 Minimum acceptable grid spacing:    90   90  190
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   86
 Minimum acceptable grid spacing:    90   90  190
 Weight matrix   0.32136831    
 Actual weight    6.0996604      is applied to the X-ray term
Norm of X_ray positional gradient                42.9
Norm of Geom. positional gradient                42.9
Norm of X_ray B-factor gradient                  104.
Norm of Geom. B-factor gradient                  103.
Product of X_ray and Geom posit. gradients     -0.178E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.345E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.1039E+07 GEOM=      8587.     TOTAL=     0.1048E+07
 function value    1047935.4    

-------------------------------------------------------------------------------
             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     1.838     1.644
Bond angles  : others                          3238     1.511     1.580
Torsion angles, period  1. refined              185     6.728     5.000
Torsion angles, period  2. refined               90    34.598    22.778
Torsion angles, period  3. refined              268    13.341    15.000
Torsion angles, period  4. refined                9    12.427    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   306     0.243     0.200
VDW repulsions.others                          1348     0.196     0.200
VDW; torsion: refined_atoms                     729     0.173     0.200
VDW; torsion.others                             735     0.087     0.200
HBOND: refined_atoms                            203     0.201     0.200
HBOND.others                                      1     0.017     0.200
VDW repulsions: symmetry: refined_atoms           8     0.196     0.200
VDW repulsions: symmetry: others                 23     0.193     0.200
HBOND: symmetry: refined_atoms                   20     0.168     0.200
M. chain bond B values: refined atoms           746     1.832     1.678
M. chain bond B values: others                  746     1.826     1.678
M. chain angle B values: refined atoms          929     2.818     2.507
M. chain angle B values: others                 930     2.816     2.507
S. chain bond B values: refined atoms           811     3.264     2.095
S. chain bond B values: others                  810     3.259     2.095
S. chain angle B values: refined atoms         1177     4.962     2.970
S. chain angle B values: others                1178     4.959     2.970
Long range B values: refined atoms             1842     7.718    22.856
Long range B values: others                    1758     7.449    21.478
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0463, B  =    0.0024
Partial structure    1: scale =     0.3938, B  =   37.3442
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.061    4875 100.00   387.7   397.3  0.17  0.18     229   381.7   385.7  0.21  0.22
 0.181    8324  99.98   211.4   188.5  0.19  0.17     468   223.2   200.3  0.22  0.20
 0.302   10593 100.00    99.5    94.6  0.22  0.19     584    99.0    94.5  0.26  0.23
 0.422   12492 100.00    41.5    51.4  0.45  0.42     628    41.7    52.0  0.45  0.43
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0608   3669   0.910   1206   0.808   4875   0.885  0.948  0.9604  0.9697  0.8998  0.9355
  0.1812   7111   0.882   1213   0.784   8324   0.868  1.086  0.9511  0.9594  0.8964  0.9350
  0.3016   9389   0.831   1204   0.750  10593   0.822  0.977  0.9340  0.9444  0.8848  0.9211
  0.4220  11286   0.461   1220   0.419  12506   0.457  0.431  0.7042  0.7012  0.6992  0.6918
 $$
Resolution limits                    =     41.964     1.440
Number of used reflections           =      36298
Percentage observed                  =    99.9921
Percentage of free reflections       =     5.0014
Overall R factor                     =     0.2154
Free R factor                        =     0.2498
Average Fourier shell correlation    =     0.8675
AverageFree Fourier shell correlation=     0.8656
Overall weighted R factor            =     0.1808
Free weighted R factor               =     0.2153
Overall weighted R2 factor           =     0.2096
Free weighted R2 factor              =     0.2511
Average correlation coefficient      =     0.8473
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9409
Cruickshanks DPI for coordinate error=     0.0794
DPI based on free R factor           =     0.0823
Overall figure of merit              =     0.7152
ML based su of positional parameters =     0.0667
ML based su of thermal parameters    =     1.9108
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    170394.59       8586.7051       1047942.7       1047935.0    

 fvalues    170394.59       8586.7051       1047943.8       1047935.8    
 fvalues    170394.59       8586.7051       1047943.8       1047935.8    

    ****                              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_1-44A.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     1.838     1.644
Bond angles  : others                          3238     1.511     1.580
Torsion angles, period  1. refined              185     6.728     5.000
Torsion angles, period  2. refined               90    34.597    22.778
Torsion angles, period  3. refined              268    13.341    15.000
Torsion angles, period  4. refined                9    12.427    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   306     0.243     0.200
VDW repulsions.others                          1349     0.196     0.200
VDW; torsion: refined_atoms                     729     0.173     0.200
VDW; torsion.others                             736     0.086     0.200
HBOND: refined_atoms                            203     0.201     0.200
HBOND.others                                      1     0.017     0.200
VDW repulsions: symmetry: refined_atoms           8     0.196     0.200
VDW repulsions: symmetry: others                 24     0.189     0.200
HBOND: symmetry: refined_atoms                   20     0.168     0.200
M. chain bond B values: refined atoms           746     1.832     1.678
M. chain bond B values: others                  746     1.826     1.678
M. chain angle B values: refined atoms          929     2.818     2.507
M. chain angle B values: others                 930     2.816     2.507
S. chain bond B values: refined atoms           811     3.264     2.095
S. chain bond B values: others                  810     3.259     2.095
S. chain angle B values: refined atoms         1177     4.962     2.970
S. chain angle B values: others                1178     4.959     2.970
Long range B values: refined atoms             1842     7.718    22.856
Long range B values: others                    1758     7.449    21.478
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0463, B  =    0.0023
Partial structure    1: scale =     0.3938, B  =   37.3793
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.061    4875 100.00   387.7   397.3  0.17  0.18     229   381.7   385.7  0.21  0.22
 0.181    8324  99.98   211.4   188.5  0.19  0.17     468   223.2   200.3  0.22  0.20
 0.302   10593 100.00    99.5    94.6  0.22  0.19     584    99.0    94.5  0.26  0.23
 0.422   12492 100.00    41.5    51.4  0.45  0.42     628    41.7    52.0  0.45  0.43
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0608   3669   0.910   1206   0.808   4875   0.885  0.948  0.9604  0.9697  0.8998  0.9355
  0.1812   7111   0.882   1213   0.784   8324   0.868  1.086  0.9511  0.9594  0.8964  0.9350
  0.3016   9389   0.831   1204   0.750  10593   0.822  0.977  0.9340  0.9444  0.8848  0.9211
  0.4220  11286   0.461   1220   0.419  12506   0.457  0.431  0.7042  0.7012  0.6992  0.6918
 $$
Resolution limits                    =     41.964     1.440
Number of used reflections           =      36298
Percentage observed                  =    99.9921
Percentage of free reflections       =     5.0014
Overall R factor                     =     0.2154
Free R factor                        =     0.2498
Average Fourier shell correlation    =     0.8675
AverageFree Fourier shell correlation=     0.8656
Overall weighted R factor            =     0.1808
Free weighted R factor               =     0.2153
Overall weighted R2 factor           =     0.2096
Free weighted R2 factor              =     0.2511
Average correlation coefficient      =     0.8473
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9409
Cruickshanks DPI for coordinate error=     0.0794
DPI based on free R factor           =     0.0823
Overall figure of merit              =     0.7152
ML based su of positional parameters =     0.0667
ML based su of thermal parameters    =     1.9108
-----------------------------------------------------------------------------
  Time in seconds: CPU =        34.37
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2155   0.2504   0.682      171749.    9225.6   0.0131  0.990   1.847  1.075   0.090
       1   0.2160   0.2494   0.712      170582.    9189.8   0.0118  0.888   1.772  1.031   0.087
       2   0.2154   0.2495   0.715      170411.    9186.5   0.0129  0.970   1.816  1.057   0.089
       3   0.2153   0.2496   0.715      170390.    9186.8   0.0129  0.975   1.831  1.065   0.090
       4   0.2154   0.2497   0.715      170389.    9187.4   0.0130  0.977   1.837  1.069   0.090
       5   0.2154   0.2498   0.715      170390.    9187.5   0.0130  0.977   1.837  1.069   0.090
       6   0.2154   0.2498   0.715      170391.    9187.6   0.0130  0.977   1.837  1.069   0.090
       7   0.2154   0.2498   0.715      170393.    9187.9   0.0130  0.977   1.838  1.069   0.090
       8   0.2154   0.2498   0.715      170395.    9187.9   0.0130  0.977   1.838  1.070   0.090
       9   0.2154   0.2498   0.715      170395.    9188.0   0.0130  0.977   1.838  1.070   0.090
      10   0.2154   0.2498   0.715      170396.    9188.1   0.0130  0.977   1.838  1.070   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2155   0.2154
             R free    0.2504   0.2498
     Rms BondLength    0.0131   0.0130
      Rms BondAngle    1.8471   1.8383
     Rms ChirVolume    0.0903   0.0899
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      65.6s System:    0.2s Elapsed:     1:06