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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: 18:59:51 


 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 1.67     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_1-68A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-67A.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_1-67A.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       0.0896
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6700
  Estimated number of reflections :      31727
  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  1.6700

  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_1-68A.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=   2.040 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=   2.203 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=   1.839 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=   2.233 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=   2.415 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=   2.398 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=   2.132 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       1262
Number of   all  reflections      24763
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          24763

   Current auto weighting coefficient =    6.6745930    

 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.= 0.906 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                 :    35   35   74
 Minimum acceptable grid spacing:    80   80  169
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    35   35   74
 Minimum acceptable grid spacing:    80   80  169
 Weight matrix   0.29927459    
 Actual weight    6.6745930      is applied to the X-ray term
Norm of X_ray positional gradient                37.5
Norm of Geom. positional gradient                82.3
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.141E+08
 Cosine of angle between them                      -0.473
Product of X_ray and Geom B-fact gradients     -0.390E+08
 Cosine of angle between them                      -0.893


Residuals: XRAY=     0.8071E+06 GEOM=     0.1374E+05 TOTAL=     0.8208E+06
 function value    820795.75    

-------------------------------------------------------------------------------
             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     2.367     1.580
Torsion angles, period  1. refined              185     6.800     5.000
Torsion angles, period  2. refined               90    35.091    22.778
Torsion angles, period  3. refined              268    13.452    15.000
Torsion angles, period  4. refined                9    12.346    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.019     0.020
VDW repulsions: refined_atoms                   299     0.247     0.200
VDW repulsions.others                          1320     0.220     0.200
VDW; torsion: refined_atoms                     723     0.174     0.200
VDW; torsion.others                             730     0.081     0.200
HBOND: refined_atoms                            214     0.203     0.200
HBOND.others                                      1     0.093     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 22     0.199     0.200
HBOND: symmetry: refined_atoms                   21     0.181     0.200
M. chain bond B values: refined atoms           746     1.718     1.412
M. chain bond B values: others                  746     1.715     1.412
M. chain angle B values: refined atoms          929     2.689     2.107
M. chain angle B values: others                 930     2.688     2.107
S. chain bond B values: refined atoms           811     3.074     1.815
S. chain bond B values: others                  810     3.068     1.814
S. chain angle B values: refined atoms         1177     4.723     2.553
S. chain angle B values: others                1178     4.721     2.553
Long range B values: refined atoms             1839     7.089    19.559
Long range B values: others                    1750     6.842    18.181
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0431, B  =    0.1108
Partial structure    1: scale =     0.3877, B  =   43.3361
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.045    3212 100.00   447.3   457.2  0.16  0.17     142   439.6   451.7  0.21  0.21
 0.135    5378  99.98   284.8   271.6  0.17  0.15     316   294.6   272.8  0.22  0.19
 0.224    6852  99.99   192.3   175.0  0.17  0.15     370   197.5   182.4  0.20  0.17
 0.314    8052 100.00    93.0   106.1  0.26  0.20     433    88.4   102.7  0.33  0.26
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0453   2312   0.911    900   0.812   3212   0.883  0.949  0.9614  0.9701  0.9046  0.9393
  0.1348   4484   0.871    894   0.765   5378   0.853  1.003  0.9465  0.9576  0.8956  0.9413
  0.2243   5953   0.882    899   0.771   6852   0.867  1.054  0.9559  0.9611  0.9128  0.9419
  0.3138   7156   0.745    901   0.675   8057   0.737  0.794  0.8929  0.9131  0.8459  0.9011
 $$
Resolution limits                    =     41.964     1.670
Number of used reflections           =      23498
Percentage observed                  =    99.9879
Percentage of free reflections       =     5.0969
Overall R factor                     =     0.1818
Free R factor                        =     0.2264
Average Fourier shell correlation    =     0.9451
AverageFree Fourier shell correlation=     0.9325
Overall weighted R factor            =     0.1614
Free weighted R factor               =     0.2005
Overall weighted R2 factor           =     0.1929
Free weighted R2 factor              =     0.2371
Average correlation coefficient      =     0.9274
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9333
Cruickshanks DPI for coordinate error=     0.1041
DPI based on free R factor           =     0.1076
Overall figure of merit              =     0.8218
ML based su of positional parameters =     0.0724
ML based su of thermal parameters    =     2.2145
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    120913.87       13744.890       820795.75      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36371729    
 Actual weight    6.6745930      is applied to the X-ray term


 function value    810105.38    

-------------------------------------------------------------------------------
             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 =     0.0431, B  =   -0.0583
Partial structure    1: scale =     0.3877, B  =   43.2289
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1819
Free R factor                        =     0.2259
Average Fourier shell correlation    =     0.9519
AverageFree Fourier shell correlation=     0.9402
Average correlation coefficient      =     0.9264
Overall figure of merit              =     0.8497
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    120062.81       8735.0146       810105.38       820795.75    


     CGMAT cycle number =      3

 Weight matrix   0.36802965    
 Actual weight    6.6745930      is applied to the X-ray term


 function value    809712.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0431, B  =   -0.0482
Partial structure    1: scale =     0.3881, B  =   43.1313
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1815
Free R factor                        =     0.2259
Average Fourier shell correlation    =     0.9525
AverageFree Fourier shell correlation=     0.9406
Average correlation coefficient      =     0.9272
Overall figure of merit              =     0.8516
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    119957.69       9043.6943       809712.44       810105.38    


     CGMAT cycle number =      4

 Weight matrix   0.36773890    
 Actual weight    6.6745930      is applied to the X-ray term


 function value    809673.31    

-------------------------------------------------------------------------------
             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 =     0.0431, B  =   -0.0194
Partial structure    1: scale =     0.3882, B  =   43.1881
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1816
Free R factor                        =     0.2259
Average Fourier shell correlation    =     0.9525
AverageFree Fourier shell correlation=     0.9406
Average correlation coefficient      =     0.9274
Overall figure of merit              =     0.8516
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    119936.91       9143.2764       809673.31       809712.44    


     CGMAT cycle number =      5

 Weight matrix   0.36742342    
 Actual weight    6.6745930      is applied to the X-ray term


 function value    809682.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0431, B  =   -0.0205
Partial structure    1: scale =     0.3883, B  =   43.1785
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1816
Free R factor                        =     0.2259
Average Fourier shell correlation    =     0.9525
AverageFree Fourier shell correlation=     0.9405
Average correlation coefficient      =     0.9274
Overall figure of merit              =     0.8516
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    119936.09       9164.4512       809706.81       809673.31    

 fvalues    119936.09       9164.4512       809694.75       809689.06    
 fvalues    119936.09       9164.4512       809694.75       809689.06    


     CGMAT cycle number =      6

 Weight matrix   0.36724865    
 Actual weight    6.6745930      is applied to the X-ray term


 function value    809697.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0431, B  =   -0.0206
Partial structure    1: scale =     0.3884, B  =   43.1919
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1817
Free R factor                        =     0.2260
Average Fourier shell correlation    =     0.9525
AverageFree Fourier shell correlation=     0.9405
Average correlation coefficient      =     0.9274
Overall figure of merit              =     0.8515
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    119937.31       9165.1563       809713.00       809689.06    

 fvalues    119937.31       9165.1563       809700.13       809697.88    
 fvalues    119937.31       9165.1563       809700.13       809697.88    


     CGMAT cycle number =      7

 Weight matrix   0.36723459    
 Actual weight    6.6745930      is applied to the X-ray term


 function value    809695.63    

-------------------------------------------------------------------------------
             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 =     0.0431, B  =   -0.0212
Partial structure    1: scale =     0.3884, B  =   43.2036
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1817
Free R factor                        =     0.2260
Average Fourier shell correlation    =     0.9525
AverageFree Fourier shell correlation=     0.9405
Average correlation coefficient      =     0.9274
Overall figure of merit              =     0.8515
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    119937.05       9164.6465       809695.63       809697.88    


     CGMAT cycle number =      8

 Weight matrix   0.36692140    
 Actual weight    6.6745930      is applied to the X-ray term


 function value    809709.94    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0431, B  =   -0.0194
Partial structure    1: scale =     0.3884, B  =   43.2319
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1817
Free R factor                        =     0.2260
Average Fourier shell correlation    =     0.9525
AverageFree Fourier shell correlation=     0.9405
Average correlation coefficient      =     0.9274
Overall figure of merit              =     0.8514
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    119939.69       9161.5234       809703.50       809695.63    
 fvalues    119939.69       9161.5234       809703.50       809710.13    


     CGMAT cycle number =      9

 Weight matrix   0.36666778    
 Actual weight    6.6745930      is applied to the X-ray term


 function value    809713.88    

-------------------------------------------------------------------------------
             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 =     0.0431, B  =   -0.0152
Partial structure    1: scale =     0.3883, B  =   43.1911
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1817
Free R factor                        =     0.2259
Average Fourier shell correlation    =     0.9525
AverageFree Fourier shell correlation=     0.9405
Average correlation coefficient      =     0.9274
Overall figure of merit              =     0.8514
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    119938.13       9161.5137       809699.69       809710.13    


     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.= 0.917 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    35   35   74
 Minimum acceptable grid spacing:    80   80  169
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    35   35   74
 Minimum acceptable grid spacing:    80   80  169
 Weight matrix   0.36676928    
 Actual weight    6.6745930      is applied to the X-ray term
Norm of X_ray positional gradient                42.8
Norm of Geom. positional gradient                42.8
Norm of X_ray B-factor gradient                  124.
Norm of Geom. B-factor gradient                  125.
Product of X_ray and Geom posit. gradients     -0.177E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.499E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.8006E+06 GEOM=      9161.     TOTAL=     0.8097E+06
 function value    809711.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.841     1.644
Bond angles  : others                          3238     1.522     1.580
Torsion angles, period  1. refined              185     6.780     5.000
Torsion angles, period  2. refined               90    34.947    22.778
Torsion angles, period  3. refined              268    13.342    15.000
Torsion angles, period  4. refined                9    12.378    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   293     0.249     0.200
VDW repulsions.others                          1329     0.197     0.200
VDW; torsion: refined_atoms                     722     0.175     0.200
VDW; torsion.others                             740     0.086     0.200
HBOND: refined_atoms                            213     0.202     0.200
HBOND.others                                      1     0.035     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 23     0.186     0.200
HBOND: symmetry: refined_atoms                   22     0.170     0.200
M. chain bond B values: refined atoms           746     1.730     1.428
M. chain bond B values: others                  746     1.727     1.428
M. chain angle B values: refined atoms          929     2.713     2.131
M. chain angle B values: others                 930     2.712     2.131
S. chain bond B values: refined atoms           811     3.087     1.833
S. chain bond B values: others                  810     3.082     1.832
S. chain angle B values: refined atoms         1177     4.737     2.580
S. chain angle B values: others                1178     4.735     2.579
Long range B values: refined atoms             1832     7.100    19.709
Long range B values: others                    1743     6.852    18.319
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0431, B  =   -0.0185
Partial structure    1: scale =     0.3883, B  =   43.1603
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.045    3212 100.00   447.9   457.5  0.16  0.17     142   440.1   453.0  0.21  0.21
 0.135    5378  99.98   285.2   271.7  0.17  0.15     316   294.9   272.9  0.22  0.19
 0.224    6852  99.99   192.5   175.3  0.17  0.15     370   197.7   182.8  0.20  0.17
 0.314    8052 100.00    93.1   106.2  0.27  0.20     433    88.5   102.7  0.33  0.26
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0453   2312   0.927    900   0.831   3212   0.900  0.951  0.9654  0.9734  0.9052  0.9396
  0.1348   4484   0.871    894   0.765   5378   0.854  1.003  0.9468  0.9576  0.8960  0.9404
  0.2243   5953   0.890    899   0.780   6852   0.876  1.054  0.9580  0.9637  0.9126  0.9428
  0.3138   7156   0.818    901   0.746   8057   0.810  0.819  0.9128  0.9311  0.8455  0.9007
 $$
Resolution limits                    =     41.964     1.670
Number of used reflections           =      23498
Percentage observed                  =    99.9879
Percentage of free reflections       =     5.0969
Overall R factor                     =     0.1817
Free R factor                        =     0.2259
Average Fourier shell correlation    =     0.9525
AverageFree Fourier shell correlation=     0.9405
Overall weighted R factor            =     0.1614
Free weighted R factor               =     0.2000
Overall weighted R2 factor           =     0.1926
Free weighted R2 factor              =     0.2368
Average correlation coefficient      =     0.9274
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9335
Cruickshanks DPI for coordinate error=     0.1041
DPI based on free R factor           =     0.1073
Overall figure of merit              =     0.8514
ML based su of positional parameters =     0.0653
ML based su of thermal parameters    =     1.9555
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    119940.18       9161.2656       809713.50       809699.69    

 fvalues    119940.18       9161.2656       809716.63       809713.13    
 fvalues    119940.18       9161.2656       809716.63       809713.13    

    ****                              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.= 0.917 id.= 3.000 dev= -2.08 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_1-67A.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     1.841     1.644
Bond angles  : others                          3238     1.522     1.580
Torsion angles, period  1. refined              185     6.780     5.000
Torsion angles, period  2. refined               90    34.946    22.778
Torsion angles, period  3. refined              268    13.341    15.000
Torsion angles, period  4. refined                9    12.379    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   293     0.249     0.200
VDW repulsions.others                          1329     0.197     0.200
VDW; torsion: refined_atoms                     722     0.175     0.200
VDW; torsion.others                             740     0.086     0.200
HBOND: refined_atoms                            213     0.202     0.200
HBOND.others                                      1     0.035     0.200
VDW repulsions: symmetry: refined_atoms           8     0.204     0.200
VDW repulsions: symmetry: others                 23     0.186     0.200
HBOND: symmetry: refined_atoms                   22     0.170     0.200
M. chain bond B values: refined atoms           746     1.730     1.428
M. chain bond B values: others                  746     1.727     1.428
M. chain angle B values: refined atoms          929     2.713     2.131
M. chain angle B values: others                 930     2.712     2.131
S. chain bond B values: refined atoms           811     3.087     1.833
S. chain bond B values: others                  810     3.082     1.832
S. chain angle B values: refined atoms         1177     4.737     2.580
S. chain angle B values: others                1178     4.735     2.579
Long range B values: refined atoms             1832     7.100    19.709
Long range B values: others                    1743     6.852    18.319
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0431, B  =   -0.0206
Partial structure    1: scale =     0.3883, B  =   43.1669
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.44 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.045    3212 100.00   447.8   457.5  0.16  0.17     142   440.1   453.0  0.21  0.21
 0.135    5378  99.98   285.2   271.7  0.17  0.15     316   294.9   272.9  0.22  0.19
 0.224    6852  99.99   192.5   175.3  0.17  0.15     370   197.7   182.8  0.20  0.17
 0.314    8052 100.00    93.1   106.2  0.27  0.20     433    88.5   102.7  0.33  0.26
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0453   2312   0.927    900   0.831   3212   0.900  0.951  0.9654  0.9734  0.9052  0.9396
  0.1348   4484   0.871    894   0.765   5378   0.854  1.003  0.9468  0.9576  0.8960  0.9404
  0.2243   5953   0.890    899   0.780   6852   0.876  1.054  0.9580  0.9637  0.9126  0.9428
  0.3138   7156   0.818    901   0.746   8057   0.810  0.819  0.9128  0.9312  0.8455  0.9007
 $$
Resolution limits                    =     41.964     1.670
Number of used reflections           =      23498
Percentage observed                  =    99.9879
Percentage of free reflections       =     5.0969
Overall R factor                     =     0.1817
Free R factor                        =     0.2259
Average Fourier shell correlation    =     0.9525
AverageFree Fourier shell correlation=     0.9405
Overall weighted R factor            =     0.1614
Free weighted R factor               =     0.2000
Overall weighted R2 factor           =     0.1926
Free weighted R2 factor              =     0.2368
Average correlation coefficient      =     0.9274
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9335
Cruickshanks DPI for coordinate error=     0.1041
DPI based on free R factor           =     0.1073
Overall figure of merit              =     0.8515
ML based su of positional parameters =     0.0653
ML based su of thermal parameters    =     1.9555
-----------------------------------------------------------------------------
  Time in seconds: CPU =        21.35
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1818   0.2264   0.822      120914.    6660.3   0.0132  0.994   1.847  1.075   0.092
       1   0.1819   0.2259   0.850      120063.    6637.4   0.0122  0.916   1.787  1.038   0.088
       2   0.1815   0.2259   0.852      119958.    6636.2   0.0130  0.979   1.822  1.059   0.091
       3   0.1816   0.2259   0.852      119937.    6636.3   0.0131  0.987   1.835  1.067   0.092
       4   0.1816   0.2259   0.852      119935.    6636.8   0.0131  0.989   1.840  1.070   0.092
       5   0.1817   0.2260   0.852      119937.    6636.9   0.0131  0.989   1.840  1.070   0.092
       6   0.1817   0.2260   0.852      119937.    6637.0   0.0131  0.989   1.841  1.070   0.092
       7   0.1817   0.2260   0.851      119940.    6637.3   0.0131  0.989   1.841  1.070   0.092
       8   0.1817   0.2259   0.851      119940.    6637.2   0.0131  0.989   1.841  1.070   0.092
       9   0.1817   0.2259   0.851      119940.    6637.4   0.0131  0.989   1.841  1.071   0.092
      10   0.1817   0.2259   0.851      119938.    6637.3   0.0131  0.989   1.841  1.071   0.092
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1818   0.1817
             R free    0.2264   0.2259
     Rms BondLength    0.0132   0.0131
      Rms BondAngle    1.8472   1.8413
     Rms ChirVolume    0.0916   0.0916
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      53.6s System:    0.1s Elapsed:     0:53