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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: 21:59:56 


 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 1.59     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_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-59A.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_1-59A.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       0.0989
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5900
  Estimated number of reflections :      36894
  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  1.5900

  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_1-60A.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=   2.193 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=   1.826 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=   2.217 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=   2.414 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=   2.393 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=   2.137 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       1457
Number of   all  reflections      28582
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28582

   Current auto weighting coefficient =    6.4745932    

 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.= 0.891 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   78
 Minimum acceptable grid spacing:    83   83  176
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   78
 Minimum acceptable grid spacing:    83   83  176
 Weight matrix   0.29059136    
 Actual weight    6.4745932      is applied to the X-ray term
Norm of X_ray positional gradient                36.7
Norm of Geom. positional gradient                82.3
Norm of X_ray B-factor gradient                  104.
Norm of Geom. B-factor gradient                  113.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.491
Product of X_ray and Geom B-fact gradients     -0.333E+08
 Cosine of angle between them                      -0.877


Residuals: XRAY=     0.8827E+06 GEOM=     0.1349E+05 TOTAL=     0.8962E+06
 function value    896156.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.857     1.644
Bond angles  : others                          3238     2.366     1.580
Torsion angles, period  1. refined              185     6.795     5.000
Torsion angles, period  2. refined               90    34.900    22.778
Torsion angles, period  3. refined              268    13.220    15.000
Torsion angles, period  4. refined                9    12.342    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   300     0.247     0.200
VDW repulsions.others                          1347     0.219     0.200
VDW; torsion: refined_atoms                     731     0.174     0.200
VDW; torsion.others                             719     0.082     0.200
HBOND: refined_atoms                            215     0.200     0.200
HBOND.others                                      2     0.047     0.200
VDW repulsions: symmetry: refined_atoms           8     0.205     0.200
VDW repulsions: symmetry: others                 22     0.208     0.200
HBOND: symmetry: refined_atoms                   22     0.224     0.200
M. chain bond B values: refined atoms           746     1.749     1.507
M. chain bond B values: others                  746     1.744     1.507
M. chain angle B values: refined atoms          929     2.726     2.251
M. chain angle B values: others                 930     2.725     2.251
S. chain bond B values: refined atoms           811     3.146     1.908
S. chain bond B values: others                  810     3.141     1.908
S. chain angle B values: refined atoms         1177     4.780     2.695
S. chain angle B values: others                1178     4.778     2.694
Long range B values: refined atoms             1848     7.281    20.822
Long range B values: others                    1759     7.033    19.427
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0443, B  =    0.1128
Partial structure    1: scale =     0.3865, B  =   41.4020
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.050    3674 100.00   429.1   438.7  0.17  0.17     173   430.8   437.3  0.20  0.21
 0.149    6229  99.97   256.2   240.6  0.17  0.15     351   260.1   239.2  0.23  0.20
 0.247    7931 100.00   162.2   146.6  0.19  0.17     421   168.0   153.1  0.22  0.19
 0.346    9275 100.00    68.9    82.9  0.33  0.26     512    66.5    81.5  0.38  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0499   2685   0.909    989   0.800   3674   0.879  0.948  0.9622  0.9689  0.9075  0.9373
  0.1487   5237   0.866    992   0.771   6229   0.851  1.022  0.9397  0.9551  0.8728  0.9375
  0.2474   6936   0.861    995   0.756   7931   0.848  1.052  0.9483  0.9552  0.9029  0.9378
  0.3462   8296   0.665    993   0.586   9289   0.656  0.700  0.8461  0.8673  0.8025  0.8630
 $$
Resolution limits                    =     41.964     1.590
Number of used reflections           =      27123
Percentage observed                  =    99.9895
Percentage of free reflections       =     5.0980
Overall R factor                     =     0.1938
Free R factor                        =     0.2368
Average Fourier shell correlation    =     0.9269
AverageFree Fourier shell correlation=     0.9120
Overall weighted R factor            =     0.1686
Free weighted R factor               =     0.2084
Overall weighted R2 factor           =     0.1994
Free weighted R2 factor              =     0.2443
Average correlation coefficient      =     0.9121
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9351
Cruickshanks DPI for coordinate error=     0.0955
DPI based on free R factor           =     0.0997
Overall figure of merit              =     0.7873
ML based su of positional parameters =     0.0723
ML based su of thermal parameters    =     2.1552
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    136327.48       13491.497       896156.50      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37706944    
 Actual weight    6.4745932      is applied to the X-ray term


 function value    883458.06    

-------------------------------------------------------------------------------
             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 =     0.0443, B  =   -0.0726
Partial structure    1: scale =     0.3862, B  =   41.5585
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1941
Free R factor                        =     0.2360
Average Fourier shell correlation    =     0.9401
AverageFree Fourier shell correlation=     0.9272
Average correlation coefficient      =     0.9107
Overall figure of merit              =     0.8278
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    135142.66       8464.4043       883458.06       896156.50    


     CGMAT cycle number =      3

 Weight matrix   0.38784251    
 Actual weight    6.4745932      is applied to the X-ray term


 function value    882526.88    

-------------------------------------------------------------------------------
             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 =     0.0443, B  =   -0.0148
Partial structure    1: scale =     0.3866, B  =   41.5859
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1936
Free R factor                        =     0.2358
Average Fourier shell correlation    =     0.9423
AverageFree Fourier shell correlation=     0.9293
Average correlation coefficient      =     0.9120
Overall figure of merit              =     0.8346
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    134937.75       8859.8330       882526.88       883458.06    


     CGMAT cycle number =      4

 Weight matrix   0.38918468    
 Actual weight    6.4745932      is applied to the X-ray term


 function value    882383.63    

-------------------------------------------------------------------------------
             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 =     0.0443, B  =   -0.0053
Partial structure    1: scale =     0.3868, B  =   41.5341
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1936
Free R factor                        =     0.2358
Average Fourier shell correlation    =     0.9426
AverageFree Fourier shell correlation=     0.9295
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8356
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    134898.36       8971.6191       882383.63       882526.88    


     CGMAT cycle number =      5

 Weight matrix   0.38895500    
 Actual weight    6.4745932      is applied to the X-ray term


 function value    882396.31    

-------------------------------------------------------------------------------
             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 =     0.0443, B  =    0.0025
Partial structure    1: scale =     0.3867, B  =   41.4432
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1936
Free R factor                        =     0.2358
Average Fourier shell correlation    =     0.9426
AverageFree Fourier shell correlation=     0.9294
Average correlation coefficient      =     0.9126
Overall figure of merit              =     0.8356
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03


 fvalues    134893.53       9016.9844       882408.31       882383.63    

 fvalues    134893.53       9016.9844       882401.94       882397.75    
 fvalues    134893.53       9016.9844       882401.94       882397.75    


     CGMAT cycle number =      6

 Weight matrix   0.38895515    
 Actual weight    6.4745932      is applied to the X-ray term


 function value    882395.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0443, B  =    0.0021
Partial structure    1: scale =     0.3867, B  =   41.4428
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1936
Free R factor                        =     0.2358
Average Fourier shell correlation    =     0.9426
AverageFree Fourier shell correlation=     0.9294
Average correlation coefficient      =     0.9126
Overall figure of merit              =     0.8356
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    134892.75       9020.0801       882395.75       882397.75    


     CGMAT cycle number =      7

 Weight matrix   0.38882139    
 Actual weight    6.4745932      is applied to the X-ray term


 function value    882395.56    

-------------------------------------------------------------------------------
             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 =     0.0443, B  =    0.0024
Partial structure    1: scale =     0.3867, B  =   41.4448
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1936
Free R factor                        =     0.2359
Average Fourier shell correlation    =     0.9426
AverageFree Fourier shell correlation=     0.9294
Average correlation coefficient      =     0.9127
Overall figure of merit              =     0.8356
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    134892.33       9022.6143       882395.56       882395.75    


     CGMAT cycle number =      8

 Weight matrix   0.38870567    
 Actual weight    6.4745932      is applied to the X-ray term


 function value    882405.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0443, B  =    0.0007
Partial structure    1: scale =     0.3867, B  =   41.4413
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1937
Free R factor                        =     0.2359
Average Fourier shell correlation    =     0.9426
AverageFree Fourier shell correlation=     0.9294
Average correlation coefficient      =     0.9127
Overall figure of merit              =     0.8355
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    134894.13       9020.1641       882402.88       882395.56    
 fvalues    134894.13       9020.1641       882402.88       882404.75    


     CGMAT cycle number =      9

 Weight matrix   0.38846108    
 Actual weight    6.4745932      is applied to the X-ray term


 function value    882405.44    

-------------------------------------------------------------------------------
             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 =     0.0443, B  =    0.0037
Partial structure    1: scale =     0.3867, B  =   41.4264
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1936
Free R factor                        =     0.2359
Average Fourier shell correlation    =     0.9426
AverageFree Fourier shell correlation=     0.9294
Average correlation coefficient      =     0.9127
Overall figure of merit              =     0.8355
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    134893.92       9021.7646       882415.81       882404.75    

 fvalues    134893.92       9021.7646       882414.19       882405.00    
 fvalues    134893.92       9021.7646       882414.19       882405.00    


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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   78
 Minimum acceptable grid spacing:    83   83  176
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   78
 Minimum acceptable grid spacing:    83   83  176
 Weight matrix   0.38836855    
 Actual weight    6.4745932      is applied to the X-ray term
Norm of X_ray positional gradient                44.0
Norm of Geom. positional gradient                44.0
Norm of X_ray B-factor gradient                  119.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.187E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.454E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8734E+06 GEOM=      9022.     TOTAL=     0.8824E+06
 function value    882413.56    

-------------------------------------------------------------------------------
             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     1.868     1.644
Bond angles  : others                          3238     1.525     1.580
Torsion angles, period  1. refined              185     6.799     5.000
Torsion angles, period  2. refined               90    34.877    22.778
Torsion angles, period  3. refined              268    13.257    15.000
Torsion angles, period  4. refined                9    12.459    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   302     0.246     0.200
VDW repulsions.others                          1354     0.196     0.200
VDW; torsion: refined_atoms                     727     0.174     0.200
VDW; torsion.others                             763     0.086     0.200
HBOND: refined_atoms                            210     0.202     0.200
HBOND.others                                      1     0.020     0.200
VDW repulsions: symmetry: refined_atoms           8     0.206     0.200
VDW repulsions: symmetry: others                 23     0.192     0.200
HBOND: symmetry: refined_atoms                   22     0.228     0.200
M. chain bond B values: refined atoms           746     1.759     1.517
M. chain bond B values: others                  746     1.755     1.517
M. chain angle B values: refined atoms          929     2.733     2.266
M. chain angle B values: others                 930     2.732     2.266
S. chain bond B values: refined atoms           811     3.157     1.918
S. chain bond B values: others                  810     3.153     1.918
S. chain angle B values: refined atoms         1177     4.797     2.710
S. chain angle B values: others                1178     4.795     2.710
Long range B values: refined atoms             1842     7.207    20.908
Long range B values: others                    1754     6.948    19.512
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0443, B  =    0.0040
Partial structure    1: scale =     0.3866, B  =   41.4194
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.050    3674 100.00   429.7   439.3  0.17  0.17     173   431.4   438.2  0.20  0.21
 0.149    6229  99.97   256.6   240.8  0.17  0.15     351   260.5   239.5  0.22  0.20
 0.247    7931 100.00   162.4   146.9  0.19  0.17     421   168.2   153.3  0.22  0.19
 0.346    9275 100.00    69.0    82.9  0.33  0.26     512    66.6    81.5  0.38  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0499   2685   0.924    989   0.822   3674   0.896  0.950  0.9659  0.9723  0.9079  0.9373
  0.1487   5237   0.871    992   0.776   6229   0.856  1.022  0.9412  0.9562  0.8747  0.9374
  0.2474   6936   0.874    995   0.769   7931   0.860  1.052  0.9520  0.9588  0.9038  0.9375
  0.3462   8296   0.785    993   0.708   9289   0.776  0.750  0.8903  0.9080  0.8036  0.8650
 $$
Resolution limits                    =     41.964     1.590
Number of used reflections           =      27123
Percentage observed                  =    99.9895
Percentage of free reflections       =     5.0980
Overall R factor                     =     0.1937
Free R factor                        =     0.2359
Average Fourier shell correlation    =     0.9426
AverageFree Fourier shell correlation=     0.9294
Overall weighted R factor            =     0.1687
Free weighted R factor               =     0.2075
Overall weighted R2 factor           =     0.1995
Free weighted R2 factor              =     0.2432
Average correlation coefficient      =     0.9127
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9356
Cruickshanks DPI for coordinate error=     0.0955
DPI based on free R factor           =     0.0993
Overall figure of merit              =     0.8355
ML based su of positional parameters =     0.0625
ML based su of thermal parameters    =     1.8100
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    134894.98       9022.1611       882417.88       882405.00    

 fvalues    134894.98       9022.1611       882413.31       882412.31    
 fvalues    134894.98       9022.1611       882413.31       882412.31    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.903 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 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_1-59A.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     1.868     1.644
Bond angles  : others                          3238     1.525     1.580
Torsion angles, period  1. refined              185     6.799     5.000
Torsion angles, period  2. refined               90    34.876    22.778
Torsion angles, period  3. refined              268    13.258    15.000
Torsion angles, period  4. refined                9    12.459    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   302     0.246     0.200
VDW repulsions.others                          1354     0.196     0.200
VDW; torsion: refined_atoms                     727     0.174     0.200
VDW; torsion.others                             763     0.086     0.200
HBOND: refined_atoms                            210     0.202     0.200
HBOND.others                                      1     0.020     0.200
VDW repulsions: symmetry: refined_atoms           8     0.206     0.200
VDW repulsions: symmetry: others                 23     0.192     0.200
HBOND: symmetry: refined_atoms                   22     0.228     0.200
M. chain bond B values: refined atoms           746     1.759     1.517
M. chain bond B values: others                  746     1.755     1.517
M. chain angle B values: refined atoms          929     2.733     2.266
M. chain angle B values: others                 930     2.732     2.266
S. chain bond B values: refined atoms           811     3.157     1.918
S. chain bond B values: others                  810     3.153     1.918
S. chain angle B values: refined atoms         1177     4.797     2.710
S. chain angle B values: others                1178     4.795     2.710
Long range B values: refined atoms             1842     7.207    20.908
Long range B values: others                    1754     6.948    19.511
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0443, B  =    0.0031
Partial structure    1: scale =     0.3866, B  =   41.4209
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.050    3674 100.00   429.7   439.3  0.17  0.17     173   431.4   438.2  0.20  0.21
 0.149    6229  99.97   256.6   240.8  0.17  0.15     351   260.5   239.5  0.22  0.20
 0.247    7931 100.00   162.4   146.9  0.19  0.17     421   168.2   153.3  0.22  0.19
 0.346    9275 100.00    69.0    82.9  0.33  0.26     512    66.6    81.5  0.38  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0499   2685   0.924    989   0.822   3674   0.896  0.950  0.9659  0.9723  0.9079  0.9374
  0.1487   5237   0.871    992   0.776   6229   0.856  1.022  0.9412  0.9562  0.8746  0.9374
  0.2474   6936   0.874    995   0.769   7931   0.860  1.052  0.9520  0.9588  0.9038  0.9375
  0.3462   8296   0.785    993   0.708   9289   0.776  0.750  0.8903  0.9080  0.8036  0.8651
 $$
Resolution limits                    =     41.964     1.590
Number of used reflections           =      27123
Percentage observed                  =    99.9895
Percentage of free reflections       =     5.0980
Overall R factor                     =     0.1937
Free R factor                        =     0.2359
Average Fourier shell correlation    =     0.9426
AverageFree Fourier shell correlation=     0.9294
Overall weighted R factor            =     0.1687
Free weighted R factor               =     0.2075
Overall weighted R2 factor           =     0.1995
Free weighted R2 factor              =     0.2432
Average correlation coefficient      =     0.9127
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9356
Cruickshanks DPI for coordinate error=     0.0955
DPI based on free R factor           =     0.0993
Overall figure of merit              =     0.8355
ML based su of positional parameters =     0.0625
ML based su of thermal parameters    =     1.8100
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.38
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1938   0.2368   0.787      136327.    7487.5   0.0132  0.987   1.857  1.081   0.090
       1   0.1941   0.2360   0.828      135143.    7443.8   0.0120  0.904   1.792  1.041   0.087
       2   0.1936   0.2358   0.835      134938.    7436.8   0.0131  0.981   1.834  1.067   0.089
       3   0.1936   0.2358   0.836      134898.    7435.9   0.0132  0.991   1.853  1.078   0.090
       4   0.1936   0.2358   0.836      134893.    7436.1   0.0133  0.994   1.862  1.084   0.090
       5   0.1936   0.2358   0.836      134893.    7436.2   0.0133  0.994   1.863  1.084   0.090
       6   0.1936   0.2359   0.836      134892.    7436.4   0.0133  0.995   1.865  1.085   0.090
       7   0.1937   0.2359   0.836      134894.    7436.8   0.0133  0.995   1.866  1.086   0.090
       8   0.1936   0.2359   0.835      134894.    7436.7   0.0133  0.995   1.867  1.087   0.090
       9   0.1937   0.2359   0.835      134895.    7436.8   0.0133  0.995   1.868  1.087   0.090
      10   0.1937   0.2359   0.835      134895.    7436.8   0.0133  0.995   1.868  1.087   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1938   0.1937
             R free    0.2368   0.2359
     Rms BondLength    0.0132   0.0133
      Rms BondAngle    1.8570   1.8679
     Rms ChirVolume    0.0900   0.0901
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      55.7s System:    0.2s Elapsed:     0:56