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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: 20:48:08 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.62     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_1-63A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-62A.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_1-62A.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       0.0953
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6200
  Estimated number of reflections :      34473
  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  1.6200

  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_1-63A.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=   2.043 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=   2.198 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=   1.831 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=   2.225 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=   2.416 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=   2.396 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=   2.141 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       1378
Number of   all  reflections      27066
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          27066

   Current auto weighting coefficient =    6.5496740    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.897 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   76
 Minimum acceptable grid spacing:    82   82  173
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   76
 Minimum acceptable grid spacing:    82   82  173
 Weight matrix   0.29525235    
 Actual weight    6.5496740      is applied to the X-ray term
Norm of X_ray positional gradient                37.1
Norm of Geom. positional gradient                82.7
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.486
Product of X_ray and Geom B-fact gradients     -0.350E+08
 Cosine of angle between them                      -0.871


Residuals: XRAY=     0.8529E+06 GEOM=     0.1362E+05 TOTAL=     0.8666E+06
 function value    866551.88    

-------------------------------------------------------------------------------
             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     1.860     1.644
Bond angles  : others                          3238     2.370     1.580
Torsion angles, period  1. refined              185     6.802     5.000
Torsion angles, period  2. refined               90    35.046    22.778
Torsion angles, period  3. refined              268    13.193    15.000
Torsion angles, period  4. refined                9    12.507    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.018     0.020
VDW repulsions: refined_atoms                   300     0.247     0.200
VDW repulsions.others                          1339     0.220     0.200
VDW; torsion: refined_atoms                     726     0.174     0.200
VDW; torsion.others                             722     0.082     0.200
HBOND: refined_atoms                            216     0.204     0.200
HBOND.others                                      2     0.041     0.200
VDW repulsions: symmetry: refined_atoms           8     0.207     0.200
VDW repulsions: symmetry: others                 23     0.203     0.200
HBOND: symmetry: refined_atoms                   22     0.173     0.200
M. chain bond B values: refined atoms           746     1.749     1.471
M. chain bond B values: others                  746     1.744     1.471
M. chain angle B values: refined atoms          929     2.718     2.197
M. chain angle B values: others                 930     2.718     2.197
S. chain bond B values: refined atoms           811     3.123     1.871
S. chain bond B values: others                  810     3.118     1.871
S. chain angle B values: refined atoms         1177     4.757     2.639
S. chain angle B values: others                1178     4.755     2.639
Long range B values: refined atoms             1847     7.206    20.454
Long range B values: others                    1754     6.900    18.987
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0439, B  =    0.1201
Partial structure    1: scale =     0.3862, B  =   41.6327
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.048    3483 100.00   436.8   446.2  0.16  0.17     162   433.4   443.2  0.20  0.21
 0.143    5892  99.97   265.6   251.5  0.17  0.15     335   272.4   251.2  0.23  0.20
 0.238    7494 100.00   174.9   157.9  0.18  0.16     409   179.7   163.3  0.21  0.19
 0.333    8811 100.00    76.7    90.7  0.30  0.24     472    72.1    87.5  0.36  0.29
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0481   2535   0.910    948   0.810   3483   0.883  0.949  0.9618  0.9693  0.9065  0.9375
  0.1432   4935   0.867    957   0.763   5892   0.850  1.013  0.9426  0.9562  0.8836  0.9383
  0.2384   6541   0.870    953   0.759   7494   0.856  1.056  0.9514  0.9574  0.9062  0.9397
  0.3335   7855   0.709    962   0.629   8817   0.700  0.743  0.8646  0.8904  0.8192  0.8784
 $$
Resolution limits                    =     41.964     1.620
Number of used reflections           =      25686
Percentage observed                  =    99.9889
Percentage of free reflections       =     5.0916
Overall R factor                     =     0.1896
Free R factor                        =     0.2325
Average Fourier shell correlation    =     0.9358
AverageFree Fourier shell correlation=     0.9207
Overall weighted R factor            =     0.1664
Free weighted R factor               =     0.2059
Overall weighted R2 factor           =     0.1977
Free weighted R2 factor              =     0.2417
Average correlation coefficient      =     0.9181
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9344
Cruickshanks DPI for coordinate error=     0.0989
DPI based on free R factor           =     0.1025
Overall figure of merit              =     0.8049
ML based su of positional parameters =     0.0722
ML based su of thermal parameters    =     2.1664
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    130225.14       13619.632       866551.88      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37545982    
 Actual weight    6.5496740      is applied to the X-ray term


 function value    854498.25    

-------------------------------------------------------------------------------
             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 =     0.0439, B  =   -0.0601
Partial structure    1: scale =     0.3869, B  =   41.8689
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1898
Free R factor                        =     0.2316
Average Fourier shell correlation    =     0.9461
AverageFree Fourier shell correlation=     0.9331
Average correlation coefficient      =     0.9172
Overall figure of merit              =     0.8404
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    129159.54       8545.3867       854498.25       866551.88    


     CGMAT cycle number =      3

 Weight matrix   0.38620844    
 Actual weight    6.5496740      is applied to the X-ray term


 function value    853864.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0439, B  =   -0.0238
Partial structure    1: scale =     0.3865, B  =   41.9808
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1894
Free R factor                        =     0.2314
Average Fourier shell correlation    =     0.9474
AverageFree Fourier shell correlation=     0.9344
Average correlation coefficient      =     0.9183
Overall figure of merit              =     0.8451
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    129008.51       8901.1113       853864.81       854498.25    


     CGMAT cycle number =      4

 Weight matrix   0.38621417    
 Actual weight    6.5496740      is applied to the X-ray term


 function value    853808.56    

-------------------------------------------------------------------------------
             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 =     0.0439, B  =   -0.0002
Partial structure    1: scale =     0.3865, B  =   41.9814
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1894
Free R factor                        =     0.2314
Average Fourier shell correlation    =     0.9475
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9187
Overall figure of merit              =     0.8454
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    128981.52       9021.6445       853808.56       853864.81    


     CGMAT cycle number =      5

 Weight matrix   0.38657084    
 Actual weight    6.5496740      is applied to the X-ray term


 function value    853802.75    

-------------------------------------------------------------------------------
             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 =     0.0439, B  =   -0.0046
Partial structure    1: scale =     0.3865, B  =   41.9406
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1894
Free R factor                        =     0.2314
Average Fourier shell correlation    =     0.9476
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9188
Overall figure of merit              =     0.8455
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    128974.74       9060.2656       853802.75       853808.56    


     CGMAT cycle number =      6

 Weight matrix   0.38618401    
 Actual weight    6.5496740      is applied to the X-ray term


 function value    853804.88    

-------------------------------------------------------------------------------
             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 =     0.0439, B  =   -0.0004
Partial structure    1: scale =     0.3865, B  =   41.9233
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1894
Free R factor                        =     0.2314
Average Fourier shell correlation    =     0.9476
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9189
Overall figure of merit              =     0.8454
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    128972.94       9075.3477       853817.88       853802.75    

 fvalues    128972.94       9075.3477       853812.50       853806.06    
 fvalues    128972.94       9075.3477       853812.50       853806.06    


     CGMAT cycle number =      7

 Weight matrix   0.38610590    
 Actual weight    6.5496740      is applied to the X-ray term


 function value    853806.38    

-------------------------------------------------------------------------------
             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 =     0.0439, B  =   -0.0000
Partial structure    1: scale =     0.3865, B  =   41.9033
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1894
Free R factor                        =     0.2314
Average Fourier shell correlation    =     0.9476
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9189
Overall figure of merit              =     0.8454
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    128973.02       9075.1318       853825.00       853806.06    

 fvalues    128973.02       9075.1318       853814.13       853806.38    
 fvalues    128973.02       9075.1318       853814.13       853806.38    


     CGMAT cycle number =      8

 Weight matrix   0.38614553    
 Actual weight    6.5496740      is applied to the X-ray term


 function value    853822.50    

-------------------------------------------------------------------------------
             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 =     0.0439, B  =   -0.0031
Partial structure    1: scale =     0.3865, B  =   41.8087
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1894
Free R factor                        =     0.2315
Average Fourier shell correlation    =     0.9476
AverageFree Fourier shell correlation=     0.9345
Average correlation coefficient      =     0.9189
Overall figure of merit              =     0.8454
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    128976.65       9073.8564       853833.19       853806.38    

 fvalues    128976.65       9073.8564       853831.81       853828.88    
 fvalues    128976.65       9073.8564       853831.81       853828.88    


     CGMAT cycle number =      9

 Weight matrix   0.38612959    
 Actual weight    6.5496740      is applied to the X-ray term


 function value    853831.63    

-------------------------------------------------------------------------------
             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 =     0.0439, B  =   -0.0035
Partial structure    1: scale =     0.3866, B  =   41.7858
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1894
Free R factor                        =     0.2315
Average Fourier shell correlation    =     0.9476
AverageFree Fourier shell correlation=     0.9344
Average correlation coefficient      =     0.9189
Overall figure of merit              =     0.8454
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    128977.05       9073.9961       853835.25       853828.88    

 fvalues    128977.05       9073.9961       853835.50       853831.69    
 fvalues    128977.05       9073.9961       853835.50       853831.69    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   76
 Minimum acceptable grid spacing:    82   82  173
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    36   36   76
 Minimum acceptable grid spacing:    82   82  173
 Weight matrix   0.38596922    
 Actual weight    6.5496740      is applied to the X-ray term
Norm of X_ray positional gradient                43.8
Norm of Geom. positional gradient                43.8
Norm of X_ray B-factor gradient                  121.
Norm of Geom. B-factor gradient                  120.
Product of X_ray and Geom posit. gradients     -0.186E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.468E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8448E+06 GEOM=      9074.     TOTAL=     0.8538E+06
 function value    853836.56    

-------------------------------------------------------------------------------
             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     1.867     1.644
Bond angles  : others                          3238     1.522     1.580
Torsion angles, period  1. refined              185     6.789     5.000
Torsion angles, period  2. refined               90    35.031    22.778
Torsion angles, period  3. refined              268    13.224    15.000
Torsion angles, period  4. refined                9    12.391    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.247     0.200
VDW repulsions.others                          1353     0.196     0.200
VDW; torsion: refined_atoms                     728     0.174     0.200
VDW; torsion.others                             741     0.087     0.200
HBOND: refined_atoms                            212     0.204     0.200
HBOND.others                                      1     0.036     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 24     0.187     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           746     1.751     1.484
M. chain bond B values: others                  746     1.747     1.484
M. chain angle B values: refined atoms          929     2.722     2.217
M. chain angle B values: others                 930     2.721     2.217
S. chain bond B values: refined atoms           811     3.130     1.883
S. chain bond B values: others                  810     3.126     1.883
S. chain angle B values: refined atoms         1177     4.766     2.658
S. chain angle B values: others                1178     4.764     2.657
Long range B values: refined atoms             1844     7.190    20.579
Long range B values: others                    1754     6.918    19.157
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0439, B  =   -0.0013
Partial structure    1: scale =     0.3866, B  =   41.7848
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.048    3483 100.00   437.3   446.6  0.17  0.17     162   433.9   443.6  0.20  0.21
 0.143    5892  99.97   265.9   251.5  0.17  0.15     335   272.7   251.3  0.23  0.20
 0.238    7494 100.00   175.1   158.2  0.18  0.16     409   179.9   163.5  0.21  0.19
 0.333    8811 100.00    76.8    90.7  0.30  0.24     472    72.2    87.5  0.36  0.29
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0481   2535   0.924    948   0.830   3483   0.898  0.951  0.9652  0.9722  0.9068  0.9371
  0.1432   4935   0.871    957   0.767   5892   0.854  1.013  0.9438  0.9573  0.8853  0.9388
  0.2384   6541   0.882    953   0.773   7494   0.868  1.056  0.9548  0.9609  0.9070  0.9399
  0.3335   7855   0.808    962   0.734   8817   0.800  0.781  0.8996  0.9201  0.8216  0.8806
 $$
Resolution limits                    =     41.964     1.620
Number of used reflections           =      25686
Percentage observed                  =    99.9889
Percentage of free reflections       =     5.0916
Overall R factor                     =     0.1894
Free R factor                        =     0.2315
Average Fourier shell correlation    =     0.9476
AverageFree Fourier shell correlation=     0.9344
Overall weighted R factor            =     0.1663
Free weighted R factor               =     0.2049
Overall weighted R2 factor           =     0.1977
Free weighted R2 factor              =     0.2406
Average correlation coefficient      =     0.9189
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9350
Cruickshanks DPI for coordinate error=     0.0988
DPI based on free R factor           =     0.1020
Overall figure of merit              =     0.8454
ML based su of positional parameters =     0.0631
ML based su of thermal parameters    =     1.8395
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    128977.89       9074.0479       853833.38       853831.69    
 fvalues    128977.89       9074.0479       853833.38       853837.19    

    ****                              VDW outliers                              ****

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

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

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_step0-01A_R00_1-62A.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     1.867     1.644
Bond angles  : others                          3238     1.522     1.580
Torsion angles, period  1. refined              185     6.789     5.000
Torsion angles, period  2. refined               90    35.031    22.778
Torsion angles, period  3. refined              268    13.224    15.000
Torsion angles, period  4. refined                9    12.390    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.247     0.200
VDW repulsions.others                          1355     0.195     0.200
VDW; torsion: refined_atoms                     728     0.174     0.200
VDW; torsion.others                             741     0.087     0.200
HBOND: refined_atoms                            212     0.204     0.200
HBOND.others                                      1     0.036     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 24     0.187     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           746     1.751     1.484
M. chain bond B values: others                  746     1.747     1.484
M. chain angle B values: refined atoms          929     2.722     2.217
M. chain angle B values: others                 930     2.721     2.217
S. chain bond B values: refined atoms           811     3.130     1.883
S. chain bond B values: others                  810     3.126     1.883
S. chain angle B values: refined atoms         1177     4.766     2.658
S. chain angle B values: others                1178     4.764     2.657
Long range B values: refined atoms             1844     7.190    20.579
Long range B values: others                    1754     6.918    19.157
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0439, B  =   -0.0026
Partial structure    1: scale =     0.3866, B  =   41.7840
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.048    3483 100.00   437.3   446.6  0.17  0.17     162   433.9   443.6  0.20  0.21
 0.143    5892  99.97   265.9   251.6  0.17  0.15     335   272.7   251.3  0.23  0.20
 0.238    7494 100.00   175.1   158.2  0.18  0.16     409   179.9   163.5  0.21  0.19
 0.333    8811 100.00    76.8    90.8  0.30  0.24     472    72.2    87.5  0.36  0.29
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0481   2535   0.924    948   0.830   3483   0.898  0.951  0.9652  0.9722  0.9068  0.9371
  0.1432   4935   0.871    957   0.767   5892   0.854  1.013  0.9438  0.9573  0.8853  0.9388
  0.2384   6541   0.882    953   0.773   7494   0.868  1.056  0.9548  0.9609  0.9070  0.9399
  0.3335   7855   0.808    962   0.734   8817   0.800  0.781  0.8996  0.9201  0.8216  0.8806
 $$
Resolution limits                    =     41.964     1.620
Number of used reflections           =      25686
Percentage observed                  =    99.9889
Percentage of free reflections       =     5.0916
Overall R factor                     =     0.1894
Free R factor                        =     0.2315
Average Fourier shell correlation    =     0.9476
AverageFree Fourier shell correlation=     0.9344
Overall weighted R factor            =     0.1663
Free weighted R factor               =     0.2049
Overall weighted R2 factor           =     0.1977
Free weighted R2 factor              =     0.2406
Average correlation coefficient      =     0.9189
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9350
Cruickshanks DPI for coordinate error=     0.0988
DPI based on free R factor           =     0.1020
Overall figure of merit              =     0.8454
ML based su of positional parameters =     0.0631
ML based su of thermal parameters    =     1.8395
-----------------------------------------------------------------------------
  Time in seconds: CPU =        25.17
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1896   0.2325   0.805      130225.    7154.1   0.0133  0.996   1.860  1.083   0.091
       1   0.1898   0.2316   0.840      129160.    7115.3   0.0121  0.909   1.790  1.041   0.087
       2   0.1894   0.2314   0.845      129009.    7110.7   0.0131  0.979   1.831  1.066   0.090
       3   0.1894   0.2314   0.845      128982.    7110.4   0.0132  0.990   1.851  1.078   0.091
       4   0.1894   0.2314   0.846      128975.    7110.5   0.0133  0.992   1.860  1.084   0.091
       5   0.1894   0.2314   0.845      128973.    7110.8   0.0133  0.994   1.865  1.087   0.091
       6   0.1894   0.2314   0.845      128973.    7110.9   0.0133  0.994   1.866  1.087   0.091
       7   0.1894   0.2315   0.845      128976.    7111.2   0.0133  0.994   1.866  1.087   0.091
       8   0.1894   0.2315   0.845      128977.    7111.3   0.0133  0.994   1.867  1.087   0.091
       9   0.1894   0.2315   0.845      128978.    7111.3   0.0133  0.994   1.867  1.087   0.091
      10   0.1894   0.2315   0.845      128977.    7111.3   0.0133  0.994   1.867  1.087   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1896   0.1894
             R free    0.2325   0.2315
     Rms BondLength    0.0133   0.0133
      Rms BondAngle    1.8599   1.8666
     Rms ChirVolume    0.0913   0.0913
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      57.3s System:    0.1s Elapsed:     0:57