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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: 15:38:18 


 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 1.79     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_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-79A.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_1-79A.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       0.0780
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7900
  Estimated number of reflections :      26299
  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  1.7900

  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_1-80A.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=   2.059 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=   2.213 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=   1.864 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=   2.204 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=   2.423 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=   2.405 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=   2.140 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       1019
Number of   all  reflections      20218
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          20218

   Current auto weighting coefficient =    6.9745569    

 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.= 0.924 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  161
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  161
 Weight matrix   0.26224557    
 Actual weight    6.9745569      is applied to the X-ray term
Norm of X_ray positional gradient                34.6
Norm of Geom. positional gradient                79.1
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.112E+08
 Cosine of angle between them                      -0.423
Product of X_ray and Geom B-fact gradients     -0.396E+08
 Cosine of angle between them                      -0.927


Residuals: XRAY=     0.7131E+06 GEOM=     0.1319E+05 TOTAL=     0.7263E+06
 function value    726259.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.801     1.644
Bond angles  : others                          3238     2.355     1.580
Torsion angles, period  1. refined              185     6.928     5.000
Torsion angles, period  2. refined               90    35.787    22.778
Torsion angles, period  3. refined              268    13.397    15.000
Torsion angles, period  4. refined                9    12.007    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   296     0.245     0.200
VDW repulsions.others                          1332     0.218     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             725     0.080     0.200
HBOND: refined_atoms                            222     0.200     0.200
HBOND.others                                      1     0.032     0.200
VDW repulsions: symmetry: refined_atoms           8     0.218     0.200
VDW repulsions: symmetry: others                 22     0.203     0.200
HBOND: symmetry: refined_atoms                   24     0.183     0.200
M. chain bond B values: refined atoms           746     1.618     1.293
M. chain bond B values: others                  746     1.616     1.293
M. chain angle B values: refined atoms          929     2.551     1.925
M. chain angle B values: others                 930     2.550     1.925
S. chain bond B values: refined atoms           811     2.779     1.660
S. chain bond B values: others                  810     2.775     1.659
S. chain angle B values: refined atoms         1177     4.331     2.333
S. chain angle B values: others                1178     4.329     2.333
Long range B values: refined atoms             1847     6.859    17.960
Long range B values: others                    1750     6.489    16.472
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0415, B  =    0.0610
Partial structure    1: scale =     0.3799, B  =   44.4066
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.040    2620 100.00   470.5   478.7  0.16  0.17     122   466.9   475.9  0.20  0.22
 0.117    4414 100.00   337.3   323.1  0.16  0.15     241   332.1   306.3  0.22  0.20
 0.195    5602  99.97   223.1   211.2  0.16  0.14     299   236.9   225.0  0.20  0.17
 0.273    6555 100.00   142.9   149.8  0.20  0.15     357   146.5   154.0  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0395   1839   0.913    781   0.809   2620   0.882  0.952  0.9619  0.9696  0.9074  0.9410
  0.1174   3635   0.874    779   0.774   4414   0.857  0.994  0.9440  0.9603  0.8860  0.9440
  0.1953   4822   0.878    780   0.763   5602   0.862  1.015  0.9522  0.9596  0.9041  0.9389
  0.2732   5776   0.815    785   0.737   6561   0.806  0.894  0.9331  0.9438  0.8718  0.9247
 $$
Resolution limits                    =     41.964     1.790
Number of used reflections           =      19197
Percentage observed                  =    99.9852
Percentage of free reflections       =     5.0406
Overall R factor                     =     0.1683
Free R factor                        =     0.2195
Average Fourier shell correlation    =     0.9557
AverageFree Fourier shell correlation=     0.9447
Overall weighted R factor            =     0.1537
Free weighted R factor               =     0.1995
Overall weighted R2 factor           =     0.1863
Free weighted R2 factor              =     0.2375
Average correlation coefficient      =     0.9355
Overall correlation coefficient      =     0.9568
Free correlation coefficient         =     0.9228
Cruickshanks DPI for coordinate error=     0.1206
DPI based on free R factor           =     0.1236
Overall figure of merit              =     0.8443
ML based su of positional parameters =     0.0791
ML based su of thermal parameters    =     2.5254
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    102238.73       13189.555       726259.44      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.29537898    
 Actual weight    6.9745569      is applied to the X-ray term


 function value    718394.06    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0788
Partial structure    1: scale =     0.3796, B  =   44.3082
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1682
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9590
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8595
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    101780.85       8517.7578       718394.06       726259.44    


     CGMAT cycle number =      3

 Weight matrix   0.29684243    
 Actual weight    6.9745569      is applied to the X-ray term


 function value    718070.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0539
Partial structure    1: scale =     0.3793, B  =   44.1288
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1678
Free R factor                        =     0.2184
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9483
Average correlation coefficient      =     0.9362
Overall figure of merit              =     0.8599
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    101699.41       8761.7988       718070.19       718394.06    


     CGMAT cycle number =      4

 Weight matrix   0.29689929    
 Actual weight    6.9745569      is applied to the X-ray term


 function value    718052.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0468
Partial structure    1: scale =     0.3792, B  =   43.9796
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1678
Free R factor                        =     0.2185
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9483
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8599
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    101688.87       8817.4639       718052.25       718070.19    


     CGMAT cycle number =      5

 Weight matrix   0.29695082    
 Actual weight    6.9745569      is applied to the X-ray term


 function value    718037.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0455
Partial structure    1: scale =     0.3791, B  =   43.9392
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1678
Free R factor                        =     0.2185
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9483
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8599
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    101684.30       8834.6514       718037.63       718052.25    


     CGMAT cycle number =      6

 Weight matrix   0.29698670    
 Actual weight    6.9745569      is applied to the X-ray term


 function value    718006.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0425
Partial structure    1: scale =     0.3792, B  =   43.9633
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1678
Free R factor                        =     0.2186
Average Fourier shell correlation    =     0.9593
AverageFree Fourier shell correlation=     0.9483
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8599
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    101679.27       8838.4912       718006.38       718037.63    


     CGMAT cycle number =      7

 Weight matrix   0.29678756    
 Actual weight    6.9745569      is applied to the X-ray term


 function value    717994.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0445
Partial structure    1: scale =     0.3793, B  =   43.9232
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1679
Free R factor                        =     0.2187
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9483
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8599
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    101678.37       8832.8691       717994.44       718006.38    


     CGMAT cycle number =      8

 Weight matrix   0.29667148    
 Actual weight    6.9745569      is applied to the X-ray term


 function value    717983.50    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0463
Partial structure    1: scale =     0.3794, B  =   43.8384
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1679
Free R factor                        =     0.2186
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9483
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8599
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    101677.50       8828.0254       717983.50       717994.44    


     CGMAT cycle number =      9

 Weight matrix   0.29638001    
 Actual weight    6.9745569      is applied to the X-ray term


 function value    718004.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0421
Partial structure    1: scale =     0.3794, B  =   43.8444
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1680
Free R factor                        =     0.2186
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9483
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8599
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    101682.74       8819.6836       718009.94       717983.50    
 fvalues    101682.74       8819.6836       718009.94       718011.75    


     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.= 0.933 id.= 3.000 dev= -2.07 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  161
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  161
 Weight matrix   0.29652563    
 Actual weight    6.9745569      is applied to the X-ray term
Norm of X_ray positional gradient                37.5
Norm of Geom. positional gradient                37.5
Norm of X_ray B-factor gradient                  121.
Norm of Geom. B-factor gradient                  123.
Product of X_ray and Geom posit. gradients     -0.136E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.480E+08
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.7092E+06 GEOM=      8820.     TOTAL=     0.7180E+06
 function value    717988.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.810     1.644
Bond angles  : others                          3238     1.483     1.580
Torsion angles, period  1. refined              185     6.921     5.000
Torsion angles, period  2. refined               90    35.749    22.778
Torsion angles, period  3. refined              268    13.305    15.000
Torsion angles, period  4. refined                9    12.001    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.242     0.200
VDW repulsions.others                          1355     0.191     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             794     0.084     0.200
HBOND: refined_atoms                            221     0.198     0.200
HBOND.others                                      1     0.002     0.200
VDW repulsions: symmetry: refined_atoms           8     0.218     0.200
VDW repulsions: symmetry: others                 22     0.186     0.200
HBOND: symmetry: refined_atoms                   23     0.191     0.200
M. chain bond B values: refined atoms           746     1.633     1.303
M. chain bond B values: others                  746     1.631     1.303
M. chain angle B values: refined atoms          929     2.568     1.940
M. chain angle B values: others                 930     2.566     1.940
S. chain bond B values: refined atoms           811     2.834     1.676
S. chain bond B values: others                  810     2.829     1.676
S. chain angle B values: refined atoms         1177     4.403     2.356
S. chain angle B values: others                1178     4.401     2.355
Long range B values: refined atoms             1851     6.850    18.107
Long range B values: others                    1756     6.536    16.658
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0422
Partial structure    1: scale =     0.3795, B  =   43.8470
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.040    2620 100.00   470.9   479.2  0.16  0.17     122   467.3   476.5  0.20  0.22
 0.117    4414 100.00   337.5   323.2  0.16  0.15     241   332.3   306.8  0.22  0.20
 0.195    5602  99.97   223.3   211.4  0.16  0.14     299   237.1   225.0  0.21  0.18
 0.273    6555 100.00   143.0   149.8  0.20  0.15     357   146.6   154.2  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0395   1839   0.926    781   0.824   2620   0.896  0.955  0.9651  0.9723  0.9084  0.9414
  0.1174   3635   0.877    779   0.776   4414   0.859  0.994  0.9454  0.9609  0.8880  0.9431
  0.1953   4822   0.881    780   0.767   5602   0.865  1.015  0.9529  0.9603  0.9052  0.9392
  0.2732   5776   0.852    785   0.769   6561   0.842  0.904  0.9407  0.9520  0.8741  0.9271
 $$
Resolution limits                    =     41.964     1.790
Number of used reflections           =      19197
Percentage observed                  =    99.9852
Percentage of free reflections       =     5.0406
Overall R factor                     =     0.1680
Free R factor                        =     0.2186
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9483
Overall weighted R factor            =     0.1537
Free weighted R factor               =     0.1985
Overall weighted R2 factor           =     0.1864
Free weighted R2 factor              =     0.2363
Average correlation coefficient      =     0.9363
Overall correlation coefficient      =     0.9569
Free correlation coefficient         =     0.9238
Cruickshanks DPI for coordinate error=     0.1204
DPI based on free R factor           =     0.1231
Overall figure of merit              =     0.8599
ML based su of positional parameters =     0.0743
ML based su of thermal parameters    =     2.3408
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    101679.38       8820.1143       717988.75       718011.75    

    ****                              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.= 0.933 id.= 3.000 dev= -2.07 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_1-79A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.810     1.644
Bond angles  : others                          3238     1.483     1.580
Torsion angles, period  1. refined              185     6.919     5.000
Torsion angles, period  2. refined               90    35.749    22.778
Torsion angles, period  3. refined              268    13.301    15.000
Torsion angles, period  4. refined                9    12.002    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   303     0.242     0.200
VDW repulsions.others                          1354     0.191     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             796     0.084     0.200
HBOND: refined_atoms                            222     0.198     0.200
HBOND.others                                      1     0.003     0.200
VDW repulsions: symmetry: refined_atoms           8     0.219     0.200
VDW repulsions: symmetry: others                 22     0.186     0.200
HBOND: symmetry: refined_atoms                   24     0.188     0.200
M. chain bond B values: refined atoms           746     1.633     1.303
M. chain bond B values: others                  746     1.631     1.303
M. chain angle B values: refined atoms          929     2.567     1.940
M. chain angle B values: others                 930     2.566     1.940
S. chain bond B values: refined atoms           811     2.835     1.676
S. chain bond B values: others                  810     2.830     1.676
S. chain angle B values: refined atoms         1177     4.405     2.356
S. chain angle B values: others                1178     4.403     2.356
Long range B values: refined atoms             1852     6.851    18.111
Long range B values: others                    1757     6.535    16.661
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0458
Partial structure    1: scale =     0.3796, B  =   43.8724
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.040    2620 100.00   470.9   479.2  0.16  0.17     122   467.3   476.6  0.20  0.22
 0.117    4414 100.00   337.6   323.2  0.16  0.15     241   332.4   306.9  0.22  0.20
 0.195    5602  99.97   223.3   211.4  0.16  0.14     299   237.1   225.0  0.21  0.18
 0.273    6555 100.00   143.0   149.8  0.20  0.15     357   146.6   154.2  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0395   1839   0.926    781   0.824   2620   0.896  0.955  0.9651  0.9723  0.9084  0.9414
  0.1174   3635   0.877    779   0.776   4414   0.859  0.994  0.9454  0.9608  0.8879  0.9431
  0.1953   4822   0.881    780   0.767   5602   0.865  1.015  0.9529  0.9603  0.9051  0.9391
  0.2732   5776   0.852    785   0.769   6561   0.842  0.904  0.9407  0.9520  0.8740  0.9271
 $$
Resolution limits                    =     41.964     1.790
Number of used reflections           =      19197
Percentage observed                  =    99.9852
Percentage of free reflections       =     5.0406
Overall R factor                     =     0.1680
Free R factor                        =     0.2187
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9483
Overall weighted R factor            =     0.1537
Free weighted R factor               =     0.1986
Overall weighted R2 factor           =     0.1864
Free weighted R2 factor              =     0.2362
Average correlation coefficient      =     0.9363
Overall correlation coefficient      =     0.9569
Free correlation coefficient         =     0.9237
Cruickshanks DPI for coordinate error=     0.1204
DPI based on free R factor           =     0.1232
Overall figure of merit              =     0.8598
ML based su of positional parameters =     0.0743
ML based su of thermal parameters    =     2.3408
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.81
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1683   0.2195   0.844      102239.    5603.0   0.0121  0.903   1.801  1.038   0.085
       1   0.1682   0.2184   0.859      101781.    5592.3   0.0116  0.868   1.765  1.018   0.084
       2   0.1678   0.2184   0.860      101699.    5590.6   0.0123  0.914   1.795  1.037   0.085
       3   0.1678   0.2185   0.860      101689.    5590.6   0.0123  0.918   1.802  1.041   0.085
       4   0.1678   0.2185   0.860      101684.    5590.4   0.0123  0.920   1.806  1.043   0.085
       5   0.1678   0.2186   0.860      101679.    5590.2   0.0123  0.920   1.808  1.044   0.085
       6   0.1679   0.2187   0.860      101678.    5590.3   0.0123  0.920   1.809  1.045   0.085
       7   0.1679   0.2186   0.860      101678.    5590.2   0.0123  0.920   1.809  1.045   0.085
       8   0.1680   0.2186   0.860      101682.    5590.3   0.0123  0.920   1.810  1.045   0.085
       9   0.1680   0.2186   0.860      101679.    5590.2   0.0123  0.920   1.810  1.045   0.085
      10   0.1680   0.2187   0.860      101683.    5590.5   0.0123  0.921   1.810  1.045   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1683   0.1680
             R free    0.2195   0.2187
     Rms BondLength    0.0121   0.0123
      Rms BondAngle    1.8012   1.8104
     Rms ChirVolume    0.0851   0.0849
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.0s System:    0.2s Elapsed:     0:47