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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: 13:14:43 


 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 1.95     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_1-96A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-01A_R00_1-95A.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_1-95A.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       0.0657
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9500
  Estimated number of reflections :      19845
  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  1.9500

  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_1-96A.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=   1.981 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=   2.210 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=   1.849 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=   2.212 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=   2.350 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=   2.436 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=   2.078 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        799
Number of   all  reflections      15753
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          15753

   Current auto weighting coefficient =    7.3745756    

 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.= 0.916 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        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  151
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  151
 Weight matrix   0.19661655    
 Actual weight    7.3745756      is applied to the X-ray term
Norm of X_ray positional gradient                31.0
Norm of Geom. positional gradient                77.3
Norm of X_ray B-factor gradient                  105.
Norm of Geom. B-factor gradient                  102.
Product of X_ray and Geom posit. gradients     -0.834E+07
 Cosine of angle between them                      -0.359
Product of X_ray and Geom B-fact gradients     -0.318E+08
 Cosine of angle between them                      -0.923


Residuals: XRAY=     0.6071E+06 GEOM=     0.1240E+05 TOTAL=     0.6195E+06
 function value    619501.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.680     1.644
Bond angles  : others                          3238     2.339     1.580
Torsion angles, period  1. refined              185     7.110     5.000
Torsion angles, period  2. refined               90    36.641    22.778
Torsion angles, period  3. refined              268    14.477    15.000
Torsion angles, period  4. refined                9    11.231    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   305     0.241     0.200
VDW repulsions.others                          1340     0.218     0.200
VDW; torsion: refined_atoms                     708     0.170     0.200
VDW; torsion.others                             703     0.079     0.200
HBOND: refined_atoms                            238     0.207     0.200
Metal-ion: refined_atoms                          1     0.019     0.200
VDW repulsions: symmetry: refined_atoms           8     0.244     0.200
VDW repulsions: symmetry: others                 24     0.193     0.200
HBOND: symmetry: refined_atoms                   17     0.237     0.200
M. chain bond B values: refined atoms           746     1.496     1.189
M. chain bond B values: others                  746     1.495     1.190
M. chain angle B values: refined atoms          929     2.435     1.770
M. chain angle B values: others                 930     2.434     1.770
S. chain bond B values: refined atoms           811     2.334     1.502
S. chain bond B values: others                  810     2.331     1.501
S. chain angle B values: refined atoms         1177     3.726     2.114
S. chain angle B values: others                1178     3.725     2.113
Long range B values: refined atoms             1862     6.698    16.643
Long range B values: others                    1762     6.338    15.209
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1010
Partial structure    1: scale =     0.3743, B  =   46.1948
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.55 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.033    2059 100.00   484.5   486.9  0.16  0.17      92   471.3   483.3  0.20  0.22
 0.099    3454 100.00   407.2   388.7  0.16  0.15     173   406.3   376.0  0.22  0.21
 0.165    4336  99.96   256.1   253.7  0.16  0.14     257   273.6   265.4  0.22  0.19
 0.230    5100 100.00   205.5   204.0  0.16  0.13     277   209.8   211.6  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0334   1406   0.909    653   0.808   2059   0.877  0.960  0.9612  0.9694  0.9143  0.9431
  0.0990   2797   0.881    657   0.761   3454   0.858  1.000  0.9441  0.9609  0.8804  0.9434
  0.1646   3673   0.853    663   0.763   4336   0.839  0.965  0.9414  0.9540  0.8810  0.9384
  0.2302   4445   0.870    658   0.749   5103   0.854  0.965  0.9450  0.9583  0.8769  0.9398
 $$
Resolution limits                    =     41.964     1.950
Number of used reflections           =      14951
Percentage observed                  =    99.9810
Percentage of free reflections       =     5.0730
Overall R factor                     =     0.1590
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9592
AverageFree Fourier shell correlation=     0.9455
Overall weighted R factor            =     0.1494
Free weighted R factor               =     0.2030
Overall weighted R2 factor           =     0.1813
Free weighted R2 factor              =     0.2450
Average correlation coefficient      =     0.9407
Overall correlation coefficient      =     0.9544
Free correlation coefficient         =     0.9087
Cruickshanks DPI for coordinate error=     0.1550
DPI based on free R factor           =     0.1515
Overall figure of merit              =     0.8539
ML based su of positional parameters =     0.0939
ML based su of thermal parameters    =     3.1778
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    82323.367       12401.470       619501.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.20304129    
 Actual weight    7.3745756      is applied to the X-ray term


 function value    613661.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1286
Partial structure    1: scale =     0.3744, B  =   46.5355
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1587
Free R factor                        =     0.2167
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9467
Average correlation coefficient      =     0.9413
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    82134.813       7952.4873       613661.88       619501.38    


     CGMAT cycle number =      3

 Weight matrix   0.20334163    
 Actual weight    7.3745756      is applied to the X-ray term


 function value    613521.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1296
Partial structure    1: scale =     0.3745, B  =   46.4817
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1584
Free R factor                        =     0.2164
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9468
Average correlation coefficient      =     0.9415
Overall figure of merit              =     0.8578
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    82109.891       7995.5830       613521.19       613661.88    


     CGMAT cycle number =      4

 Weight matrix   0.20308506    
 Actual weight    7.3745756      is applied to the X-ray term


 function value    613513.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1346
Partial structure    1: scale =     0.3746, B  =   46.4429
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9467
Average correlation coefficient      =     0.9415
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    82106.969       8009.5405       613513.63       613521.19    


     CGMAT cycle number =      5

 Weight matrix   0.20288841    
 Actual weight    7.3745756      is applied to the X-ray term


 function value    613489.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1369
Partial structure    1: scale =     0.3745, B  =   46.2670
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9467
Average correlation coefficient      =     0.9415
Overall figure of merit              =     0.8576
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    82103.914       8008.3906       613489.88       613513.63    


     CGMAT cycle number =      6

 Weight matrix   0.20254759    
 Actual weight    7.3745756      is applied to the X-ray term


 function value    613514.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1455
Partial structure    1: scale =     0.3746, B  =   46.0992
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2164
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9467
Average correlation coefficient      =     0.9415
Overall figure of merit              =     0.8575
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    82106.945       7999.4004       613529.50       613489.88    

 fvalues    82106.945       7999.4004       613503.25       613503.25    
 fvalues    82106.945       7999.4004       613503.25       613503.25    


     CGMAT cycle number =      7

 Weight matrix   0.20232967    
 Actual weight    7.3745756      is applied to the X-ray term


 function value    613527.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1463
Partial structure    1: scale =     0.3746, B  =   46.0673
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2164
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9415
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    82109.422       7995.1846       613540.56       613503.25    

 fvalues    82109.422       7995.1846       613549.69       613517.31    
 fvalues    82109.422       7995.1846       613549.69       613517.31    


     CGMAT cycle number =      8

 Weight matrix   0.20228882    
 Actual weight    7.3745756      is applied to the X-ray term


 function value    613525.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1483
Partial structure    1: scale =     0.3746, B  =   46.0911
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9415
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    82110.969       7991.8652       613527.25       613517.31    

 fvalues    82110.969       7991.8652       613519.38       613525.44    
 fvalues    82110.969       7991.8652       613519.38       613525.44    


     CGMAT cycle number =      9

 Weight matrix   0.20226203    
 Actual weight    7.3745756      is applied to the X-ray term


 function value    613522.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1462
Partial structure    1: scale =     0.3746, B  =   46.1017
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9466
Average correlation coefficient      =     0.9415
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    82110.625       7991.9609       613522.94       613525.44    


     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.= 0.929 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        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  151
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    30   30   63
 Minimum acceptable grid spacing:    71   71  151
 Weight matrix   0.20220307    
 Actual weight    7.3745756      is applied to the X-ray term
Norm of X_ray positional gradient                30.5
Norm of Geom. positional gradient                30.6
Norm of X_ray B-factor gradient                  102.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.904E+07
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.349E+08
 Cosine of angle between them                      -0.981


Residuals: XRAY=     0.6055E+06 GEOM=      7991.     TOTAL=     0.6135E+06
 function value    613523.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.687     1.644
Bond angles  : others                          3238     1.413     1.580
Torsion angles, period  1. refined              185     7.075     5.000
Torsion angles, period  2. refined               90    36.664    22.778
Torsion angles, period  3. refined              268    14.490    15.000
Torsion angles, period  4. refined                9    11.098    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   302     0.242     0.200
VDW repulsions.others                          1337     0.196     0.200
VDW; torsion: refined_atoms                     713     0.170     0.200
VDW; torsion.others                             752     0.083     0.200
HBOND: refined_atoms                            234     0.207     0.200
HBOND.others                                      1     0.010     0.200
Metal-ion: refined_atoms                          1     0.017     0.200
VDW repulsions: symmetry: refined_atoms           9     0.231     0.200
VDW repulsions: symmetry: others                 24     0.186     0.200
HBOND: symmetry: refined_atoms                   19     0.220     0.200
M. chain bond B values: refined atoms           746     1.506     1.197
M. chain bond B values: others                  746     1.506     1.197
M. chain angle B values: refined atoms          929     2.449     1.781
M. chain angle B values: others                 930     2.448     1.781
S. chain bond B values: refined atoms           811     2.368     1.514
S. chain bond B values: others                  810     2.365     1.514
S. chain angle B values: refined atoms         1177     3.780     2.130
S. chain angle B values: others                1178     3.778     2.130
Long range B values: refined atoms             1857     6.685    16.750
Long range B values: others                    1759     6.358    15.335
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1452
Partial structure    1: scale =     0.3747, B  =   46.0912
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.033    2059 100.00   484.8   487.5  0.16  0.17      92   471.6   482.7  0.20  0.22
 0.099    3454 100.00   407.4   388.4  0.16  0.15     173   406.5   376.4  0.22  0.21
 0.165    4336  99.96   256.2   253.8  0.16  0.14     257   273.7   265.0  0.22  0.19
 0.230    5100 100.00   205.6   204.1  0.15  0.12     277   209.9   211.6  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0334   1406   0.923    653   0.824   2059   0.892  0.960  0.9644  0.9725  0.9155  0.9441
  0.0990   2797   0.884    657   0.765   3454   0.862  1.000  0.9461  0.9619  0.8833  0.9428
  0.1646   3673   0.853    663   0.763   4336   0.839  0.965  0.9414  0.9538  0.8812  0.9378
  0.2302   4445   0.872    658   0.750   5103   0.856  0.965  0.9458  0.9598  0.8778  0.9428
 $$
Resolution limits                    =     41.964     1.950
Number of used reflections           =      14951
Percentage observed                  =    99.9810
Percentage of free reflections       =     5.0730
Overall R factor                     =     0.1582
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9466
Overall weighted R factor            =     0.1490
Free weighted R factor               =     0.2015
Overall weighted R2 factor           =     0.1810
Free weighted R2 factor              =     0.2429
Average correlation coefficient      =     0.9415
Overall correlation coefficient      =     0.9546
Free correlation coefficient         =     0.9099
Cruickshanks DPI for coordinate error=     0.1542
DPI based on free R factor           =     0.1505
Overall figure of merit              =     0.8574
ML based su of positional parameters =     0.0925
ML based su of thermal parameters    =     3.1421
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    82110.758       7991.4756       613519.38       613522.94    
 fvalues    82110.758       7991.4756       613519.38       613523.50    

    ****                              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.= 0.929 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_1-95A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.011     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.687     1.644
Bond angles  : others                          3238     1.413     1.580
Torsion angles, period  1. refined              185     7.075     5.000
Torsion angles, period  2. refined               90    36.666    22.778
Torsion angles, period  3. refined              268    14.492    15.000
Torsion angles, period  4. refined                9    11.100    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   302     0.242     0.200
VDW repulsions.others                          1337     0.196     0.200
VDW; torsion: refined_atoms                     714     0.170     0.200
VDW; torsion.others                             752     0.083     0.200
HBOND: refined_atoms                            234     0.207     0.200
HBOND.others                                      1     0.010     0.200
Metal-ion: refined_atoms                          1     0.017     0.200
VDW repulsions: symmetry: refined_atoms           9     0.232     0.200
VDW repulsions: symmetry: others                 24     0.186     0.200
HBOND: symmetry: refined_atoms                   19     0.220     0.200
M. chain bond B values: refined atoms           746     1.506     1.197
M. chain bond B values: others                  746     1.506     1.197
M. chain angle B values: refined atoms          929     2.449     1.781
M. chain angle B values: others                 930     2.448     1.781
S. chain bond B values: refined atoms           811     2.368     1.514
S. chain bond B values: others                  810     2.365     1.514
S. chain angle B values: refined atoms         1177     3.780     2.130
S. chain angle B values: others                1178     3.778     2.130
Long range B values: refined atoms             1858     6.683    16.749
Long range B values: others                    1760     6.356    15.335
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0398, B  =   -0.1449
Partial structure    1: scale =     0.3747, B  =   46.0951
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.033    2059 100.00   484.8   487.5  0.16  0.17      92   471.6   482.7  0.20  0.22
 0.099    3454 100.00   407.4   388.4  0.16  0.15     173   406.5   376.4  0.22  0.21
 0.165    4336  99.96   256.3   253.8  0.16  0.14     257   273.7   265.0  0.22  0.19
 0.230    5100 100.00   205.7   204.1  0.15  0.12     277   209.9   211.6  0.22  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0334   1406   0.923    653   0.824   2059   0.892  0.960  0.9645  0.9725  0.9156  0.9441
  0.0990   2797   0.884    657   0.765   3454   0.862  1.000  0.9461  0.9619  0.8833  0.9428
  0.1646   3673   0.853    663   0.763   4336   0.839  0.965  0.9413  0.9538  0.8811  0.9378
  0.2302   4445   0.872    658   0.750   5103   0.856  0.965  0.9458  0.9598  0.8778  0.9428
 $$
Resolution limits                    =     41.964     1.950
Number of used reflections           =      14951
Percentage observed                  =    99.9810
Percentage of free reflections       =     5.0730
Overall R factor                     =     0.1582
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9466
Overall weighted R factor            =     0.1490
Free weighted R factor               =     0.2015
Overall weighted R2 factor           =     0.1810
Free weighted R2 factor              =     0.2429
Average correlation coefficient      =     0.9415
Overall correlation coefficient      =     0.9546
Free correlation coefficient         =     0.9099
Cruickshanks DPI for coordinate error=     0.1542
DPI based on free R factor           =     0.1506
Overall figure of merit              =     0.8573
ML based su of positional parameters =     0.0925
ML based su of thermal parameters    =     3.1421
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.45
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1590   0.2178   0.854       82323.    4560.9   0.0111  0.813   1.680  0.978   0.082
       1   0.1587   0.2167   0.858       82135.    4557.6   0.0109  0.794   1.668  0.972   0.082
       2   0.1584   0.2164   0.858       82110.    4556.8   0.0111  0.815   1.681  0.979   0.082
       3   0.1583   0.2165   0.858       82107.    4557.1   0.0111  0.818   1.685  0.982   0.082
       4   0.1582   0.2165   0.858       82104.    4557.3   0.0111  0.818   1.686  0.982   0.082
       5   0.1582   0.2164   0.858       82108.    4557.7   0.0111  0.817   1.686  0.983   0.082
       6   0.1582   0.2164   0.857       82111.    4558.0   0.0111  0.817   1.687  0.983   0.082
       7   0.1582   0.2165   0.857       82111.    4558.1   0.0111  0.817   1.687  0.983   0.082
       8   0.1582   0.2165   0.857       82111.    4558.1   0.0111  0.817   1.687  0.983   0.082
       9   0.1582   0.2165   0.857       82111.    4558.2   0.0111  0.817   1.687  0.983   0.082
      10   0.1582   0.2165   0.857       82114.    4558.3   0.0111  0.817   1.687  0.983   0.082
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1590   0.1582
             R free    0.2178   0.2165
     Rms BondLength    0.0111   0.0111
      Rms BondAngle    1.6803   1.6867
     Rms ChirVolume    0.0816   0.0823
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      49.5s System:    0.2s Elapsed:     0:50