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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: 10:37:32 


 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 1.80     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_step0-10A_R00_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_step0-10A_R00_1-80A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_step0-10A_R00_1-80A.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       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  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  1.8000

  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_step0-10A_R00_1-90A.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=   2.009 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=   2.201 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=   1.861 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=   2.208 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=   2.398 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=   2.430 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=   2.114 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       1001
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 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.= 0.927 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  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.23593636    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                36.7
Norm of Geom. positional gradient                77.7
Norm of X_ray B-factor gradient                  123.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.856E+07
 Cosine of angle between them                      -0.310
Product of X_ray and Geom B-fact gradients     -0.351E+08
 Cosine of angle between them                      -0.823


Residuals: XRAY=     0.7097E+06 GEOM=     0.1280E+05 TOTAL=     0.7224E+06
 function value    722447.69    

-------------------------------------------------------------------------------
             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     1.725     1.644
Bond angles  : others                          3238     2.340     1.580
Torsion angles, period  1. refined              185     6.999     5.000
Torsion angles, period  2. refined               90    36.496    22.778
Torsion angles, period  3. refined              268    14.369    15.000
Torsion angles, period  4. refined                9    11.572    15.000
Chiral centres: refined atoms                   196     0.082     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   294     0.248     0.200
VDW repulsions.others                          1334     0.220     0.200
VDW; torsion: refined_atoms                     717     0.170     0.200
VDW; torsion.others                             709     0.079     0.200
HBOND: refined_atoms                            228     0.202     0.200
VDW repulsions: symmetry: refined_atoms           9     0.224     0.200
VDW repulsions: symmetry: others                 22     0.215     0.200
HBOND: symmetry: refined_atoms                   20     0.211     0.200
M. chain bond B values: refined atoms           746     1.542     1.215
M. chain bond B values: others                  746     1.541     1.215
M. chain angle B values: refined atoms          929     2.481     1.808
M. chain angle B values: others                 930     2.479     1.808
S. chain bond B values: refined atoms           811     2.538     1.555
S. chain bond B values: others                  810     2.534     1.555
S. chain angle B values: refined atoms         1177     4.009     2.185
S. chain angle B values: others                1178     4.007     2.185
Long range B values: refined atoms             1848     6.659    16.889
Long range B values: others                    1752     6.363    15.521
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =    0.8412
Partial structure    1: scale =     0.3785, B  =   46.0704
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2575 100.00   474.1   481.3  0.16  0.17     118   467.6   477.5  0.20  0.22
 0.116    4340 100.00   342.4   328.5  0.16  0.15     239   339.6   313.8  0.22  0.20
 0.193    5512  99.97   226.0   215.2  0.16  0.14     296   237.0   226.5  0.21  0.18
 0.270    6440 100.00   147.9   154.5  0.21  0.16     347   153.5   159.2  0.26  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1808   0.913    767   0.813   2575   0.883  0.956  0.9605  0.9691  0.9074  0.9408
  0.1161   3566   0.875    774   0.773   4340   0.857  0.993  0.9448  0.9609  0.8882  0.9450
  0.1931   4740   0.869    772   0.753   5512   0.853  1.008  0.9468  0.9575  0.8931  0.9398
  0.2701   5670   0.811    777   0.722   6447   0.800  0.888  0.9264  0.9361  0.8571  0.9070
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18874
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0365
Overall R factor                     =     0.1700
Free R factor                        =     0.2222
Average Fourier shell correlation    =     0.9526
AverageFree Fourier shell correlation=     0.9409
Overall weighted R factor            =     0.1535
Free weighted R factor               =     0.2014
Overall weighted R2 factor           =     0.1848
Free weighted R2 factor              =     0.2407
Average correlation coefficient      =     0.9299
Overall correlation coefficient      =     0.9557
Free correlation coefficient         =     0.9191
Cruickshanks DPI for coordinate error=     0.1242
DPI based on free R factor           =     0.1269
Overall figure of merit              =     0.8400
ML based su of positional parameters =     0.0835
ML based su of thermal parameters    =     2.6925
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    101385.13       12796.236       722447.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.26864454    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    713533.25    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0582
Partial structure    1: scale =     0.3785, B  =   46.3993
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                     =     0.1691
Free R factor                        =     0.2193
Average Fourier shell correlation    =     0.9569
AverageFree Fourier shell correlation=     0.9454
Average correlation coefficient      =     0.9326
Overall figure of merit              =     0.8550
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100809.14       7913.4868       713533.25       722447.69    


     CGMAT cycle number =      3

 Weight matrix   0.27557743    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    712230.69    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =    0.0004
Partial structure    1: scale =     0.3784, B  =   46.2737
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                     =     0.1677
Free R factor                        =     0.2173
Average Fourier shell correlation    =     0.9580
AverageFree Fourier shell correlation=     0.9468
Average correlation coefficient      =     0.9345
Overall figure of merit              =     0.8572
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100554.92       8390.4004       712230.69       713533.25    


     CGMAT cycle number =      4

 Weight matrix   0.27895144    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711727.19    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =    0.0101
Partial structure    1: scale =     0.3784, B  =   46.2619
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                     =     0.1675
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9584
AverageFree Fourier shell correlation=     0.9474
Average correlation coefficient      =     0.9352
Overall figure of merit              =     0.8582
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100457.99       8565.2930       711727.19       712230.69    


     CGMAT cycle number =      5

 Weight matrix   0.28053853    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711424.88    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =    0.0230
Partial structure    1: scale =     0.3786, B  =   46.0967
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                     =     0.1672
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9586
AverageFree Fourier shell correlation=     0.9477
Average correlation coefficient      =     0.9355
Overall figure of merit              =     0.8587
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100402.27       8652.9854       711424.88       711727.19    


     CGMAT cycle number =      6

 Weight matrix   0.28188807    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711233.63    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =    0.0378
Partial structure    1: scale =     0.3789, B  =   45.9656
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                     =     0.1672
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9587
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100369.56       8690.7188       711233.63       711424.88    


     CGMAT cycle number =      7

 Weight matrix   0.28208926    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711145.56    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =    0.0033
Partial structure    1: scale =     0.3792, B  =   45.9061
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                     =     0.1671
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9358
Overall figure of merit              =     0.8592
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100357.51       8687.0879       711145.56       711233.63    


     CGMAT cycle number =      8

 Weight matrix   0.28223476    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711126.63    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =    0.0050
Partial structure    1: scale =     0.3791, B  =   45.8745
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                     =     0.1671
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9359
Overall figure of merit              =     0.8592
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    100351.93       8707.1465       711126.63       711145.56    


     CGMAT cycle number =      9

 Weight matrix   0.28230557    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711085.31    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =    0.0069
Partial structure    1: scale =     0.3792, B  =   45.7860
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                     =     0.1670
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8592
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    100346.41       8704.5273       711085.31       711126.63    


     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.= 0.938 id.= 3.000 dev= -2.06 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  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.28259921    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                36.3
Norm of Geom. positional gradient                36.2
Norm of X_ray B-factor gradient                  121.
Norm of Geom. B-factor gradient                  121.
Product of X_ray and Geom posit. gradients     -0.127E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.473E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7023E+06 GEOM=      8710.     TOTAL=     0.7111E+06
 function value    711050.69    

-------------------------------------------------------------------------------
             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     1.793     1.644
Bond angles  : others                          3238     1.474     1.580
Torsion angles, period  1. refined              185     6.963     5.000
Torsion angles, period  2. refined               90    36.378    22.778
Torsion angles, period  3. refined              268    14.231    15.000
Torsion angles, period  4. refined                9    12.086    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   294     0.248     0.200
VDW repulsions.others                          1357     0.191     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             788     0.084     0.200
HBOND: refined_atoms                            220     0.193     0.200
HBOND.others                                      1     0.038     0.200
VDW repulsions: symmetry: refined_atoms           8     0.214     0.200
VDW repulsions: symmetry: others                 22     0.184     0.200
HBOND: symmetry: refined_atoms                   21     0.200     0.200
M. chain bond B values: refined atoms           746     1.625     1.290
M. chain bond B values: others                  746     1.623     1.290
M. chain angle B values: refined atoms          929     2.561     1.921
M. chain angle B values: others                 930     2.560     1.920
S. chain bond B values: refined atoms           811     2.782     1.663
S. chain bond B values: others                  810     2.778     1.663
S. chain angle B values: refined atoms         1177     4.371     2.335
S. chain angle B values: others                1178     4.369     2.334
Long range B values: refined atoms             1842     6.824    17.817
Long range B values: others                    1750     6.493    16.398
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0062
Partial structure    1: scale =     0.3793, B  =   45.7406
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2575 100.00   473.4   481.6  0.16  0.17     118   466.9   476.5  0.20  0.22
 0.116    4340 100.00   341.9   327.1  0.16  0.15     239   339.1   312.0  0.22  0.20
 0.193    5512  99.97   225.7   214.4  0.16  0.14     296   236.7   226.1  0.21  0.17
 0.270    6440 100.00   147.7   154.0  0.19  0.15     347   153.2   159.4  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1808   0.928    767   0.829   2575   0.899  0.956  0.9649  0.9723  0.9105  0.9410
  0.1161   3566   0.881    774   0.782   4340   0.863  0.993  0.9484  0.9625  0.8947  0.9445
  0.1931   4740   0.876    772   0.762   5512   0.860  1.008  0.9506  0.9592  0.9011  0.9387
  0.2701   5670   0.850    777   0.766   6447   0.840  0.904  0.9399  0.9507  0.8734  0.9259
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18874
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0365
Overall R factor                     =     0.1670
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9589
AverageFree Fourier shell correlation=     0.9480
Overall weighted R factor            =     0.1529
Free weighted R factor               =     0.1968
Overall weighted R2 factor           =     0.1852
Free weighted R2 factor              =     0.2339
Average correlation coefficient      =     0.9360
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9237
Cruickshanks DPI for coordinate error=     0.1221
DPI based on free R factor           =     0.1233
Overall figure of merit              =     0.8592
ML based su of positional parameters =     0.0762
ML based su of thermal parameters    =     2.4235
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    100340.72       8709.6895       711050.69       711085.31    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.938 id.= 3.000 dev= -2.06 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_step0-10A_R00_1-80A.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     1.794     1.644
Bond angles  : others                          3238     1.474     1.580
Torsion angles, period  1. refined              185     6.959     5.000
Torsion angles, period  2. refined               90    36.376    22.778
Torsion angles, period  3. refined              268    14.241    15.000
Torsion angles, period  4. refined                9    12.090    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1743     0.009     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   293     0.248     0.200
VDW repulsions.others                          1359     0.191     0.200
VDW; torsion: refined_atoms                     723     0.171     0.200
VDW; torsion.others                             791     0.084     0.200
HBOND: refined_atoms                            220     0.193     0.200
HBOND.others                                      1     0.039     0.200
VDW repulsions: symmetry: refined_atoms           8     0.214     0.200
VDW repulsions: symmetry: others                 22     0.185     0.200
HBOND: symmetry: refined_atoms                   21     0.199     0.200
M. chain bond B values: refined atoms           746     1.625     1.290
M. chain bond B values: others                  746     1.624     1.290
M. chain angle B values: refined atoms          929     2.561     1.920
M. chain angle B values: others                 930     2.560     1.920
S. chain bond B values: refined atoms           811     2.784     1.663
S. chain bond B values: others                  810     2.780     1.662
S. chain angle B values: refined atoms         1177     4.373     2.334
S. chain angle B values: others                1178     4.371     2.334
Long range B values: refined atoms             1842     6.830    17.819
Long range B values: others                    1750     6.499    16.399
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0003
Partial structure    1: scale =     0.3793, B  =   45.7397
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2575 100.00   473.4   481.6  0.16  0.17     118   466.9   476.4  0.20  0.22
 0.116    4340 100.00   341.9   327.2  0.16  0.15     239   339.1   312.2  0.22  0.20
 0.193    5512  99.97   225.7   214.5  0.16  0.14     296   236.7   226.2  0.21  0.17
 0.270    6440 100.00   147.7   154.1  0.19  0.15     347   153.2   159.5  0.24  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1808   0.928    767   0.829   2575   0.898  0.956  0.9648  0.9723  0.9103  0.9410
  0.1161   3566   0.881    774   0.783   4340   0.863  0.993  0.9484  0.9625  0.8947  0.9445
  0.1931   4740   0.876    772   0.762   5512   0.860  1.008  0.9506  0.9592  0.9010  0.9386
  0.2701   5670   0.850    777   0.766   6447   0.840  0.904  0.9399  0.9508  0.8735  0.9261
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18874
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0365
Overall R factor                     =     0.1671
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9589
AverageFree Fourier shell correlation=     0.9480
Overall weighted R factor            =     0.1529
Free weighted R factor               =     0.1968
Overall weighted R2 factor           =     0.1853
Free weighted R2 factor              =     0.2339
Average correlation coefficient      =     0.9360
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9237
Cruickshanks DPI for coordinate error=     0.1221
DPI based on free R factor           =     0.1234
Overall figure of merit              =     0.8593
ML based su of positional parameters =     0.0762
ML based su of thermal parameters    =     2.4235
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.04
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1700   0.2222   0.840      101385.    5550.3   0.0113  0.841   1.725  0.997   0.082
       1   0.1691   0.2193   0.855      100809.    5532.6   0.0111  0.823   1.713  0.988   0.083
       2   0.1677   0.2173   0.857      100555.    5522.6   0.0119  0.877   1.750  1.008   0.084
       3   0.1675   0.2165   0.858      100458.    5518.0   0.0120  0.889   1.769  1.018   0.084
       4   0.1672   0.2161   0.859      100402.    5515.3   0.0121  0.896   1.779  1.023   0.084
       5   0.1672   0.2159   0.859      100370.    5513.9   0.0121  0.899   1.785  1.026   0.084
       6   0.1671   0.2158   0.859      100358.    5513.5   0.0121  0.901   1.789  1.028   0.084
       7   0.1671   0.2159   0.859      100352.    5513.1   0.0121  0.901   1.791  1.029   0.084
       8   0.1670   0.2160   0.859      100346.    5512.8   0.0121  0.902   1.792  1.030   0.084
       9   0.1670   0.2159   0.859      100341.    5512.4   0.0121  0.902   1.793  1.030   0.084
      10   0.1671   0.2160   0.859      100338.    5512.5   0.0121  0.903   1.794  1.031   0.084
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1700   0.1671
             R free    0.2222   0.2160
     Rms BondLength    0.0113   0.0121
      Rms BondAngle    1.7255   1.7942
     Rms ChirVolume    0.0825   0.0844
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      45.6s System:    0.1s Elapsed:     0:46