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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: 18:07:06 


 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 1.60     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 11
  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_complete_R11_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R11_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R11_1-60A.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       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:    11
  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  1.6000

  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_complete_R11_1-70A.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=   2.026 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=   2.185 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=   1.836 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=   2.388 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=   2.408 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=   2.080 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:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  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:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                           11
Number of "free" reflections       1379
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 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.= 0.908 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.29937741    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                39.9
Norm of Geom. positional gradient                79.1
Norm of X_ray B-factor gradient                  119.
Norm of Geom. B-factor gradient                 0.213E+05
Product of X_ray and Geom posit. gradients     -0.132E+08
 Cosine of angle between them                      -0.431
Product of X_ray and Geom B-fact gradients     -0.391E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8743E+06 GEOM=     0.2598E+05 TOTAL=     0.9002E+06
 function value    900246.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.777     1.644
Bond angles  : others                          3242     2.340     1.582
Torsion angles, period  1. refined              184     6.882     5.000
Torsion angles, period  2. refined               90    36.151    22.778
Torsion angles, period  3. refined              268    13.662    15.000
Torsion angles, period  4. refined                9    10.888    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   305     0.264     0.200
VDW repulsions.others                          1325     0.232     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             724     0.080     0.200
HBOND: refined_atoms                            218     0.200     0.200
HBOND.others                                      2     0.082     0.200
VDW repulsions: symmetry: refined_atoms           8     0.228     0.200
VDW repulsions: symmetry: others                 25     0.170     0.200
HBOND: symmetry: refined_atoms                   21     0.246     0.200
M. chain bond B values: refined atoms           745     1.680     1.390
M. chain bond B values: others                  745     1.678     1.390
M. chain angle B values: refined atoms          926     2.634     2.071
M. chain angle B values: others                 927     2.633     2.071
S. chain bond B values: refined atoms           812     2.979     1.786
S. chain bond B values: others                  811     2.972     1.785
S. chain angle B values: refined atoms         1177     4.626     2.514
S. chain angle B values: others                1178     4.624     2.513
Long range B values: refined atoms             1850     7.530    19.635
Long range B values: others                    1758     7.219    18.169
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    1.2275
Partial structure    1: scale =     0.3845, B  =   48.4659
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3600 100.00   432.2   442.0  0.17  0.18     182   431.7   457.4  0.20  0.21
 0.147    6142  99.97   258.8   243.1  0.16  0.15     302   255.2   239.3  0.20  0.18
 0.244    7819 100.00   167.4   151.7  0.19  0.17     399   163.4   146.9  0.23  0.20
 0.342    9094 100.00    71.3    85.7  0.33  0.26     496    70.8    87.2  0.37  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2640   0.906    960   0.807   3600   0.880  0.944  0.9635  0.9675  0.9167  0.9353
  0.1468   5160   0.893    982   0.796   6142   0.877  1.029  0.9551  0.9648  0.9082  0.9437
  0.2444   6842   0.856    977   0.755   7819   0.843  1.049  0.9396  0.9522  0.8900  0.9347
  0.3419   8113   0.669    986   0.589   9099   0.660  0.703  0.8531  0.8671  0.8186  0.8555
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26659
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.9183
Overall R factor                     =     0.1926
Free R factor                        =     0.2333
Average Fourier shell correlation    =     0.9281
AverageFree Fourier shell correlation=     0.9150
Overall weighted R factor            =     0.1669
Free weighted R factor               =     0.2014
Overall weighted R2 factor           =     0.1976
Free weighted R2 factor              =     0.2327
Average correlation coefficient      =     0.9098
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9403
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0996
Overall figure of merit              =     0.7936
ML based su of positional parameters =     0.0714
ML based su of thermal parameters    =     2.1707
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134509.38       25982.137       900246.31      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.38360384    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    875856.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0581
Partial structure    1: scale =     0.3849, B  =   48.2996
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2340
Average Fourier shell correlation    =     0.9423
AverageFree Fourier shell correlation=     0.9305
Average correlation coefficient      =     0.9107
Overall figure of merit              =     0.8348
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133241.64       9832.0020       875856.38       900246.31    


     CGMAT cycle number =      3

 Weight matrix   0.39730036    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    873460.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0073
Partial structure    1: scale =     0.3853, B  =   44.4058
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1911
Free R factor                        =     0.2332
Average Fourier shell correlation    =     0.9448
AverageFree Fourier shell correlation=     0.9326
Average correlation coefficient      =     0.9132
Overall figure of merit              =     0.8417
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132941.03       9390.3525       873460.88       875856.38    


     CGMAT cycle number =      4

 Weight matrix   0.36295283    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    794310.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0039
Partial structure    1: scale =     0.3855, B  =   44.1228
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1908
Free R factor                        =     0.2327
Average Fourier shell correlation    =     0.9452
AverageFree Fourier shell correlation=     0.9329
Average correlation coefficient      =     0.9142
Overall figure of merit              =     0.8425
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132855.45       9297.7139       794310.63       873460.88    


     CGMAT cycle number =      5

 Weight matrix   0.32968113    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722835.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    0.0023
Partial structure    1: scale =     0.3863, B  =   44.0240
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1911
Free R factor                        =     0.2326
Average Fourier shell correlation    =     0.9452
AverageFree Fourier shell correlation=     0.9329
Average correlation coefficient      =     0.9142
Overall figure of merit              =     0.8425
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132878.58       9062.8994       722835.25       794310.63    


     CGMAT cycle number =      6

 Weight matrix   0.32901564    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722813.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0002
Partial structure    1: scale =     0.3863, B  =   43.9765
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1916
Free R factor                        =     0.2326
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9327
Average correlation coefficient      =     0.9138
Overall figure of merit              =     0.8424
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    132931.66       8755.8320       722813.31       722835.25    


     CGMAT cycle number =      7

 Weight matrix   0.32864809    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722866.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0012
Partial structure    1: scale =     0.3867, B  =   43.9511
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1917
Free R factor                        =     0.2323
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9327
Average correlation coefficient      =     0.9137
Overall figure of merit              =     0.8423
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    132955.97       8679.5117       722875.69       722813.31    

 fvalues    132955.97       8679.5117       722879.50       722867.56    
 fvalues    132955.97       8679.5117       722879.50       722867.56    


     CGMAT cycle number =      8

 Weight matrix   0.32859278    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722879.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0001
Partial structure    1: scale =     0.3870, B  =   43.9308
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1917
Free R factor                        =     0.2323
Average Fourier shell correlation    =     0.9450
AverageFree Fourier shell correlation=     0.9327
Average correlation coefficient      =     0.9137
Overall figure of merit              =     0.8423
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    132960.13       8669.4443       722878.69       722867.56    
 fvalues    132960.13       8669.4443       722878.69       722879.81    


     CGMAT cycle number =      9

 Weight matrix   0.32853568    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722877.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    0.0018
Partial structure    1: scale =     0.3871, B  =   43.9136
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1917
Free R factor                        =     0.2323
Average Fourier shell correlation    =     0.9449
AverageFree Fourier shell correlation=     0.9327
Average correlation coefficient      =     0.9137
Overall figure of merit              =     0.8423
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    132961.50       8659.6279       722877.44       722879.81    


     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.= 0.917 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.32854035    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                38.5
Norm of Geom. positional gradient                38.6
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  108.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.372E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7142E+06 GEOM=      8650.     TOTAL=     0.7229E+06
 function value    722879.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.776     1.644
Bond angles  : others                          3242     1.501     1.582
Torsion angles, period  1. refined              184     6.873     5.000
Torsion angles, period  2. refined               90    35.805    22.778
Torsion angles, period  3. refined              268    13.406    15.000
Torsion angles, period  4. refined                9    10.675    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   306     0.265     0.200
VDW repulsions.others                          1363     0.206     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             788     0.083     0.200
HBOND: refined_atoms                            221     0.199     0.200
HBOND.others                                      1     0.121     0.200
VDW repulsions: symmetry: refined_atoms           9     0.215     0.200
VDW repulsions: symmetry: others                 25     0.169     0.200
HBOND: symmetry: refined_atoms                   21     0.267     0.200
HBOND: symmetry: others                           1     0.003     0.200
M. chain bond B values: refined atoms           745     1.716     1.509
M. chain bond B values: others                  745     1.713     1.509
M. chain angle B values: refined atoms          926     2.681     2.251
M. chain angle B values: others                 927     2.680     2.251
S. chain bond B values: refined atoms           811     3.056     1.907
S. chain bond B values: others                  810     3.050     1.906
S. chain angle B values: refined atoms         1177     4.707     2.694
S. chain angle B values: others                1178     4.705     2.694
Long range B values: refined atoms             1853     7.738    21.192
Long range B values: others                    1761     7.469    19.732
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    0.0012
Partial structure    1: scale =     0.3872, B  =   43.9290
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3600 100.00   432.4   442.0  0.17  0.18     182   431.9   458.7  0.20  0.20
 0.147    6142  99.97   258.9   243.2  0.16  0.14     302   255.4   239.2  0.20  0.18
 0.244    7819 100.00   167.5   151.7  0.19  0.17     399   163.5   146.7  0.24  0.20
 0.342    9094 100.00    71.4    85.4  0.32  0.25     496    70.9    87.2  0.37  0.31
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2640   0.927    960   0.843   3600   0.904  0.948  0.9689  0.9725  0.9202  0.9351
  0.1468   5160   0.901    982   0.806   6142   0.886  1.029  0.9581  0.9670  0.9116  0.9444
  0.2444   6842   0.866    977   0.766   7819   0.853  1.049  0.9431  0.9556  0.8880  0.9332
  0.3419   8113   0.788    986   0.707   9099   0.779  0.756  0.8956  0.9100  0.8172  0.8677
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26659
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.9183
Overall R factor                     =     0.1918
Free R factor                        =     0.2322
Average Fourier shell correlation    =     0.9449
AverageFree Fourier shell correlation=     0.9327
Overall weighted R factor            =     0.1665
Free weighted R factor               =     0.1997
Overall weighted R2 factor           =     0.1971
Free weighted R2 factor              =     0.2302
Average correlation coefficient      =     0.9137
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9415
Cruickshanks DPI for coordinate error=     0.0962
DPI based on free R factor           =     0.0992
Overall figure of merit              =     0.8423
ML based su of positional parameters =     0.0619
ML based su of thermal parameters    =     1.8350
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    132963.92       8649.8115       722876.00       722877.44    
 fvalues    132963.92       8649.8115       722876.00       722880.63    

    ****                              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.= 0.917 id.= 3.000 dev= -2.08 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_complete_R11_1-60A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.775     1.644
Bond angles  : others                          3242     1.501     1.582
Torsion angles, period  1. refined              184     6.875     5.000
Torsion angles, period  2. refined               90    35.789    22.778
Torsion angles, period  3. refined              268    13.396    15.000
Torsion angles, period  4. refined                9    10.671    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   307     0.264     0.200
VDW repulsions.others                          1361     0.206     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             787     0.083     0.200
HBOND: refined_atoms                            221     0.199     0.200
HBOND.others                                      1     0.121     0.200
VDW repulsions: symmetry: refined_atoms           9     0.215     0.200
VDW repulsions: symmetry: others                 25     0.169     0.200
HBOND: symmetry: refined_atoms                   21     0.268     0.200
HBOND: symmetry: others                           1     0.004     0.200
M. chain bond B values: refined atoms           745     1.715     1.509
M. chain bond B values: others                  745     1.712     1.509
M. chain angle B values: refined atoms          926     2.680     2.251
M. chain angle B values: others                 927     2.678     2.251
S. chain bond B values: refined atoms           811     3.053     1.906
S. chain bond B values: others                  810     3.048     1.906
S. chain angle B values: refined atoms         1177     4.703     2.694
S. chain angle B values: others                1178     4.701     2.693
Long range B values: refined atoms             1854     7.732    21.217
Long range B values: others                    1761     7.462    19.738
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    0.0034
Partial structure    1: scale =     0.3874, B  =   43.9607
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3600 100.00   432.4   441.9  0.17  0.18     182   431.9   458.8  0.20  0.20
 0.147    6142  99.97   258.9   243.2  0.16  0.14     302   255.4   239.3  0.20  0.18
 0.244    7819 100.00   167.5   151.7  0.19  0.17     399   163.5   146.7  0.24  0.21
 0.342    9094 100.00    71.4    85.3  0.32  0.25     496    70.9    87.2  0.37  0.31
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2640   0.927    960   0.843   3600   0.905  0.948  0.9691  0.9726  0.9202  0.9352
  0.1468   5160   0.901    982   0.806   6142   0.886  1.029  0.9581  0.9670  0.9118  0.9443
  0.2444   6842   0.866    977   0.766   7819   0.853  1.049  0.9430  0.9555  0.8879  0.9332
  0.3419   8113   0.787    986   0.707   9099   0.779  0.756  0.8956  0.9100  0.8171  0.8677
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26659
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.9183
Overall R factor                     =     0.1917
Free R factor                        =     0.2321
Average Fourier shell correlation    =     0.9449
AverageFree Fourier shell correlation=     0.9327
Overall weighted R factor            =     0.1665
Free weighted R factor               =     0.1995
Overall weighted R2 factor           =     0.1971
Free weighted R2 factor              =     0.2301
Average correlation coefficient      =     0.9137
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9415
Cruickshanks DPI for coordinate error=     0.0962
DPI based on free R factor           =     0.0991
Overall figure of merit              =     0.8423
ML based su of positional parameters =     0.0619
ML based su of thermal parameters    =     1.8350
-----------------------------------------------------------------------------
  Time in seconds: CPU =        20.20
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1926   0.2333   0.794      134509.    7081.2   0.0122  0.914   1.777  1.033   0.087
       1   0.1924   0.2340   0.835      133242.    7042.3   0.0123  0.917   1.759  1.024   0.087
       2   0.1911   0.2332   0.842      132941.    7035.2   0.0134  1.001   1.808  1.054   0.090
       3   0.1908   0.2327   0.843      132855.    7033.0   0.0136  1.017   1.833  1.069   0.091
       4   0.1911   0.2326   0.842      132879.    7032.9   0.0131  0.978   1.817  1.059   0.089
       5   0.1916   0.2326   0.842      132932.    7033.7   0.0125  0.935   1.787  1.041   0.087
       6   0.1917   0.2323   0.842      132956.    7034.2   0.0124  0.932   1.779  1.035   0.086
       7   0.1917   0.2323   0.842      132960.    7034.5   0.0124  0.932   1.778  1.035   0.086
       8   0.1917   0.2323   0.842      132962.    7034.6   0.0124  0.931   1.777  1.034   0.086
       9   0.1918   0.2322   0.842      132964.    7034.7   0.0124  0.931   1.776  1.034   0.086
      10   0.1917   0.2321   0.842      132962.    7034.6   0.0124  0.931   1.775  1.033   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1926   0.1917
             R free    0.2333   0.2321
     Rms BondLength    0.0122   0.0124
      Rms BondAngle    1.7766   1.7755
     Rms ChirVolume    0.0873   0.0862
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      52.4s System:    0.2s Elapsed:     0:53