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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: 17:06:21 


 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 1.70     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 16
  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_R16_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R16_1-70A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R16_1-70A.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       0.0865
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7000
  Estimated number of reflections :      29131
  Free R exclusion - flag equals:    16
  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  1.7000

  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_R16_1-80A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.037 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=   1.836 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=   2.182 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=   2.404 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=   2.424 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=   2.066 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                           16
Number of "free" reflections       1174
Number of   all  reflections      23491
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23491

   Current auto weighting coefficient =    6.7496872    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.29809216    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                39.1
Norm of Geom. positional gradient                80.5
Norm of X_ray B-factor gradient                  128.
Norm of Geom. B-factor gradient                 0.214E+05
Product of X_ray and Geom posit. gradients     -0.130E+08
 Cosine of angle between them                      -0.428
Product of X_ray and Geom B-fact gradients     -0.447E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7821E+06 GEOM=     0.2648E+05 TOTAL=     0.8086E+06
 function value    808574.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.816     1.644
Bond angles  : others                          3242     2.350     1.582
Torsion angles, period  1. refined              184     6.957     5.000
Torsion angles, period  2. refined               90    36.621    22.778
Torsion angles, period  3. refined              268    13.966    15.000
Torsion angles, period  4. refined                9    11.845    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   302     0.269     0.200
VDW repulsions.others                          1331     0.233     0.200
VDW; torsion: refined_atoms                     714     0.173     0.200
VDW; torsion.others                             717     0.081     0.200
HBOND: refined_atoms                            225     0.198     0.200
HBOND.others                                      1     0.096     0.200
VDW repulsions: symmetry: refined_atoms           8     0.217     0.200
VDW repulsions: symmetry: others                 22     0.176     0.200
HBOND: symmetry: refined_atoms                   20     0.226     0.200
M. chain bond B values: refined atoms           745     1.692     1.295
M. chain bond B values: others                  745     1.691     1.295
M. chain angle B values: refined atoms          926     2.638     1.923
M. chain angle B values: others                 927     2.636     1.923
S. chain bond B values: refined atoms           811     2.921     1.686
S. chain bond B values: others                  810     2.917     1.686
S. chain angle B values: refined atoms         1177     4.604     2.363
S. chain angle B values: others                1178     4.602     2.363
Long range B values: refined atoms             1850     6.982    18.029
Long range B values: others                    1756     6.675    16.562
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =    1.0931
Partial structure    1: scale =     0.3899, B  =   49.2389
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3004 100.00   452.1   461.3  0.16  0.17     167   464.7   474.7  0.18  0.19
 0.130    5143 100.00   299.5   286.4  0.16  0.14     257   275.4   267.9  0.22  0.19
 0.216    6502  99.97   202.1   186.0  0.17  0.15     370   198.5   183.8  0.22  0.19
 0.303    7663 100.00   103.9   116.5  0.26  0.20     380   104.9   119.4  0.30  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2160   0.923    844   0.830   3004   0.897  0.947  0.9694  0.9731  0.9189  0.9388
  0.1301   4274   0.895    869   0.792   5143   0.878  1.004  0.9483  0.9668  0.8953  0.9489
  0.2165   5622   0.879    880   0.769   6502   0.864  1.045  0.9443  0.9592  0.8854  0.9388
  0.3028   6798   0.749    868   0.682   7666   0.741  0.807  0.9021  0.9137  0.8423  0.8925
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22315
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9981
Overall R factor                     =     0.1785
Free R factor                        =     0.2185
Average Fourier shell correlation    =     0.9472
AverageFree Fourier shell correlation=     0.9351
Overall weighted R factor            =     0.1569
Free weighted R factor               =     0.1944
Overall weighted R2 factor           =     0.1881
Free weighted R2 factor              =     0.2206
Average correlation coefficient      =     0.9252
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9376
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.1084
Overall figure of merit              =     0.8296
ML based su of positional parameters =     0.0730
ML based su of thermal parameters    =     2.3027
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    115871.97       26475.012       808574.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35177454    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    787574.94    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =   -0.0759
Partial structure    1: scale =     0.3898, B  =   48.5602
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1784
Free R factor                        =     0.2169
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9421
Average correlation coefficient      =     0.9263
Overall figure of merit              =     0.8546
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115184.38       10116.436       787574.94       808574.56    


     CGMAT cycle number =      3

 Weight matrix   0.36324358    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785220.94    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =   -0.0258
Partial structure    1: scale =     0.3892, B  =   45.4712
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1775
Free R factor                        =     0.2164
Average Fourier shell correlation    =     0.9554
AverageFree Fourier shell correlation=     0.9433
Average correlation coefficient      =     0.9284
Overall figure of merit              =     0.8583
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    114924.45       9516.9043       785220.94       787574.94    


     CGMAT cycle number =      4

 Weight matrix   0.36619797    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784450.94    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =   -0.0003
Partial structure    1: scale =     0.3893, B  =   45.4796
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1772
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9558
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8592
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    114830.68       9379.7607       784450.94       785220.94    


     CGMAT cycle number =      5

 Weight matrix   0.36715031    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784194.94    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =   -0.0000
Partial structure    1: scale =     0.3893, B  =   45.4795
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1770
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9559
AverageFree Fourier shell correlation=     0.9439
Average correlation coefficient      =     0.9296
Overall figure of merit              =     0.8595
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114789.83       9399.5264       784194.94       784450.94    


     CGMAT cycle number =      6

 Weight matrix   0.36784518    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784110.44    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =   -0.0033
Partial structure    1: scale =     0.3897, B  =   45.5383
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1770
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9560
AverageFree Fourier shell correlation=     0.9440
Average correlation coefficient      =     0.9298
Overall figure of merit              =     0.8596
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114771.84       9436.4258       784110.44       784194.94    


     CGMAT cycle number =      7

 Weight matrix   0.36758628    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784076.25    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =   -0.0015
Partial structure    1: scale =     0.3903, B  =   45.6922
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1770
Free R factor                        =     0.2163
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9439
Average correlation coefficient      =     0.9299
Overall figure of merit              =     0.8596
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    114764.40       9452.4316       784076.25       784110.44    


     CGMAT cycle number =      8

 Weight matrix   0.36695230    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784102.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =   -0.0016
Partial structure    1: scale =     0.3906, B  =   45.8458
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1770
Free R factor                        =     0.2165
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9439
Average correlation coefficient      =     0.9300
Overall figure of merit              =     0.8595
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    114767.41       9458.6982       784094.25       784076.25    
 fvalues    114767.41       9458.6982       784094.25       784102.81    


     CGMAT cycle number =      9

 Weight matrix   0.36672714    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784080.56    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =   -0.0006
Partial structure    1: scale =     0.3907, B  =   45.8304
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1770
Free R factor                        =     0.2166
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9301
Overall figure of merit              =     0.8595
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    114765.27       9450.9590       784080.56       784102.81    


     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.= 0.912 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        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.36681652    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                42.7
Norm of Geom. positional gradient                42.6
Norm of X_ray B-factor gradient                  129.
Norm of Geom. B-factor gradient                  129.
Product of X_ray and Geom posit. gradients     -0.176E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.537E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7746E+06 GEOM=      9453.     TOTAL=     0.7841E+06
 function value    784090.56    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.829     1.644
Bond angles  : others                          3242     1.505     1.582
Torsion angles, period  1. refined              184     6.902     5.000
Torsion angles, period  2. refined               90    36.243    22.778
Torsion angles, period  3. refined              268    14.012    15.000
Torsion angles, period  4. refined                9    11.761    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   305     0.269     0.200
VDW repulsions.others                          1357     0.206     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             776     0.085     0.200
HBOND: refined_atoms                            215     0.201     0.200
HBOND.others                                      1     0.129     0.200
VDW repulsions: symmetry: refined_atoms           8     0.199     0.200
VDW repulsions: symmetry: others                 21     0.171     0.200
HBOND: symmetry: refined_atoms                   19     0.220     0.200
M. chain bond B values: refined atoms           745     1.733     1.388
M. chain bond B values: others                  745     1.731     1.389
M. chain angle B values: refined atoms          926     2.696     2.067
M. chain angle B values: others                 927     2.695     2.067
S. chain bond B values: refined atoms           811     3.090     1.797
S. chain bond B values: others                  810     3.081     1.797
S. chain angle B values: refined atoms         1177     4.790     2.524
S. chain angle B values: others                1178     4.788     2.523
Long range B values: refined atoms             1844     7.067    19.448
Long range B values: others                    1752     6.751    17.979
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =   -0.0023
Partial structure    1: scale =     0.3901, B  =   45.8163
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3004 100.00   452.6   462.5  0.16  0.17     167   465.2   474.4  0.18  0.19
 0.130    5143 100.00   299.8   286.1  0.16  0.14     257   275.7   268.0  0.21  0.19
 0.216    6502  99.97   202.4   186.2  0.17  0.15     370   198.7   183.3  0.22  0.19
 0.303    7663 100.00   104.1   116.1  0.25  0.19     380   105.0   119.0  0.30  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2160   0.927    844   0.837   3004   0.901  0.947  0.9699  0.9734  0.9170  0.9376
  0.1301   4274   0.900    869   0.801   5143   0.883  1.004  0.9503  0.9677  0.8976  0.9484
  0.2165   5622   0.886    880   0.777   6502   0.871  1.045  0.9473  0.9613  0.8889  0.9391
  0.3028   6798   0.825    868   0.752   7666   0.817  0.837  0.9246  0.9371  0.8528  0.9073
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22315
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9981
Overall R factor                     =     0.1769
Free R factor                        =     0.2168
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9438
Overall weighted R factor            =     0.1577
Free weighted R factor               =     0.1943
Overall weighted R2 factor           =     0.1901
Free weighted R2 factor              =     0.2215
Average correlation coefficient      =     0.9301
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9383
Cruickshanks DPI for coordinate error=     0.1071
DPI based on free R factor           =     0.1075
Overall figure of merit              =     0.8595
ML based su of positional parameters =     0.0657
ML based su of thermal parameters    =     2.0160
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    114766.69       9452.7568       784088.31       784080.56    
 fvalues    114766.69       9452.7568       784088.31       784092.00    

    ****                              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.= 0.912 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R16_1-70A.mtz 




-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.830     1.644
Bond angles  : others                          3242     1.505     1.582
Torsion angles, period  1. refined              184     6.896     5.000
Torsion angles, period  2. refined               90    36.217    22.778
Torsion angles, period  3. refined              268    13.959    15.000
Torsion angles, period  4. refined                9    11.756    15.000
Chiral centres: refined atoms                   196     0.092     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   305     0.269     0.200
VDW repulsions.others                          1360     0.206     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             777     0.085     0.200
HBOND: refined_atoms                            214     0.202     0.200
HBOND.others                                      1     0.129     0.200
VDW repulsions: symmetry: refined_atoms           8     0.199     0.200
VDW repulsions: symmetry: others                 21     0.172     0.200
HBOND: symmetry: refined_atoms                   19     0.220     0.200
M. chain bond B values: refined atoms           745     1.731     1.388
M. chain bond B values: others                  745     1.729     1.388
M. chain angle B values: refined atoms          926     2.692     2.066
M. chain angle B values: others                 927     2.690     2.066
S. chain bond B values: refined atoms           811     3.089     1.796
S. chain bond B values: others                  810     3.080     1.796
S. chain angle B values: refined atoms         1177     4.786     2.522
S. chain angle B values: others                1178     4.784     2.522
Long range B values: refined atoms             1843     7.066    19.474
Long range B values: others                    1751     6.751    18.007
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =   -0.0010
Partial structure    1: scale =     0.3899, B  =   45.7993
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3004 100.00   452.7   462.6  0.16  0.17     167   465.2   474.4  0.18  0.19
 0.130    5143 100.00   299.8   286.1  0.16  0.14     257   275.7   268.1  0.21  0.19
 0.216    6502  99.97   202.4   186.2  0.17  0.15     370   198.7   183.3  0.22  0.19
 0.303    7663 100.00   104.1   116.1  0.25  0.19     380   105.0   119.0  0.30  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2160   0.927    844   0.836   3004   0.901  0.947  0.9699  0.9734  0.9170  0.9375
  0.1301   4274   0.900    869   0.801   5143   0.883  1.004  0.9502  0.9677  0.8976  0.9484
  0.2165   5622   0.886    880   0.777   6502   0.871  1.045  0.9473  0.9613  0.8890  0.9391
  0.3028   6798   0.825    868   0.752   7666   0.817  0.837  0.9247  0.9372  0.8529  0.9074
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22315
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9981
Overall R factor                     =     0.1769
Free R factor                        =     0.2169
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9439
Overall weighted R factor            =     0.1577
Free weighted R factor               =     0.1944
Overall weighted R2 factor           =     0.1901
Free weighted R2 factor              =     0.2216
Average correlation coefficient      =     0.9302
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9383
Cruickshanks DPI for coordinate error=     0.1071
DPI based on free R factor           =     0.1076
Overall figure of merit              =     0.8595
ML based su of positional parameters =     0.0657
ML based su of thermal parameters    =     2.0160
-----------------------------------------------------------------------------
  Time in seconds: CPU =        16.32
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1785   0.2185   0.830      115872.    6279.5   0.0129  0.960   1.816  1.047   0.088
       1   0.1784   0.2169   0.855      115184.    6255.4   0.0124  0.925   1.779  1.025   0.087
       2   0.1775   0.2164   0.858      114924.    6248.2   0.0131  0.981   1.800  1.041   0.090
       3   0.1772   0.2159   0.859      114831.    6244.2   0.0132  0.993   1.812  1.050   0.091
       4   0.1770   0.2159   0.860      114790.    6242.6   0.0133  0.997   1.819  1.055   0.091
       5   0.1770   0.2161   0.860      114772.    6242.2   0.0133  0.999   1.824  1.059   0.092
       6   0.1770   0.2163   0.860      114764.    6242.3   0.0133  0.999   1.827  1.060   0.092
       7   0.1770   0.2165   0.859      114767.    6243.1   0.0133  0.999   1.828  1.061   0.092
       8   0.1770   0.2166   0.859      114765.    6243.3   0.0133  0.998   1.829  1.062   0.092
       9   0.1769   0.2168   0.859      114766.    6243.2   0.0133  0.998   1.829  1.062   0.092
      10   0.1769   0.2169   0.860      114764.    6243.1   0.0133  0.998   1.830  1.062   0.092
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1785   0.1769
             R free    0.2185   0.2169
     Rms BondLength    0.0129   0.0133
      Rms BondAngle    1.8164   1.8296
     Rms ChirVolume    0.0877   0.0921
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      48.3s System:    0.2s Elapsed:     0:48