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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: 16:48:12 


 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 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_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R11_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_R11_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:    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  1.7000

  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_R11_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=   2.032 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=   2.180 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=   1.846 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=   2.191 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=   2.417 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=   2.099 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       1149
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.= 0.913 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   0.29064727    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                39.8
Norm of Geom. positional gradient                80.2
Norm of X_ray B-factor gradient                  128.
Norm of Geom. B-factor gradient                 0.209E+05
Product of X_ray and Geom posit. gradients     -0.129E+08
 Cosine of angle between them                      -0.416
Product of X_ray and Geom B-fact gradients     -0.439E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7848E+06 GEOM=     0.2630E+05 TOTAL=     0.8111E+06
 function value    811125.63    

-------------------------------------------------------------------------------
             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     1.850     1.644
Bond angles  : others                          3242     2.353     1.582
Torsion angles, period  1. refined              184     7.031     5.000
Torsion angles, period  2. refined               90    36.573    22.778
Torsion angles, period  3. refined              268    14.232    15.000
Torsion angles, period  4. refined                9    11.209    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                   309     0.262     0.200
VDW repulsions.others                          1332     0.232     0.200
VDW; torsion: refined_atoms                     708     0.174     0.200
VDW; torsion.others                             711     0.082     0.200
HBOND: refined_atoms                            227     0.205     0.200
HBOND.others                                      2     0.074     0.200
VDW repulsions: symmetry: refined_atoms           9     0.236     0.200
VDW repulsions: symmetry: others                 27     0.166     0.200
HBOND: symmetry: refined_atoms                   22     0.221     0.200
M. chain bond B values: refined atoms           745     1.693     1.285
M. chain bond B values: others                  745     1.692     1.286
M. chain angle B values: refined atoms          926     2.627     1.910
M. chain angle B values: others                 927     2.626     1.910
S. chain bond B values: refined atoms           811     2.964     1.677
S. chain bond B values: others                  810     2.960     1.677
S. chain angle B values: refined atoms         1177     4.646     2.350
S. chain angle B values: others                1178     4.644     2.349
Long range B values: refined atoms             1855     7.555    18.234
Long range B values: others                    1757     7.199    16.722
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.1384
Partial structure    1: scale =     0.3814, B  =   48.4401
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.47 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3021 100.00   453.5   462.2  0.16  0.17     150   458.7   486.5  0.21  0.21
 0.130    5148 100.00   299.2   285.8  0.16  0.14     252   293.4   278.8  0.19  0.17
 0.216    6532  99.97   202.5   186.3  0.17  0.15     340   199.6   181.3  0.21  0.18
 0.303    7637 100.00   104.5   117.0  0.26  0.20     406    99.1   115.8  0.32  0.25
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.907    842   0.818   3021   0.882  0.946  0.9631  0.9684  0.9181  0.9389
  0.1301   4282   0.898    866   0.795   5148   0.881  1.009  0.9575  0.9672  0.9144  0.9490
  0.2165   5660   0.875    872   0.771   6532   0.861  1.043  0.9467  0.9591  0.8932  0.9389
  0.3028   6782   0.746    857   0.681   7639   0.738  0.802  0.8943  0.9127  0.8474  0.8909
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22340
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.8917
Overall R factor                     =     0.1787
Free R factor                        =     0.2234
Average Fourier shell correlation    =     0.9463
AverageFree Fourier shell correlation=     0.9327
Overall weighted R factor            =     0.1573
Free weighted R factor               =     0.1950
Overall weighted R2 factor           =     0.1875
Free weighted R2 factor              =     0.2266
Average correlation coefficient      =     0.9248
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9372
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.1107
Overall figure of merit              =     0.8266
ML based su of positional parameters =     0.0739
ML based su of thermal parameters    =     2.3243
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    116276.38       26296.441       811125.63      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36124796    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788809.06    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0717
Partial structure    1: scale =     0.3810, B  =   47.6882
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                     =     0.1783
Free R factor                        =     0.2232
Average Fourier shell correlation    =     0.9548
AverageFree Fourier shell correlation=     0.9423
Average correlation coefficient      =     0.9263
Overall figure of merit              =     0.8592
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115375.48       10060.600       788809.06       811125.63    


     CGMAT cycle number =      3

 Weight matrix   0.36918053    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786418.00    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0021
Partial structure    1: scale =     0.3810, B  =   44.2655
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                     =     0.1771
Free R factor                        =     0.2219
Average Fourier shell correlation    =     0.9559
AverageFree Fourier shell correlation=     0.9434
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8613
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    115084.16       9635.8818       786418.00       788809.06    


     CGMAT cycle number =      4

 Weight matrix   0.37219381    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785567.50    

-------------------------------------------------------------------------------
             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  =    0.0317
Partial structure    1: scale =     0.3881, B  =   45.2960
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                     =     0.1768
Free R factor                        =     0.2219
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8620
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    114974.10       9528.2490       785567.50       786418.00    


     CGMAT cycle number =      5

 Weight matrix   0.37597308    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785199.06    

-------------------------------------------------------------------------------
             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  =    0.0319
Partial structure    1: scale =     0.3884, B  =   45.2211
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                     =     0.1767
Free R factor                        =     0.2214
Average Fourier shell correlation    =     0.9565
AverageFree Fourier shell correlation=     0.9442
Average correlation coefficient      =     0.9296
Overall figure of merit              =     0.8628
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114914.24       9563.8535       785199.06       785567.50    


     CGMAT cycle number =      6

 Weight matrix   0.34286699    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    714541.94    

-------------------------------------------------------------------------------
             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  =   -0.0040
Partial structure    1: scale =     0.3886, B  =   45.2295
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                     =     0.1766
Free R factor                        =     0.2208
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9442
Average correlation coefficient      =     0.9298
Overall figure of merit              =     0.8630
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114885.63       9594.5615       714541.94       785199.06    


     CGMAT cycle number =      7

 Weight matrix   0.31180304    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650390.75    

-------------------------------------------------------------------------------
             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  =   -0.0039
Partial structure    1: scale =     0.3887, B  =   45.2309
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                        =     0.2205
Average Fourier shell correlation    =     0.9565
AverageFree Fourier shell correlation=     0.9442
Average correlation coefficient      =     0.9295
Overall figure of merit              =     0.8630
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    114924.24       9314.1934       650390.75       714541.94    


     CGMAT cycle number =      8

 Weight matrix   0.31130895    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650436.06    

-------------------------------------------------------------------------------
             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  =   -0.0122
Partial structure    1: scale =     0.3888, B  =   45.1408
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                     =     0.1776
Free R factor                        =     0.2205
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9441
Average correlation coefficient      =     0.9290
Overall figure of merit              =     0.8629
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    115004.45       8955.6133       650488.81       650390.75    

 fvalues    115004.45       8955.6133       650489.75       650479.63    
 fvalues    115004.45       8955.6133       650489.75       650479.63    


     CGMAT cycle number =      9

 Weight matrix   0.31124052    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    650503.06    

-------------------------------------------------------------------------------
             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  =   -0.0196
Partial structure    1: scale =     0.3890, B  =   45.1017
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                     =     0.1776
Free R factor                        =     0.2205
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9440
Average correlation coefficient      =     0.9289
Overall figure of merit              =     0.8629
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    115013.51       8932.3555       650516.25       650479.63    

 fvalues    115013.51       8932.3555       650516.69       650506.88    
 fvalues    115013.51       8932.3555       650516.69       650506.88    


     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.= 0.920 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    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   0.31124696    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                37.2
Norm of Geom. positional gradient                37.5
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.135E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.437E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.6416E+06 GEOM=      8925.     TOTAL=     0.6505E+06
 function value    650503.69    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.779     1.644
Bond angles  : others                          3242     1.500     1.582
Torsion angles, period  1. refined              184     6.885     5.000
Torsion angles, period  2. refined               90    36.156    22.778
Torsion angles, period  3. refined              268    13.671    15.000
Torsion angles, period  4. refined                9    10.880    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   305     0.264     0.200
VDW repulsions.others                          1353     0.205     0.200
VDW; torsion: refined_atoms                     721     0.172     0.200
VDW; torsion.others                             803     0.083     0.200
HBOND: refined_atoms                            218     0.200     0.200
HBOND.others                                      1     0.118     0.200
VDW repulsions: symmetry: refined_atoms           8     0.228     0.200
VDW repulsions: symmetry: others                 26     0.160     0.200
HBOND: symmetry: refined_atoms                   22     0.240     0.200
M. chain bond B values: refined atoms           745     1.681     1.390
M. chain bond B values: others                  745     1.679     1.390
M. chain angle B values: refined atoms          926     2.636     2.071
M. chain angle B values: others                 927     2.635     2.071
S. chain bond B values: refined atoms           812     2.982     1.786
S. chain bond B values: others                  811     2.975     1.786
S. chain angle B values: refined atoms         1177     4.631     2.514
S. chain angle B values: others                1178     4.629     2.514
Long range B values: refined atoms             1849     7.534    19.640
Long range B values: others                    1757     7.223    18.173
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =   -0.0190
Partial structure    1: scale =     0.3890, B  =   45.1460
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3021 100.00   453.3   462.4  0.16  0.17     150   458.5   488.0  0.21  0.21
 0.130    5148 100.00   299.1   285.1  0.16  0.14     252   293.3   279.3  0.19  0.17
 0.216    6532  99.97   202.4   186.4  0.17  0.15     340   199.5   180.7  0.21  0.18
 0.303    7637 100.00   104.4   116.3  0.25  0.19     406    99.1   115.2  0.31  0.25
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.924    842   0.846   3021   0.902  0.946  0.9672  0.9718  0.9187  0.9362
  0.1301   4282   0.902    866   0.800   5148   0.885  1.009  0.9589  0.9678  0.9152  0.9478
  0.2165   5660   0.887    872   0.783   6532   0.873  1.043  0.9517  0.9620  0.8993  0.9386
  0.3028   6782   0.832    857   0.759   7639   0.824  0.841  0.9199  0.9374  0.8539  0.9050
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22340
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.8917
Overall R factor                     =     0.1776
Free R factor                        =     0.2205
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9440
Overall weighted R factor            =     0.1583
Free weighted R factor               =     0.1929
Overall weighted R2 factor           =     0.1900
Free weighted R2 factor              =     0.2244
Average correlation coefficient      =     0.9289
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9383
Cruickshanks DPI for coordinate error=     0.1074
DPI based on free R factor           =     0.1093
Overall figure of merit              =     0.8629
ML based su of positional parameters =     0.0648
ML based su of thermal parameters    =     1.9844
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    115014.34       8924.5762       650503.69       650506.88    

    ****                              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.= 0.920 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_1-70A.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     1.777     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.885     5.000
Torsion angles, period  2. refined               90    36.149    22.778
Torsion angles, period  3. refined              268    13.662    15.000
Torsion angles, period  4. refined                9    10.875    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   305     0.264     0.200
VDW repulsions.others                          1354     0.205     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             801     0.083     0.200
HBOND: refined_atoms                            218     0.200     0.200
HBOND.others                                      1     0.118     0.200
VDW repulsions: symmetry: refined_atoms           8     0.228     0.200
VDW repulsions: symmetry: others                 26     0.160     0.200
HBOND: symmetry: refined_atoms                   22     0.241     0.200
M. chain bond B values: refined atoms           745     1.679     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    19.658
Long range B values: others                    1758     7.219    18.192
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =   -0.0123
Partial structure    1: scale =     0.3890, B  =   45.1068
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3021 100.00   453.3   462.4  0.16  0.17     150   458.5   488.1  0.21  0.21
 0.130    5148 100.00   299.1   285.1  0.16  0.14     252   293.3   279.3  0.19  0.17
 0.216    6532  99.97   202.4   186.3  0.17  0.15     340   199.6   180.7  0.21  0.18
 0.303    7637 100.00   104.4   116.2  0.25  0.19     406    99.1   115.2  0.31  0.25
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.924    842   0.846   3021   0.902  0.946  0.9672  0.9718  0.9186  0.9362
  0.1301   4282   0.902    866   0.800   5148   0.885  1.009  0.9589  0.9678  0.9153  0.9478
  0.2165   5660   0.887    872   0.783   6532   0.873  1.043  0.9517  0.9620  0.8993  0.9386
  0.3028   6782   0.832    857   0.759   7639   0.824  0.841  0.9198  0.9373  0.8538  0.9050
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22340
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.8917
Overall R factor                     =     0.1776
Free R factor                        =     0.2205
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9440
Overall weighted R factor            =     0.1583
Free weighted R factor               =     0.1928
Overall weighted R2 factor           =     0.1901
Free weighted R2 factor              =     0.2244
Average correlation coefficient      =     0.9289
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9383
Cruickshanks DPI for coordinate error=     0.1074
DPI based on free R factor           =     0.1093
Overall figure of merit              =     0.8629
ML based su of positional parameters =     0.0648
ML based su of thermal parameters    =     1.9844
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.81
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1787   0.2234   0.827      116276.    6110.9   0.0131  0.966   1.850  1.067   0.087
       1   0.1783   0.2232   0.859      115375.    6079.5   0.0124  0.919   1.797  1.038   0.086
       2   0.1771   0.2219   0.861      115084.    6068.4   0.0133  0.991   1.826  1.059   0.090
       3   0.1768   0.2219   0.862      114974.    6063.4   0.0134  0.999   1.837  1.067   0.091
       4   0.1767   0.2214   0.863      114914.    6061.1   0.0134  1.002   1.843  1.071   0.091
       5   0.1766   0.2208   0.863      114886.    6059.7   0.0134  1.005   1.848  1.074   0.092
       6   0.1770   0.2205   0.863      114924.    6059.0   0.0128  0.961   1.820  1.058   0.090
       7   0.1776   0.2205   0.863      114997.    6060.1   0.0122  0.916   1.782  1.036   0.088
       8   0.1776   0.2205   0.863      115013.    6060.9   0.0122  0.915   1.780  1.034   0.088
       9   0.1776   0.2205   0.863      115014.    6060.9   0.0122  0.915   1.779  1.034   0.088
      10   0.1776   0.2205   0.863      115019.    6060.8   0.0122  0.914   1.777  1.033   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1787   0.1776
             R free    0.2234   0.2205
     Rms BondLength    0.0131   0.0122
      Rms BondAngle    1.8495   1.7770
     Rms ChirVolume    0.0868   0.0875
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      50.0s System:    0.1s Elapsed:     0:50