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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: 15:41:27 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.80     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 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_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R11_1-80A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R11_1-80A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  Free R exclusion - flag equals:    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  1.8000

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R11_1-90A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.003 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=   2.188 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=   1.839 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=   2.210 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=   2.375 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=   2.446 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=   2.049 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        964
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.907 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  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.26825711    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                40.5
Norm of Geom. positional gradient                79.4
Norm of X_ray B-factor gradient                  134.
Norm of Geom. B-factor gradient                 0.210E+05
Product of X_ray and Geom posit. gradients     -0.105E+08
 Cosine of angle between them                      -0.338
Product of X_ray and Geom B-fact gradients     -0.422E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7076E+06 GEOM=     0.2607E+05 TOTAL=     0.7337E+06
 function value    733658.81    

-------------------------------------------------------------------------------
             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     1.812     1.644
Bond angles  : others                          3242     2.343     1.582
Torsion angles, period  1. refined              184     6.932     5.000
Torsion angles, period  2. refined               90    36.939    22.778
Torsion angles, period  3. refined              268    14.133    15.000
Torsion angles, period  4. refined                9    10.008    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   312     0.261     0.200
VDW repulsions.others                          1340     0.231     0.200
VDW; torsion: refined_atoms                     726     0.170     0.200
VDW; torsion.others                             721     0.080     0.200
HBOND: refined_atoms                            230     0.216     0.200
HBOND.others                                      1     0.002     0.200
VDW repulsions: symmetry: refined_atoms           9     0.248     0.200
VDW repulsions: symmetry: others                 28     0.167     0.200
HBOND: symmetry: refined_atoms                   19     0.219     0.200
HBOND: symmetry: others                           1     0.015     0.200
M. chain bond B values: refined atoms           745     1.642     1.203
M. chain bond B values: others                  745     1.641     1.203
M. chain angle B values: refined atoms          926     2.586     1.786
M. chain angle B values: others                 927     2.584     1.786
S. chain bond B values: refined atoms           812     2.719     1.563
S. chain bond B values: others                  811     2.716     1.563
S. chain angle B values: refined atoms         1177     4.260     2.192
S. chain angle B values: others                1178     4.258     2.191
Long range B values: refined atoms             1871     7.237    17.091
Long range B values: others                    1772     6.901    15.677
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =    0.8643
Partial structure    1: scale =     0.3779, B  =   50.5352
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2568 100.00   473.9   481.1  0.16  0.17     125   475.0   504.2  0.21  0.22
 0.116    4366 100.00   342.5   327.7  0.16  0.15     213   338.9   323.2  0.20  0.18
 0.193    5514  99.97   226.7   215.6  0.15  0.13     294   225.7   213.4  0.20  0.17
 0.270    6455 100.00   148.5   155.6  0.22  0.17     332   142.5   153.7  0.26  0.20
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1811   0.919    757   0.827   2568   0.892  0.953  0.9647  0.9700  0.9225  0.9399
  0.1161   3594   0.892    772   0.792   4366   0.874  1.000  0.9556  0.9652  0.9137  0.9458
  0.1931   4748   0.884    766   0.777   5514   0.870  1.014  0.9506  0.9635  0.8880  0.9448
  0.2701   5685   0.819    778   0.738   6463   0.809  0.892  0.9223  0.9365  0.8602  0.9035
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18911
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.8503
Overall R factor                     =     0.1688
Free R factor                        =     0.2146
Average Fourier shell correlation    =     0.9556
AverageFree Fourier shell correlation=     0.9438
Overall weighted R factor            =     0.1521
Free weighted R factor               =     0.1925
Overall weighted R2 factor           =     0.1839
Free weighted R2 factor              =     0.2235
Average correlation coefficient      =     0.9303
Overall correlation coefficient      =     0.9558
Free correlation coefficient         =     0.9317
Cruickshanks DPI for coordinate error=     0.1231
DPI based on free R factor           =     0.1224
Overall figure of merit              =     0.8531
ML based su of positional parameters =     0.0783
ML based su of thermal parameters    =     2.5512
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    101090.47       26069.900       733658.81      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30561507    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    714180.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0462
Partial structure    1: scale =     0.3773, B  =   49.9180
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1678
Free R factor                        =     0.2125
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9479
Average correlation coefficient      =     0.9330
Overall figure of merit              =     0.8675
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100577.27       10183.584       714180.38       733658.81    


     CGMAT cycle number =      3

 Weight matrix   0.31119379    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711728.06    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0097
Partial structure    1: scale =     0.3766, B  =   47.4504
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1666
Free R factor                        =     0.2106
Average Fourier shell correlation    =     0.9604
AverageFree Fourier shell correlation=     0.9488
Average correlation coefficient      =     0.9350
Overall figure of merit              =     0.8690
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100314.95       9567.4590       711728.06       714180.38    


     CGMAT cycle number =      4

 Weight matrix   0.31285518    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710833.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0065
Partial structure    1: scale =     0.3765, B  =   47.1615
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2100
Average Fourier shell correlation    =     0.9607
AverageFree Fourier shell correlation=     0.9491
Average correlation coefficient      =     0.9356
Overall figure of merit              =     0.8694
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100211.54       9397.0566       710833.88       711728.06    


     CGMAT cycle number =      5

 Weight matrix   0.31335419    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710561.94    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0016
Partial structure    1: scale =     0.3766, B  =   47.1565
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1661
Free R factor                        =     0.2096
Average Fourier shell correlation    =     0.9608
AverageFree Fourier shell correlation=     0.9492
Average correlation coefficient      =     0.9358
Overall figure of merit              =     0.8697
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100171.77       9403.4551       710561.94       710833.88    


     CGMAT cycle number =      6

 Weight matrix   0.31279922    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710430.06    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =    0.0026
Partial structure    1: scale =     0.3765, B  =   47.1107
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1659
Free R factor                        =     0.2096
Average Fourier shell correlation    =     0.9608
AverageFree Fourier shell correlation=     0.9491
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8696
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100147.84       9439.0918       710430.06       710561.94    


     CGMAT cycle number =      7

 Weight matrix   0.31216773    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710392.56    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =    0.0005
Partial structure    1: scale =     0.3765, B  =   47.0852
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1659
Free R factor                        =     0.2095
Average Fourier shell correlation    =     0.9608
AverageFree Fourier shell correlation=     0.9490
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8695
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100141.85       9443.5420       710392.56       710430.06    


     CGMAT cycle number =      8

 Weight matrix   0.31177524    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710382.31    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =    0.0013
Partial structure    1: scale =     0.3765, B  =   47.0331
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1660
Free R factor                        =     0.2096
Average Fourier shell correlation    =     0.9607
AverageFree Fourier shell correlation=     0.9490
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8694
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    100140.02       9446.0625       710382.31       710392.56    


     CGMAT cycle number =      9

 Weight matrix   0.31113857    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710396.13    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0000
Partial structure    1: scale =     0.3765, B  =   47.0333
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1660
Free R factor                        =     0.2097
Average Fourier shell correlation    =     0.9607
AverageFree Fourier shell correlation=     0.9489
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8693
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    100143.26       9437.3467       710383.19       710382.31    
 fvalues    100143.26       9437.3467       710383.19       710396.25    


     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.= 0.926 id.= 3.000 dev= -2.07 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.31072500    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                39.3
Norm of Geom. positional gradient                39.3
Norm of X_ray B-factor gradient                  129.
Norm of Geom. B-factor gradient                  129.
Product of X_ray and Geom posit. gradients     -0.149E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.539E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7010E+06 GEOM=      9441.     TOTAL=     0.7104E+06
 function value    710406.69    

-------------------------------------------------------------------------------
             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     1.849     1.644
Bond angles  : others                          3242     1.491     1.582
Torsion angles, period  1. refined              184     7.034     5.000
Torsion angles, period  2. refined               90    36.590    22.778
Torsion angles, period  3. refined              268    14.222    15.000
Torsion angles, period  4. refined                9    11.216    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                   310     0.262     0.200
VDW repulsions.others                          1349     0.205     0.200
VDW; torsion: refined_atoms                     710     0.173     0.200
VDW; torsion.others                             796     0.084     0.200
HBOND: refined_atoms                            227     0.205     0.200
HBOND.others                                      1     0.108     0.200
VDW repulsions: symmetry: refined_atoms           9     0.233     0.200
VDW repulsions: symmetry: others                 29     0.155     0.200
HBOND: symmetry: refined_atoms                   22     0.218     0.200
M. chain bond B values: refined atoms           745     1.693     1.285
M. chain bond B values: others                  745     1.692     1.285
M. chain angle B values: refined atoms          926     2.626     1.910
M. chain angle B values: others                 927     2.625     1.909
S. chain bond B values: refined atoms           811     2.961     1.677
S. chain bond B values: others                  810     2.958     1.677
S. chain angle B values: refined atoms         1177     4.642     2.350
S. chain angle B values: others                1178     4.640     2.349
Long range B values: refined atoms             1857     7.573    18.253
Long range B values: others                    1759     7.224    16.743
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0002
Partial structure    1: scale =     0.3766, B  =   47.0650
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2568 100.00   472.7   481.2  0.16  0.17     125   473.7   505.3  0.20  0.21
 0.116    4366 100.00   341.6   326.2  0.16  0.15     213   338.0   321.0  0.19  0.17
 0.193    5514  99.97   226.1   214.6  0.16  0.13     294   225.1   211.8  0.20  0.17
 0.270    6455 100.00   148.1   154.6  0.20  0.16     332   142.1   152.8  0.26  0.19
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1811   0.934    757   0.850   2568   0.909  0.955  0.9684  0.9732  0.9254  0.9414
  0.1161   3594   0.899    772   0.802   4366   0.882  1.000  0.9591  0.9673  0.9202  0.9468
  0.1931   4748   0.889    766   0.783   5514   0.874  1.014  0.9527  0.9639  0.8929  0.9422
  0.2701   5685   0.850    778   0.769   6463   0.841  0.904  0.9314  0.9485  0.8632  0.9213
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18911
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.8503
Overall R factor                     =     0.1660
Free R factor                        =     0.2099
Average Fourier shell correlation    =     0.9607
AverageFree Fourier shell correlation=     0.9488
Overall weighted R factor            =     0.1512
Free weighted R factor               =     0.1875
Overall weighted R2 factor           =     0.1828
Free weighted R2 factor              =     0.2196
Average correlation coefficient      =     0.9360
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9344
Cruickshanks DPI for coordinate error=     0.1210
DPI based on free R factor           =     0.1197
Overall figure of merit              =     0.8693
ML based su of positional parameters =     0.0727
ML based su of thermal parameters    =     2.3448
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    100144.09       9441.0508       710391.88       710396.25    
 fvalues    100144.09       9441.0508       710391.88       710405.75    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.927 id.= 3.000 dev= -2.07 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 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_1-80A.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     1.849     1.644
Bond angles  : others                          3242     1.492     1.582
Torsion angles, period  1. refined              184     7.029     5.000
Torsion angles, period  2. refined               90    36.568    22.778
Torsion angles, period  3. refined              268    14.236    15.000
Torsion angles, period  4. refined                9    11.226    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                   309     0.262     0.200
VDW repulsions.others                          1355     0.205     0.200
VDW; torsion: refined_atoms                     710     0.173     0.200
VDW; torsion.others                             798     0.084     0.200
HBOND: refined_atoms                            227     0.205     0.200
HBOND.others                                      1     0.111     0.200
VDW repulsions: symmetry: refined_atoms           9     0.236     0.200
VDW repulsions: symmetry: others                 29     0.155     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     2.625     1.910
S. chain bond B values: refined atoms           811     2.964     1.677
S. chain bond B values: others                  810     2.961     1.677
S. chain angle B values: refined atoms         1177     4.646     2.350
S. chain angle B values: others                1178     4.645     2.349
Long range B values: refined atoms             1857     7.553    18.242
Long range B values: others                    1759     7.198    16.732
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0045
Partial structure    1: scale =     0.3769, B  =   46.9836
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2568 100.00   472.5   481.1  0.16  0.17     125   473.5   505.3  0.20  0.21
 0.116    4366 100.00   341.5   326.2  0.16  0.15     213   337.8   320.9  0.19  0.18
 0.193    5514  99.97   226.0   214.5  0.16  0.13     294   225.0   211.7  0.20  0.17
 0.270    6455 100.00   148.1   154.5  0.20  0.16     332   142.1   152.7  0.26  0.19
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1811   0.934    757   0.850   2568   0.909  0.955  0.9682  0.9732  0.9249  0.9414
  0.1161   3594   0.899    772   0.803   4366   0.882  1.000  0.9592  0.9673  0.9202  0.9467
  0.1931   4748   0.888    766   0.783   5514   0.874  1.014  0.9526  0.9638  0.8929  0.9421
  0.2701   5685   0.851    778   0.770   6463   0.841  0.907  0.9314  0.9485  0.8631  0.9214
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18911
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.8503
Overall R factor                     =     0.1660
Free R factor                        =     0.2101
Average Fourier shell correlation    =     0.9607
AverageFree Fourier shell correlation=     0.9488
Overall weighted R factor            =     0.1512
Free weighted R factor               =     0.1877
Overall weighted R2 factor           =     0.1826
Free weighted R2 factor              =     0.2199
Average correlation coefficient      =     0.9360
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9342
Cruickshanks DPI for coordinate error=     0.1210
DPI based on free R factor           =     0.1198
Overall figure of merit              =     0.8693
ML based su of positional parameters =     0.0727
ML based su of thermal parameters    =     2.3448
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.18
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1688   0.2146   0.853      101090.    5283.8   0.0126  0.929   1.812  1.047   0.087
       1   0.1678   0.2125   0.867      100577.    5271.2   0.0121  0.894   1.785  1.030   0.086
       2   0.1666   0.2106   0.869      100315.    5263.6   0.0130  0.958   1.821  1.050   0.087
       3   0.1662   0.2100   0.869      100212.    5260.4   0.0131  0.966   1.837  1.059   0.087
       4   0.1661   0.2096   0.870      100172.    5258.7   0.0131  0.968   1.844  1.064   0.087
       5   0.1659   0.2096   0.870      100148.    5259.3   0.0131  0.969   1.848  1.066   0.087
       6   0.1659   0.2095   0.869      100142.    5260.0   0.0131  0.968   1.849  1.066   0.087
       7   0.1660   0.2096   0.869      100140.    5261.1   0.0131  0.968   1.848  1.066   0.087
       8   0.1660   0.2097   0.869      100143.    5261.6   0.0131  0.967   1.849  1.066   0.087
       9   0.1660   0.2099   0.869      100144.    5262.1   0.0131  0.966   1.849  1.067   0.087
      10   0.1660   0.2101   0.869      100134.    5262.5   0.0131  0.966   1.849  1.067   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1688   0.1660
             R free    0.2146   0.2101
     Rms BondLength    0.0126   0.0131
      Rms BondAngle    1.8117   1.8493
     Rms ChirVolume    0.0870   0.0867
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.2s System:    0.1s Elapsed:     0:48