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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 18:32:33 


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


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

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

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

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

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

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

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

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

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.60     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 17
  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_R17_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R17_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R17_1-60A.mtz

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

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

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


  Residual                               : Rice Maximum Likelihood for Fs

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

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


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

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:    17
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.6000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R17_1-70A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.028 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=   2.218 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=   1.827 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=   2.223 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=   2.377 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=   2.383 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=   2.125 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                           17
Number of "free" reflections       1416
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.27871928    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                37.1
Norm of Geom. positional gradient                80.5
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                 0.217E+05
Product of X_ray and Geom posit. gradients     -0.133E+08
 Cosine of angle between them                      -0.461
Product of X_ray and Geom B-fact gradients     -0.380E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8747E+06 GEOM=     0.2639E+05 TOTAL=     0.9011E+06
 function value    901125.00    

-------------------------------------------------------------------------------
             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     1.811     1.644
Bond angles  : others                          3242     2.348     1.582
Torsion angles, period  1. refined              184     6.848     5.000
Torsion angles, period  2. refined               90    36.604    22.778
Torsion angles, period  3. refined              268    13.904    15.000
Torsion angles, period  4. refined                9    11.351    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   300     0.267     0.200
VDW repulsions.others                          1340     0.231     0.200
VDW; torsion: refined_atoms                     728     0.172     0.200
VDW; torsion.others                             719     0.082     0.200
HBOND: refined_atoms                            218     0.195     0.200
HBOND.others                                      1     0.030     0.200
VDW repulsions: symmetry: refined_atoms           8     0.209     0.200
VDW repulsions: symmetry: others                 24     0.160     0.200
HBOND: symmetry: refined_atoms                   22     0.209     0.200
M. chain bond B values: refined atoms           745     1.671     1.385
M. chain bond B values: others                  745     1.669     1.385
M. chain angle B values: refined atoms          926     2.624     2.063
M. chain angle B values: others                 927     2.623     2.063
S. chain bond B values: refined atoms           811     2.992     1.778
S. chain bond B values: others                  810     2.986     1.777
S. chain angle B values: refined atoms         1177     4.624     2.503
S. chain angle B values: others                1178     4.622     2.502
Long range B values: refined atoms             1848     7.502    19.523
Long range B values: others                    1758     7.189    18.103
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    1.2782
Partial structure    1: scale =     0.3887, B  =   48.5263
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.42 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3607 100.00   432.1   441.8  0.17  0.18     175   447.7   451.3  0.19  0.20
 0.147    6124  99.97   258.0   242.5  0.16  0.15     320   278.0   258.3  0.19  0.18
 0.244    7802 100.00   167.6   151.7  0.19  0.17     416   164.7   149.3  0.24  0.21
 0.342    9085 100.00    71.4    85.9  0.33  0.26     505    71.3    85.6  0.36  0.29
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2634   0.910    973   0.818   3607   0.885  0.946  0.9645  0.9691  0.9156  0.9353
  0.1468   5150   0.881    974   0.787   6124   0.866  1.025  0.9567  0.9626  0.9106  0.9442
  0.2444   6825   0.849    977   0.741   7802   0.835  1.047  0.9375  0.9506  0.8892  0.9350
  0.3419   8107   0.661    983   0.584   9090   0.652  0.698  0.8499  0.8634  0.8000  0.8545
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26622
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0503
Overall R factor                     =     0.1934
Free R factor                        =     0.2268
Average Fourier shell correlation    =     0.9261
AverageFree Fourier shell correlation=     0.9139
Overall weighted R factor            =     0.1671
Free weighted R factor               =     0.1938
Overall weighted R2 factor           =     0.1970
Free weighted R2 factor              =     0.2233
Average correlation coefficient      =     0.9097
Overall correlation coefficient      =     0.9580
Free correlation coefficient         =     0.9433
Cruickshanks DPI for coordinate error=     0.0972
DPI based on free R factor           =     0.0970
Overall figure of merit              =     0.7867
ML based su of positional parameters =     0.0740
ML based su of thermal parameters    =     2.2422
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134581.50       26392.080       901125.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.34071076    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    878022.25    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0647
Partial structure    1: scale =     0.3886, B  =   48.1512
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1936
Free R factor                        =     0.2262
Average Fourier shell correlation    =     0.9380
AverageFree Fourier shell correlation=     0.9266
Average correlation coefficient      =     0.9104
Overall figure of merit              =     0.8226
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133604.53       9639.2725       878022.25       901125.00    


     CGMAT cycle number =      3

 Weight matrix   0.35420859    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    875620.31    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0288
Partial structure    1: scale =     0.3892, B  =   44.1528
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1926
Free R factor                        =     0.2256
Average Fourier shell correlation    =     0.9405
AverageFree Fourier shell correlation=     0.9288
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8299
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    133322.80       9068.4785       875620.31       878022.25    


     CGMAT cycle number =      4

 Weight matrix   0.35544086    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    875053.75    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0254
Partial structure    1: scale =     0.3903, B  =   43.7791
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2257
Average Fourier shell correlation    =     0.9409
AverageFree Fourier shell correlation=     0.9291
Average correlation coefficient      =     0.9132
Overall figure of merit              =     0.8305
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    133255.08       8942.0654       875053.75       875620.31    


     CGMAT cycle number =      5

 Weight matrix   0.35472900    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874940.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0001
Partial structure    1: scale =     0.3903, B  =   43.7787
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1923
Free R factor                        =     0.2256
Average Fourier shell correlation    =     0.9409
AverageFree Fourier shell correlation=     0.9290
Average correlation coefficient      =     0.9136
Overall figure of merit              =     0.8303
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    133233.52       8968.8887       874940.44       875053.75    


     CGMAT cycle number =      6

 Weight matrix   0.35570300    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874853.00    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0091
Partial structure    1: scale =     0.3905, B  =   43.7779
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1923
Free R factor                        =     0.2255
Average Fourier shell correlation    =     0.9410
AverageFree Fourier shell correlation=     0.9291
Average correlation coefficient      =     0.9137
Overall figure of merit              =     0.8305
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    133216.55       8991.7314       874853.00       874940.44    


     CGMAT cycle number =      7

 Weight matrix   0.35567269    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874832.13    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0072
Partial structure    1: scale =     0.3900, B  =   43.6861
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1923
Free R factor                        =     0.2253
Average Fourier shell correlation    =     0.9410
AverageFree Fourier shell correlation=     0.9291
Average correlation coefficient      =     0.9138
Overall figure of merit              =     0.8305
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    133210.77       9008.4180       874832.13       874853.00    


     CGMAT cycle number =      8

 Weight matrix   0.35536230    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874855.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0001
Partial structure    1: scale =     0.3900, B  =   43.6869
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1923
Free R factor                        =     0.2252
Average Fourier shell correlation    =     0.9410
AverageFree Fourier shell correlation=     0.9291
Average correlation coefficient      =     0.9138
Overall figure of merit              =     0.8304
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    133212.95       9017.3164       874839.38       874832.13    
 fvalues    133212.95       9017.3164       874839.38       874855.19    


     CGMAT cycle number =      9

 Weight matrix   0.35540476    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874853.00    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0033
Partial structure    1: scale =     0.3899, B  =   43.7125
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1923
Free R factor                        =     0.2252
Average Fourier shell correlation    =     0.9410
AverageFree Fourier shell correlation=     0.9291
Average correlation coefficient      =     0.9139
Overall figure of merit              =     0.8305
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    133213.00       9014.7842       874853.00       874855.19    


     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.= 0.900 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.35513178    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                41.8
Norm of Geom. positional gradient                41.8
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  114.
Product of X_ray and Geom posit. gradients     -0.169E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.423E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8658E+06 GEOM=      9019.     TOTAL=     0.8749E+06
 function value    874861.38    

-------------------------------------------------------------------------------
             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     1.837     1.644
Bond angles  : others                          3242     1.511     1.582
Torsion angles, period  1. refined              184     6.853     5.000
Torsion angles, period  2. refined               90    36.190    22.778
Torsion angles, period  3. refined              268    13.669    15.000
Torsion angles, period  4. refined                9    11.669    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   308     0.266     0.200
VDW repulsions.others                          1371     0.205     0.200
VDW; torsion: refined_atoms                     730     0.173     0.200
VDW; torsion.others                             810     0.084     0.200
HBOND: refined_atoms                            218     0.201     0.200
HBOND.others                                      1     0.063     0.200
VDW repulsions: symmetry: refined_atoms           8     0.220     0.200
VDW repulsions: symmetry: others                 25     0.165     0.200
HBOND: symmetry: refined_atoms                   18     0.223     0.200
M. chain bond B values: refined atoms           745     1.749     1.508
M. chain bond B values: others                  745     1.747     1.508
M. chain angle B values: refined atoms          926     2.727     2.250
M. chain angle B values: others                 927     2.725     2.250
S. chain bond B values: refined atoms           811     3.161     1.911
S. chain bond B values: others                  810     3.155     1.911
S. chain angle B values: refined atoms         1177     4.829     2.700
S. chain angle B values: others                1178     4.827     2.699
Long range B values: refined atoms             1858     7.757    21.131
Long range B values: others                    1769     7.357    19.697
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0000
Partial structure    1: scale =     0.3899, B  =   43.7124
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3607 100.00   432.4   441.7  0.17  0.17     175   447.9   452.3  0.19  0.19
 0.147    6124  99.97   258.1   242.4  0.16  0.15     320   278.2   258.6  0.19  0.17
 0.244    7802 100.00   167.7   151.6  0.19  0.17     416   164.7   150.2  0.24  0.20
 0.342    9085 100.00    71.5    85.4  0.32  0.26     505    71.4    85.5  0.36  0.28
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2634   0.921    973   0.839   3607   0.899  0.948  0.9667  0.9715  0.9157  0.9358
  0.1468   5150   0.889    974   0.796   6124   0.874  1.025  0.9588  0.9646  0.9112  0.9440
  0.2444   6825   0.858    977   0.751   7802   0.845  1.047  0.9415  0.9541  0.8901  0.9342
  0.3419   8107   0.770    983   0.690   9090   0.762  0.751  0.8868  0.9017  0.8051  0.8674
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26622
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0503
Overall R factor                     =     0.1923
Free R factor                        =     0.2251
Average Fourier shell correlation    =     0.9410
AverageFree Fourier shell correlation=     0.9290
Overall weighted R factor            =     0.1667
Free weighted R factor               =     0.1922
Overall weighted R2 factor           =     0.1958
Free weighted R2 factor              =     0.2221
Average correlation coefficient      =     0.9139
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9437
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0962
Overall figure of merit              =     0.8304
ML based su of positional parameters =     0.0655
ML based su of thermal parameters    =     1.9400
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    133213.66       9018.6836       874861.56       874853.00    

 fvalues    133213.66       9018.6836       874862.19       874861.13    
 fvalues    133213.66       9018.6836       874862.19       874861.13    

    ****                              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.= 0.900 id.= 3.000 dev= -2.10 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_R17_1-60A.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     1.838     1.644
Bond angles  : others                          3242     1.511     1.582
Torsion angles, period  1. refined              184     6.853     5.000
Torsion angles, period  2. refined               90    36.181    22.778
Torsion angles, period  3. refined              268    13.663    15.000
Torsion angles, period  4. refined                9    11.672    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   309     0.265     0.200
VDW repulsions.others                          1370     0.205     0.200
VDW; torsion: refined_atoms                     730     0.173     0.200
VDW; torsion.others                             810     0.084     0.200
HBOND: refined_atoms                            217     0.201     0.200
HBOND.others                                      1     0.063     0.200
VDW repulsions: symmetry: refined_atoms           8     0.220     0.200
VDW repulsions: symmetry: others                 24     0.168     0.200
HBOND: symmetry: refined_atoms                   18     0.224     0.200
M. chain bond B values: refined atoms           745     1.749     1.508
M. chain bond B values: others                  745     1.747     1.508
M. chain angle B values: refined atoms          926     2.727     2.250
M. chain angle B values: others                 927     2.725     2.250
S. chain bond B values: refined atoms           811     3.161     1.911
S. chain bond B values: others                  810     3.155     1.911
S. chain angle B values: refined atoms         1177     4.829     2.700
S. chain angle B values: others                1178     4.827     2.699
Long range B values: refined atoms             1858     7.761    21.135
Long range B values: others                    1769     7.358    19.701
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0019
Partial structure    1: scale =     0.3898, B  =   43.7303
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3607 100.00   432.4   441.7  0.17  0.17     175   447.9   452.3  0.19  0.19
 0.147    6124  99.97   258.1   242.5  0.16  0.15     320   278.2   258.6  0.19  0.17
 0.244    7802 100.00   167.7   151.6  0.19  0.17     416   164.8   150.3  0.24  0.20
 0.342    9085 100.00    71.5    85.5  0.32  0.26     505    71.4    85.6  0.36  0.28
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2634   0.921    973   0.839   3607   0.899  0.948  0.9668  0.9715  0.9158  0.9359
  0.1468   5150   0.889    974   0.796   6124   0.874  1.025  0.9588  0.9646  0.9113  0.9440
  0.2444   6825   0.858    977   0.751   7802   0.845  1.047  0.9415  0.9541  0.8902  0.9342
  0.3419   8107   0.770    983   0.690   9090   0.762  0.751  0.8869  0.9018  0.8052  0.8674
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26622
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0503
Overall R factor                     =     0.1923
Free R factor                        =     0.2250
Average Fourier shell correlation    =     0.9410
AverageFree Fourier shell correlation=     0.9291
Overall weighted R factor            =     0.1667
Free weighted R factor               =     0.1921
Overall weighted R2 factor           =     0.1957
Free weighted R2 factor              =     0.2220
Average correlation coefficient      =     0.9139
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9438
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0962
Overall figure of merit              =     0.8305
ML based su of positional parameters =     0.0655
ML based su of thermal parameters    =     1.9400
-----------------------------------------------------------------------------
  Time in seconds: CPU =        19.53
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1934   0.2268   0.787      134582.    7315.8   0.0129  0.962   1.811  1.045   0.088
       1   0.1936   0.2262   0.823      133605.    7278.6   0.0122  0.908   1.765  1.020   0.086
       2   0.1926   0.2256   0.830      133323.    7270.0   0.0130  0.969   1.796  1.040   0.088
       3   0.1924   0.2257   0.830      133255.    7269.5   0.0132  0.982   1.815  1.051   0.089
       4   0.1923   0.2256   0.830      133234.    7269.3   0.0132  0.984   1.824  1.056   0.089
       5   0.1923   0.2255   0.831      133217.    7269.0   0.0132  0.984   1.829  1.059   0.089
       6   0.1923   0.2253   0.831      133211.    7269.2   0.0132  0.986   1.832  1.061   0.089
       7   0.1923   0.2252   0.830      133213.    7269.1   0.0132  0.986   1.835  1.062   0.089
       8   0.1923   0.2252   0.830      133213.    7269.6   0.0132  0.986   1.836  1.063   0.089
       9   0.1923   0.2251   0.830      133214.    7269.7   0.0132  0.986   1.837  1.063   0.089
      10   0.1923   0.2250   0.830      133212.    7269.6   0.0132  0.986   1.838  1.063   0.089
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1934   0.1923
             R free    0.2268   0.2250
     Rms BondLength    0.0129   0.0132
      Rms BondAngle    1.8106   1.8376
     Rms ChirVolume    0.0878   0.0892
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      51.7s System:    0.1s Elapsed:     0:52