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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 16:08:35 


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


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

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

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

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

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

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

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

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

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.70     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  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_R00_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R00_1-70A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R00_1-70A.mtz

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

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

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


  Residual                               : Rice Maximum Likelihood for Fs

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

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


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

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0865
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7000
  Estimated number of reflections :      29131
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.7000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R00_1-80A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.049 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=   2.216 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=   1.865 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=   2.435 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.408 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.137 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                            0
Number of "free" reflections       1202
Number of   all  reflections      23491
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23491

   Current auto weighting coefficient =    6.7496872    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.926 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  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.27055562    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                37.7
Norm of Geom. positional gradient                78.9
Norm of X_ray B-factor gradient                  125.
Norm of Geom. B-factor gradient                 0.214E+05
Product of X_ray and Geom posit. gradients     -0.110E+08
 Cosine of angle between them                      -0.381
Product of X_ray and Geom B-fact gradients     -0.401E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7857E+06 GEOM=     0.2587E+05 TOTAL=     0.8115E+06
 function value    811528.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.796     1.644
Bond angles  : others                          3242     2.349     1.582
Torsion angles, period  1. refined              184     6.967     5.000
Torsion angles, period  2. refined               90    36.593    22.778
Torsion angles, period  3. refined              268    14.025    15.000
Torsion angles, period  4. refined                9    11.924    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   304     0.262     0.200
VDW repulsions.others                          1338     0.226     0.200
VDW; torsion: refined_atoms                     715     0.172     0.200
VDW; torsion.others                             725     0.081     0.200
HBOND: refined_atoms                            222     0.193     0.200
HBOND.others                                      1     0.001     0.200
VDW repulsions: symmetry: refined_atoms           8     0.211     0.200
VDW repulsions: symmetry: others                 24     0.185     0.200
HBOND: symmetry: refined_atoms                   21     0.205     0.200
M. chain bond B values: refined atoms           745     1.614     1.290
M. chain bond B values: others                  745     1.612     1.290
M. chain angle B values: refined atoms          926     2.537     1.916
M. chain angle B values: others                 927     2.536     1.916
S. chain bond B values: refined atoms           811     2.737     1.658
S. chain bond B values: others                  810     2.733     1.658
S. chain angle B values: refined atoms         1177     4.295     2.330
S. chain angle B values: others                1178     4.293     2.330
Long range B values: refined atoms             1849     6.808    17.936
Long range B values: others                    1757     6.488    16.509
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.1146
Partial structure    1: scale =     0.3877, B  =   48.5138
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3036 100.00   454.7   462.8  0.16  0.17     135   453.1   461.8  0.21  0.22
 0.130    5109 100.00   299.2   286.4  0.16  0.15     291   305.3   281.4  0.22  0.20
 0.216    6518  99.97   202.5   186.2  0.17  0.15     354   207.9   192.8  0.21  0.18
 0.303    7621 100.00   104.5   117.1  0.26  0.20     422   102.5   114.9  0.32  0.24
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.905    857   0.807   3036   0.878  0.949  0.9585  0.9682  0.8974  0.9377
  0.1301   4247   0.866    862   0.760   5109   0.848  0.997  0.9443  0.9578  0.8938  0.9436
  0.2165   5641   0.877    877   0.768   6518   0.863  1.043  0.9516  0.9598  0.9051  0.9413
  0.3028   6772   0.756    852   0.687   7624   0.749  0.813  0.9034  0.9154  0.8501  0.8924
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22287
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1173
Overall R factor                     =     0.1804
Free R factor                        =     0.2295
Average Fourier shell correlation    =     0.9453
AverageFree Fourier shell correlation=     0.9337
Overall weighted R factor            =     0.1598
Free weighted R factor               =     0.2044
Overall weighted R2 factor           =     0.1910
Free weighted R2 factor              =     0.2415
Average correlation coefficient      =     0.9246
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9284
Cruickshanks DPI for coordinate error=     0.1094
DPI based on free R factor           =     0.1140
Overall figure of merit              =     0.8224
ML based su of positional parameters =     0.0766
ML based su of thermal parameters    =     2.3699
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    116399.38       25869.090       811528.44      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.32664451    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    789745.50    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0640
Partial structure    1: scale =     0.3874, B  =   47.3266
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1802
Free R factor                        =     0.2273
Average Fourier shell correlation    =     0.9521
AverageFree Fourier shell correlation=     0.9412
Average correlation coefficient      =     0.9260
Overall figure of merit              =     0.8483
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115585.14       9581.9414       789745.50       811528.44    


     CGMAT cycle number =      3

 Weight matrix   0.33764422    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    787154.06    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0185
Partial structure    1: scale =     0.3868, B  =   44.1220
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1790
Free R factor                        =     0.2254
Average Fourier shell correlation    =     0.9535
AverageFree Fourier shell correlation=     0.9428
Average correlation coefficient      =     0.9281
Overall figure of merit              =     0.8516
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    115272.58       9100.1680       787154.06       789745.50    


     CGMAT cycle number =      4

 Weight matrix   0.34257895    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786278.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0132
Partial structure    1: scale =     0.3869, B  =   44.0847
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1787
Free R factor                        =     0.2245
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9433
Average correlation coefficient      =     0.9288
Overall figure of merit              =     0.8528
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    115154.14       9024.3584       786278.81       787154.06    


     CGMAT cycle number =      5

 Weight matrix   0.34380001    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785952.88    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0053
Partial structure    1: scale =     0.3875, B  =   44.0445
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1785
Free R factor                        =     0.2241
Average Fourier shell correlation    =     0.9542
AverageFree Fourier shell correlation=     0.9436
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8533
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    115100.21       9062.4551       785952.88       786278.81    


     CGMAT cycle number =      6

 Weight matrix   0.34517497    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785804.88    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0026
Partial structure    1: scale =     0.3875, B  =   44.0583
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1784
Free R factor                        =     0.2239
Average Fourier shell correlation    =     0.9543
AverageFree Fourier shell correlation=     0.9437
Average correlation coefficient      =     0.9293
Overall figure of merit              =     0.8536
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    115070.19       9117.1006       785804.88       785952.88    


     CGMAT cycle number =      7

 Weight matrix   0.34519309    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785744.44    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0134
Partial structure    1: scale =     0.3880, B  =   44.1775
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1784
Free R factor                        =     0.2240
Average Fourier shell correlation    =     0.9543
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9294
Overall figure of merit              =     0.8537
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    115056.58       9148.5293       785744.44       785804.88    


     CGMAT cycle number =      8

 Weight matrix   0.34536347    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785652.31    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0173
Partial structure    1: scale =     0.3874, B  =   43.9850
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1783
Free R factor                        =     0.2237
Average Fourier shell correlation    =     0.9544
AverageFree Fourier shell correlation=     0.9438
Average correlation coefficient      =     0.9295
Overall figure of merit              =     0.8538
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    115040.81       9162.8066       785652.31       785744.44    


     CGMAT cycle number =      9

 Weight matrix   0.34560841    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785624.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0124
Partial structure    1: scale =     0.3872, B  =   43.9586
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1783
Free R factor                        =     0.2236
Average Fourier shell correlation    =     0.9544
AverageFree Fourier shell correlation=     0.9439
Average correlation coefficient      =     0.9295
Overall figure of merit              =     0.8539
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    115036.05       9166.8926       785624.25       785652.31    


     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.= 0.918 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.34562492    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                41.3
Norm of Geom. positional gradient                41.3
Norm of X_ray B-factor gradient                  128.
Norm of Geom. B-factor gradient                  126.
Product of X_ray and Geom posit. gradients     -0.165E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.522E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7764E+06 GEOM=      9180.     TOTAL=     0.7856E+06
 function value    785600.81    

-------------------------------------------------------------------------------
             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     1.831     1.644
Bond angles  : others                          3242     1.509     1.582
Torsion angles, period  1. refined              184     6.860     5.000
Torsion angles, period  2. refined               90    36.130    22.778
Torsion angles, period  3. refined              268    13.881    15.000
Torsion angles, period  4. refined                9    11.901    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.266     0.200
VDW repulsions.others                          1373     0.200     0.200
VDW; torsion: refined_atoms                     717     0.174     0.200
VDW; torsion.others                             782     0.085     0.200
HBOND: refined_atoms                            207     0.195     0.200
HBOND.others                                      1     0.017     0.200
VDW repulsions: symmetry: refined_atoms           8     0.198     0.200
VDW repulsions: symmetry: others                 22     0.176     0.200
HBOND: symmetry: refined_atoms                   21     0.195     0.200
M. chain bond B values: refined atoms           745     1.698     1.384
M. chain bond B values: others                  745     1.695     1.384
M. chain angle B values: refined atoms          926     2.654     2.060
M. chain angle B values: others                 927     2.652     2.060
S. chain bond B values: refined atoms           811     3.001     1.784
S. chain bond B values: others                  810     2.993     1.784
S. chain angle B values: refined atoms         1177     4.635     2.508
S. chain angle B values: others                1178     4.633     2.508
Long range B values: refined atoms             1828     6.906    19.167
Long range B values: others                    1741     6.675    17.798
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0161
Partial structure    1: scale =     0.3872, B  =   43.9701
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3036 100.00   454.5   463.4  0.16  0.17     135   452.9   463.4  0.21  0.21
 0.130    5109 100.00   299.1   285.7  0.16  0.15     291   305.2   282.3  0.21  0.19
 0.216    6518  99.97   202.4   186.2  0.17  0.15     354   207.8   192.3  0.20  0.17
 0.303    7621 100.00   104.5   116.4  0.25  0.19     422   102.4   115.2  0.31  0.24
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.924    857   0.832   3036   0.898  0.951  0.9639  0.9723  0.9003  0.9384
  0.1301   4247   0.872    862   0.767   5109   0.855  0.997  0.9477  0.9592  0.9000  0.9426
  0.2165   5641   0.888    877   0.781   6518   0.874  1.043  0.9564  0.9628  0.9121  0.9414
  0.3028   6772   0.828    852   0.750   7624   0.819  0.839  0.9244  0.9369  0.8608  0.9072
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22287
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1173
Overall R factor                     =     0.1783
Free R factor                        =     0.2236
Average Fourier shell correlation    =     0.9544
AverageFree Fourier shell correlation=     0.9439
Overall weighted R factor            =     0.1597
Free weighted R factor               =     0.1982
Overall weighted R2 factor           =     0.1920
Free weighted R2 factor              =     0.2349
Average correlation coefficient      =     0.9296
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9318
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.1110
Overall figure of merit              =     0.8539
ML based su of positional parameters =     0.0677
ML based su of thermal parameters    =     2.0471
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    115030.64       9179.9834       785600.81       785624.25    

    ****                              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.= 0.918 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R00_1-70A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.832     1.644
Bond angles  : others                          3242     1.509     1.582
Torsion angles, period  1. refined              184     6.856     5.000
Torsion angles, period  2. refined               90    36.097    22.778
Torsion angles, period  3. refined              268    13.836    15.000
Torsion angles, period  4. refined                9    11.904    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.266     0.200
VDW repulsions.others                          1373     0.200     0.200
VDW; torsion: refined_atoms                     717     0.174     0.200
VDW; torsion.others                             787     0.085     0.200
HBOND: refined_atoms                            206     0.195     0.200
HBOND.others                                      1     0.016     0.200
VDW repulsions: symmetry: refined_atoms           8     0.198     0.200
VDW repulsions: symmetry: others                 22     0.176     0.200
HBOND: symmetry: refined_atoms                   21     0.195     0.200
M. chain bond B values: refined atoms           745     1.697     1.384
M. chain bond B values: others                  745     1.694     1.384
M. chain angle B values: refined atoms          926     2.652     2.060
M. chain angle B values: others                 927     2.651     2.060
S. chain bond B values: refined atoms           811     3.005     1.785
S. chain bond B values: others                  810     2.997     1.784
S. chain angle B values: refined atoms         1177     4.640     2.509
S. chain angle B values: others                1178     4.638     2.508
Long range B values: refined atoms             1828     6.937    19.138
Long range B values: others                    1742     6.675    17.800
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0168
Partial structure    1: scale =     0.3872, B  =   43.9548
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3036 100.00   454.4   463.4  0.16  0.17     135   452.9   463.4  0.21  0.21
 0.130    5109 100.00   299.0   285.7  0.16  0.15     291   305.2   282.3  0.21  0.19
 0.216    6518  99.97   202.3   186.1  0.17  0.15     354   207.8   192.3  0.20  0.17
 0.303    7621 100.00   104.5   116.4  0.25  0.19     422   102.4   115.2  0.31  0.24
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2179   0.924    857   0.832   3036   0.898  0.951  0.9639  0.9723  0.9002  0.9384
  0.1301   4247   0.873    862   0.767   5109   0.855  0.997  0.9477  0.9592  0.9001  0.9426
  0.2165   5641   0.888    877   0.781   6518   0.874  1.043  0.9564  0.9628  0.9122  0.9414
  0.3028   6772   0.828    852   0.750   7624   0.819  0.839  0.9244  0.9369  0.8608  0.9073
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22287
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1173
Overall R factor                     =     0.1782
Free R factor                        =     0.2235
Average Fourier shell correlation    =     0.9544
AverageFree Fourier shell correlation=     0.9439
Overall weighted R factor            =     0.1597
Free weighted R factor               =     0.1982
Overall weighted R2 factor           =     0.1920
Free weighted R2 factor              =     0.2349
Average correlation coefficient      =     0.9296
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9318
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.1110
Overall figure of merit              =     0.8539
ML based su of positional parameters =     0.0677
ML based su of thermal parameters    =     2.0471
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.13
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1804   0.2295   0.822      116399.    6444.9   0.0121  0.899   1.796  1.031   0.086
       1   0.1802   0.2273   0.848      115585.    6415.9   0.0117  0.872   1.759  1.011   0.085
       2   0.1790   0.2254   0.852      115273.    6403.8   0.0125  0.940   1.791  1.032   0.088
       3   0.1787   0.2245   0.853      115154.    6398.8   0.0127  0.954   1.808  1.044   0.090
       4   0.1785   0.2241   0.853      115100.    6395.9   0.0128  0.960   1.817  1.050   0.090
       5   0.1784   0.2239   0.854      115070.    6394.3   0.0128  0.961   1.823  1.054   0.091
       6   0.1784   0.2240   0.854      115057.    6393.8   0.0128  0.963   1.826  1.056   0.091
       7   0.1783   0.2237   0.854      115041.    6392.8   0.0128  0.963   1.828  1.057   0.091
       8   0.1783   0.2236   0.854      115036.    6392.4   0.0128  0.963   1.829  1.059   0.091
       9   0.1783   0.2236   0.854      115031.    6392.4   0.0128  0.964   1.831  1.060   0.091
      10   0.1782   0.2235   0.854      115026.    6392.1   0.0128  0.964   1.832  1.060   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1804   0.1782
             R free    0.2295   0.2235
     Rms BondLength    0.0121   0.0128
      Rms BondAngle    1.7955   1.8315
     Rms ChirVolume    0.0855   0.0914
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.2s System:    0.1s Elapsed:     0:46