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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 15:38:28 


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


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

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

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

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

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

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

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

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

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.80     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 10
  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_R10_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R10_1-80A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R10_1-80A.mtz

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

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

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


  Residual                               : Rice Maximum Likelihood for Fs

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

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


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

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  Free R exclusion - flag equals:    10
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.8000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R10_1-90A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.014 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=   2.220 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=   1.844 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=   2.174 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=   2.413 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=   2.410 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=   2.077 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                           10
Number of "free" reflections       1021
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.911 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.28948247    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                42.6
Norm of Geom. positional gradient                80.1
Norm of X_ray B-factor gradient                  137.
Norm of Geom. B-factor gradient                 0.222E+05
Product of X_ray and Geom posit. gradients     -0.116E+08
 Cosine of angle between them                      -0.350
Product of X_ray and Geom B-fact gradients     -0.452E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7036E+06 GEOM=     0.2697E+05 TOTAL=     0.7306E+06
 function value    730593.69    

-------------------------------------------------------------------------------
             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     1.818     1.644
Bond angles  : others                          3242     2.347     1.582
Torsion angles, period  1. refined              184     6.907     5.000
Torsion angles, period  2. refined               90    36.887    22.778
Torsion angles, period  3. refined              268    13.965    15.000
Torsion angles, period  4. refined                9    10.231    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.019     0.020
VDW repulsions: refined_atoms                   314     0.264     0.200
VDW repulsions.others                          1333     0.234     0.200
VDW; torsion: refined_atoms                     712     0.171     0.200
VDW; torsion.others                             691     0.082     0.200
HBOND: refined_atoms                            239     0.206     0.200
HBOND.others                                      2     0.009     0.200
VDW repulsions: symmetry: refined_atoms          10     0.238     0.200
VDW repulsions: symmetry: others                 25     0.214     0.200
HBOND: symmetry: refined_atoms                   24     0.208     0.200
HBOND: symmetry: others                           1     0.113     0.200
M. chain bond B values: refined atoms           745     1.607     1.202
M. chain bond B values: others                  745     1.606     1.202
M. chain angle B values: refined atoms          926     2.537     1.785
M. chain angle B values: others                 927     2.536     1.784
S. chain bond B values: refined atoms           812     2.717     1.553
S. chain bond B values: others                  811     2.714     1.553
S. chain angle B values: refined atoms         1177     4.183     2.181
S. chain angle B values: others                1178     4.181     2.180
Long range B values: refined atoms             1873     6.879    17.141
Long range B values: others                    1775     6.582    15.766
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.8572
Partial structure    1: scale =     0.3786, B  =   49.5384
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2556 100.00   473.4   482.5  0.16  0.17     137   462.8   468.1  0.21  0.22
 0.116    4332 100.00   341.6   327.3  0.16  0.15     247   341.6   322.2  0.20  0.18
 0.193    5544  99.97   226.6   216.2  0.16  0.13     264   215.2   208.1  0.22  0.18
 0.270    6414 100.00   147.8   154.6  0.21  0.16     373   149.8   154.4  0.23  0.18
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1796   0.913    760   0.808   2556   0.882  0.951  0.9572  0.9686  0.8843  0.9377
  0.1161   3552   0.896    780   0.789   4332   0.877  0.999  0.9541  0.9647  0.9098  0.9461
  0.1931   4767   0.882    777   0.772   5544   0.867  1.010  0.9459  0.9618  0.8910  0.9411
  0.2701   5639   0.835    783   0.756   6422   0.826  0.899  0.9382  0.9447  0.8859  0.9113
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18854
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1371
Overall R factor                     =     0.1688
Free R factor                        =     0.2128
Average Fourier shell correlation    =     0.9576
AverageFree Fourier shell correlation=     0.9466
Overall weighted R factor            =     0.1537
Free weighted R factor               =     0.1938
Overall weighted R2 factor           =     0.1883
Free weighted R2 factor              =     0.2375
Average correlation coefficient      =     0.9316
Overall correlation coefficient      =     0.9553
Free correlation coefficient         =     0.9268
Cruickshanks DPI for coordinate error=     0.1235
DPI based on free R factor           =     0.1217
Overall figure of merit              =     0.8571
ML based su of positional parameters =     0.0754
ML based su of thermal parameters    =     2.4271
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100523.92       26970.313       730593.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.32090381    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710871.25    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0640
Partial structure    1: scale =     0.3790, B  =   49.0857
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1677
Free R factor                        =     0.2118
Average Fourier shell correlation    =     0.9608
AverageFree Fourier shell correlation=     0.9501
Average correlation coefficient      =     0.9340
Overall figure of merit              =     0.8688
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100075.85       10384.219       710871.25       730593.69    


     CGMAT cycle number =      3

 Weight matrix   0.32614067    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708506.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0152
Partial structure    1: scale =     0.3791, B  =   46.5539
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1664
Free R factor                        =     0.2107
Average Fourier shell correlation    =     0.9616
AverageFree Fourier shell correlation=     0.9508
Average correlation coefficient      =     0.9359
Overall figure of merit              =     0.8703
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    99852.148       9585.0957       708506.38       710871.25    


     CGMAT cycle number =      4

 Weight matrix   0.32769573    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707667.75    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0008
Partial structure    1: scale =     0.3791, B  =   46.1674
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1660
Free R factor                        =     0.2103
Average Fourier shell correlation    =     0.9619
AverageFree Fourier shell correlation=     0.9511
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8707
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    99766.359       9347.0313       707667.75       708506.38    


     CGMAT cycle number =      5

 Weight matrix   0.32966205    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707288.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0065
Partial structure    1: scale =     0.3794, B  =   46.1204
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1659
Free R factor                        =     0.2101
Average Fourier shell correlation    =     0.9621
AverageFree Fourier shell correlation=     0.9513
Average correlation coefficient      =     0.9367
Overall figure of merit              =     0.8713
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    99714.031       9334.1895       707288.69       707667.75    


     CGMAT cycle number =      6

 Weight matrix   0.33001280    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707180.00    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0263
Partial structure    1: scale =     0.3794, B  =   46.0766
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1657
Free R factor                        =     0.2102
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9514
Average correlation coefficient      =     0.9370
Overall figure of merit              =     0.8714
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    99697.664       9340.0654       707180.00       707288.69    


     CGMAT cycle number =      7

 Weight matrix   0.33009446    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707136.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0133
Partial structure    1: scale =     0.3793, B  =   46.1149
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1657
Free R factor                        =     0.2104
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9514
Average correlation coefficient      =     0.9371
Overall figure of merit              =     0.8714
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    99688.508       9360.7588       707136.56       707180.00    


     CGMAT cycle number =      8

 Weight matrix   0.33082595    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707043.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0114
Partial structure    1: scale =     0.3793, B  =   45.9617
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1657
Free R factor                        =     0.2105
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9515
Average correlation coefficient      =     0.9371
Overall figure of merit              =     0.8716
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    99675.164       9361.3838       707043.81       707136.56    


     CGMAT cycle number =      9

 Weight matrix   0.33080605    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    706993.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0113
Partial structure    1: scale =     0.3794, B  =   45.9886
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1657
Free R factor                        =     0.2106
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9515
Average correlation coefficient      =     0.9372
Overall figure of merit              =     0.8716
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    99668.609       9356.9395       706993.50       707043.81    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.915 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.33079320    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                40.1
Norm of Geom. positional gradient                40.1
Norm of X_ray B-factor gradient                  130.
Norm of Geom. B-factor gradient                  131.
Product of X_ray and Geom posit. gradients     -0.156E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.550E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.6976E+06 GEOM=      9358.     TOTAL=     0.7070E+06
 function value    706983.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.837     1.644
Bond angles  : others                          3242     1.486     1.582
Torsion angles, period  1. refined              184     6.881     5.000
Torsion angles, period  2. refined               90    36.275    22.778
Torsion angles, period  3. refined              268    13.741    15.000
Torsion angles, period  4. refined                9    11.040    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   313     0.264     0.200
VDW repulsions.others                          1348     0.206     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             792     0.084     0.200
HBOND: refined_atoms                            237     0.195     0.200
HBOND.others                                      2     0.043     0.200
VDW repulsions: symmetry: refined_atoms          10     0.216     0.200
VDW repulsions: symmetry: others                 25     0.187     0.200
HBOND: symmetry: refined_atoms                   25     0.199     0.200
HBOND: symmetry: others                           1     0.035     0.200
M. chain bond B values: refined atoms           745     1.657     1.285
M. chain bond B values: others                  745     1.656     1.285
M. chain angle B values: refined atoms          926     2.581     1.909
M. chain angle B values: others                 927     2.580     1.908
S. chain bond B values: refined atoms           811     2.886     1.662
S. chain bond B values: others                  810     2.881     1.661
S. chain angle B values: refined atoms         1177     4.459     2.333
S. chain angle B values: others                1178     4.458     2.333
Long range B values: refined atoms             1874     7.029    18.238
Long range B values: others                    1774     6.715    16.738
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0135
Partial structure    1: scale =     0.3793, B  =   46.0426
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2556 100.00   473.2   482.6  0.16  0.17     137   462.7   466.7  0.20  0.21
 0.116    4332 100.00   341.4   326.1  0.16  0.15     247   341.4   321.8  0.20  0.19
 0.193    5544  99.97   226.5   215.5  0.16  0.14     264   215.1   208.1  0.22  0.18
 0.270    6414 100.00   147.7   154.2  0.19  0.15     373   149.7   154.7  0.22  0.17
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1796   0.927    760   0.823   2556   0.896  0.951  0.9622  0.9717  0.8890  0.9393
  0.1161   3552   0.898    780   0.793   4332   0.879  0.999  0.9552  0.9653  0.9109  0.9455
  0.1931   4767   0.886    777   0.776   5544   0.870  1.010  0.9467  0.9624  0.8903  0.9403
  0.2701   5639   0.867    783   0.791   6422   0.858  0.911  0.9486  0.9566  0.8950  0.9281
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18854
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1371
Overall R factor                     =     0.1657
Free R factor                        =     0.2107
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9515
Overall weighted R factor            =     0.1527
Free weighted R factor               =     0.1929
Overall weighted R2 factor           =     0.1875
Free weighted R2 factor              =     0.2346
Average correlation coefficient      =     0.9372
Overall correlation coefficient      =     0.9566
Free correlation coefficient         =     0.9287
Cruickshanks DPI for coordinate error=     0.1213
DPI based on free R factor           =     0.1205
Overall figure of merit              =     0.8716
ML based su of positional parameters =     0.0705
ML based su of thermal parameters    =     2.2351
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    99667.008       9358.1611       706983.50       706993.50    

    ****                              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.= 0.915 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R10_1-80A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.837     1.644
Bond angles  : others                          3242     1.486     1.582
Torsion angles, period  1. refined              184     6.873     5.000
Torsion angles, period  2. refined               90    36.211    22.778
Torsion angles, period  3. refined              268    13.668    15.000
Torsion angles, period  4. refined                9    11.064    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   312     0.264     0.200
VDW repulsions.others                          1345     0.206     0.200
VDW; torsion: refined_atoms                     723     0.171     0.200
VDW; torsion.others                             797     0.084     0.200
HBOND: refined_atoms                            239     0.193     0.200
HBOND.others                                      2     0.043     0.200
VDW repulsions: symmetry: refined_atoms          10     0.215     0.200
VDW repulsions: symmetry: others                 25     0.187     0.200
HBOND: symmetry: refined_atoms                   24     0.203     0.200
HBOND: symmetry: others                           1     0.031     0.200
M. chain bond B values: refined atoms           745     1.656     1.285
M. chain bond B values: others                  745     1.655     1.285
M. chain angle B values: refined atoms          926     2.579     1.908
M. chain angle B values: others                 927     2.577     1.908
S. chain bond B values: refined atoms           811     2.886     1.661
S. chain bond B values: others                  810     2.882     1.661
S. chain angle B values: refined atoms         1177     4.460     2.333
S. chain angle B values: others                1178     4.458     2.332
Long range B values: refined atoms             1875     7.006    18.270
Long range B values: others                    1775     6.686    16.746
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0110
Partial structure    1: scale =     0.3792, B  =   45.9693
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2556 100.00   473.2   482.6  0.16  0.17     137   462.7   466.5  0.20  0.21
 0.116    4332 100.00   341.5   326.1  0.16  0.15     247   341.5   321.8  0.20  0.19
 0.193    5544  99.97   226.6   215.5  0.16  0.14     264   215.1   208.0  0.22  0.18
 0.270    6414 100.00   147.7   154.2  0.19  0.15     373   149.7   154.8  0.22  0.17
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1796   0.927    760   0.823   2556   0.896  0.951  0.9621  0.9717  0.8887  0.9393
  0.1161   3552   0.898    780   0.793   4332   0.879  0.999  0.9552  0.9652  0.9109  0.9454
  0.1931   4767   0.886    777   0.776   5544   0.870  1.010  0.9466  0.9623  0.8902  0.9403
  0.2701   5639   0.868    783   0.791   6422   0.858  0.911  0.9486  0.9567  0.8951  0.9283
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18854
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1371
Overall R factor                     =     0.1657
Free R factor                        =     0.2108
Average Fourier shell correlation    =     0.9623
AverageFree Fourier shell correlation=     0.9515
Overall weighted R factor            =     0.1528
Free weighted R factor               =     0.1930
Overall weighted R2 factor           =     0.1876
Free weighted R2 factor              =     0.2348
Average correlation coefficient      =     0.9372
Overall correlation coefficient      =     0.9566
Free correlation coefficient         =     0.9287
Cruickshanks DPI for coordinate error=     0.1213
DPI based on free R factor           =     0.1205
Overall figure of merit              =     0.8716
ML based su of positional parameters =     0.0705
ML based su of thermal parameters    =     2.2351
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.52
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1688   0.2128   0.857      100524.    5579.6   0.0125  0.921   1.818  1.054   0.087
       1   0.1677   0.2118   0.869      100076.    5565.5   0.0122  0.898   1.790  1.036   0.087
       2   0.1664   0.2107   0.870       99852.    5559.2   0.0128  0.946   1.814  1.049   0.088
       3   0.1660   0.2103   0.871       99766.    5556.1   0.0129  0.953   1.825  1.055   0.088
       4   0.1659   0.2101   0.871       99714.    5554.0   0.0129  0.955   1.830  1.058   0.088
       5   0.1657   0.2102   0.871       99698.    5554.1   0.0129  0.957   1.833  1.059   0.088
       6   0.1657   0.2104   0.871       99689.    5554.2   0.0129  0.957   1.835  1.060   0.087
       7   0.1657   0.2105   0.872       99675.    5553.5   0.0129  0.956   1.835  1.060   0.087
       8   0.1657   0.2106   0.872       99669.    5553.4   0.0129  0.957   1.836  1.060   0.087
       9   0.1657   0.2107   0.872       99667.    5553.8   0.0129  0.957   1.837  1.061   0.087
      10   0.1657   0.2108   0.872       99666.    5554.0   0.0129  0.957   1.837  1.061   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1688   0.1657
             R free    0.2128   0.2108
     Rms BondLength    0.0125   0.0129
      Rms BondAngle    1.8182   1.8372
     Rms ChirVolume    0.0873   0.0871
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      45.6s System:    0.2s Elapsed:     0:46