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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: 16:19:18 


 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 3
  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_R03_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R03_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_R03_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:     3
  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_R03_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=   2.040 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=   2.203 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=   1.832 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=   2.200 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=   2.374 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=   2.401 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=   2.127 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  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  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:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            3
Number of "free" reflections       1103
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

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A    171 THR C   . - A    172 GLY N   . mod.= 1.724 id.= 1.337 dev= -0.387 sig.= 0.011

    ****                              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.= 0.894 id.= 3.000 dev= -2.11 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   0.31321999    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                43.2
Norm of Geom. positional gradient                92.1
Norm of X_ray B-factor gradient                  140.
Norm of Geom. B-factor gradient                  113.
Product of X_ray and Geom posit. gradients     -0.122E+08
 Cosine of angle between them                      -0.318
Product of X_ray and Geom B-fact gradients     -0.426E+08
 Cosine of angle between them                      -0.839


Residuals: XRAY=     0.7849E+06 GEOM=     0.1387E+05 TOTAL=     0.7987E+06
 function value    798731.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.016     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.803     1.644
Bond angles  : others                          3238     2.359     1.580
Torsion angles, period  1. refined              185     7.069     5.000
Torsion angles, period  2. refined               90    36.894    22.778
Torsion angles, period  3. refined              268    14.114    15.000
Torsion angles, period  4. refined                9    12.161    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.013     0.020
VDW repulsions: refined_atoms                   303     0.241     0.200
VDW repulsions.others                          1319     0.223     0.200
VDW; torsion: refined_atoms                     719     0.170     0.200
VDW; torsion.others                             704     0.082     0.200
HBOND: refined_atoms                            222     0.200     0.200
HBOND.others                                      2     0.116     0.200
VDW repulsions: symmetry: refined_atoms           9     0.235     0.200
VDW repulsions: symmetry: others                 27     0.181     0.200
HBOND: symmetry: refined_atoms                   23     0.192     0.200
HBOND: symmetry: others                           1     0.032     0.200
M. chain bond B values: refined atoms           746     1.588     1.293
M. chain bond B values: others                  746     1.587     1.293
M. chain angle B values: refined atoms          929     2.525     1.926
M. chain angle B values: others                 930     2.524     1.926
S. chain bond B values: refined atoms           811     2.836     1.672
S. chain bond B values: others                  810     2.832     1.672
S. chain angle B values: refined atoms         1177     4.468     2.348
S. chain angle B values: others                1178     4.466     2.348
Long range B values: refined atoms             1846     7.098    18.113
Long range B values: others                    1751     6.759    16.651
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.0550
Partial structure    1: scale =     0.3872, B  =   45.1889
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    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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3017 100.00   453.5   462.7  0.16  0.17     154   468.4   465.5  0.19  0.20
 0.130    5132 100.00   299.4   286.9  0.16  0.14     268   296.0   280.3  0.20  0.18
 0.216    6565  99.97   202.1   185.9  0.17  0.15     307   213.0   197.7  0.20  0.17
 0.303    7669 100.00   104.2   116.8  0.27  0.20     374   107.1   119.9  0.29  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2166   0.922    851   0.818   3017   0.892  0.948  0.9664  0.9720  0.9022  0.9404
  0.1301   4269   0.893    863   0.790   5132   0.876  1.003  0.9557  0.9652  0.9146  0.9450
  0.2165   5674   0.882    891   0.773   6565   0.867  1.046  0.9549  0.9616  0.9004  0.9409
  0.3028   6802   0.761    870   0.699   7672   0.754  0.812  0.9099  0.9172  0.8644  0.8896
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22386
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.6958
Overall R factor                     =     0.1796
Free R factor                        =     0.2100
Average Fourier shell correlation    =     0.9486
AverageFree Fourier shell correlation=     0.9415
Overall weighted R factor            =     0.1583
Free weighted R factor               =     0.1860
Overall weighted R2 factor           =     0.1888
Free weighted R2 factor              =     0.2227
Average correlation coefficient      =     0.9242
Overall correlation coefficient      =     0.9578
Free correlation coefficient         =     0.9365
Cruickshanks DPI for coordinate error=     0.1084
DPI based on free R factor           =     0.1039
Overall figure of merit              =     0.8337
ML based su of positional parameters =     0.0712
ML based su of thermal parameters    =     2.2398
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    116280.80       13872.045       798731.13      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36639875    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    787897.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0624
Partial structure    1: scale =     0.3872, B  =   45.1715
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                     =     0.1782
Free R factor                        =     0.2093
Average Fourier shell correlation    =     0.9549
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9267
Overall figure of merit              =     0.8551
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115465.28       8543.1377       787897.63       798731.13    


     CGMAT cycle number =      3

 Weight matrix   0.37447804    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786800.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.014     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0262
Partial structure    1: scale =     0.3875, B  =   45.1777
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                     =     0.1771
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8585
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    115212.78       9150.6084       786800.88       787897.63    


     CGMAT cycle number =      4

 Weight matrix   0.34196341    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    715782.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.014     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =   -0.0200
Partial structure    1: scale =     0.3881, B  =   45.2894
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                     =     0.1768
Free R factor                        =     0.2089
Average Fourier shell correlation    =     0.9564
AverageFree Fourier shell correlation=     0.9482
Average correlation coefficient      =     0.9293
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    115123.39       9375.8047       715782.06       786800.88    


     CGMAT cycle number =      5

 Weight matrix   0.31088573    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651484.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =   -0.0259
Partial structure    1: scale =     0.3883, B  =   45.4668
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                     =     0.1771
Free R factor                        =     0.2090
Average Fourier shell correlation    =     0.9564
AverageFree Fourier shell correlation=     0.9481
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8591
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    115145.98       9170.6143       651484.13       715782.06    


     CGMAT cycle number =      6

 Weight matrix   0.30947486    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651499.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0351
Partial structure    1: scale =     0.3883, B  =   45.4621
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                     =     0.1776
Free R factor                        =     0.2093
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9288
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    115205.30       8843.3564       651490.56       651484.13    

 fvalues    115205.30       8843.3564       651487.81       651487.75    
 fvalues    115205.30       8843.3564       651487.81       651487.75    


     CGMAT cycle number =      7

 Weight matrix   0.30993769    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651498.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0477
Partial structure    1: scale =     0.3883, B  =   45.4581
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                     =     0.1776
Free R factor                        =     0.2093
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9288
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    115209.61       8822.8975       651507.94       651487.75    

 fvalues    115209.61       8822.8975       651489.56       651491.31    
 fvalues    115209.61       8822.8975       651489.56       651491.31    


     CGMAT cycle number =      8

 Weight matrix   0.30985469    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651484.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0456
Partial structure    1: scale =     0.3884, B  =   45.5016
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                     =     0.1777
Free R factor                        =     0.2093
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9288
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    115211.46       8806.1699       651484.94       651491.31    


     CGMAT cycle number =      9

 Weight matrix   0.30979735    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651483.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0438
Partial structure    1: scale =     0.3884, B  =   45.4976
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                     =     0.1777
Free R factor                        =     0.2093
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9480
Average correlation coefficient      =     0.9288
Overall figure of merit              =     0.8589
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    115213.62       8792.3262       651483.13       651484.94    


     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.= 0.902 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.30938208    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                37.6
Norm of Geom. positional gradient                37.8
Norm of X_ray B-factor gradient                  113.
Norm of Geom. B-factor gradient                  116.
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.419E+08
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.6427E+06 GEOM=      8780.     TOTAL=     0.6515E+06
 function value    651500.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.776     1.644
Bond angles  : others                          3238     1.485     1.580
Torsion angles, period  1. refined              185     6.897     5.000
Torsion angles, period  2. refined               90    36.681    22.778
Torsion angles, period  3. refined              268    14.023    15.000
Torsion angles, period  4. refined                9    12.103    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   296     0.245     0.200
VDW repulsions.others                          1342     0.198     0.200
VDW; torsion: refined_atoms                     728     0.171     0.200
VDW; torsion.others                             751     0.085     0.200
HBOND: refined_atoms                            216     0.196     0.200
HBOND.others                                      1     0.055     0.200
VDW repulsions: symmetry: refined_atoms           7     0.243     0.200
VDW repulsions: symmetry: others                 28     0.160     0.200
HBOND: symmetry: refined_atoms                   20     0.201     0.200
HBOND: symmetry: others                           1     0.047     0.200
M. chain bond B values: refined atoms           746     1.626     1.394
M. chain bond B values: others                  746     1.624     1.394
M. chain angle B values: refined atoms          929     2.575     2.079
M. chain angle B values: others                 930     2.574     2.079
S. chain bond B values: refined atoms           811     3.005     1.794
S. chain bond B values: others                  810     2.998     1.794
S. chain angle B values: refined atoms         1177     4.684     2.524
S. chain angle B values: others                1178     4.682     2.524
Long range B values: refined atoms             1839     7.199    19.482
Long range B values: others                    1747     6.923    18.048
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0390
Partial structure    1: scale =     0.3884, B  =   45.5108
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3017 100.00   453.0   463.0  0.16  0.17     154   467.9   466.6  0.19  0.20
 0.130    5132 100.00   299.1   286.0  0.16  0.14     268   295.7   278.9  0.20  0.17
 0.216    6565  99.97   201.9   185.5  0.17  0.15     307   212.8   197.8  0.20  0.17
 0.303    7669 100.00   104.1   116.0  0.25  0.19     374   107.0   119.4  0.28  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2166   0.935    851   0.841   3017   0.909  0.951  0.9688  0.9747  0.9000  0.9400
  0.1301   4269   0.896    863   0.792   5132   0.878  1.003  0.9566  0.9657  0.9166  0.9450
  0.2165   5674   0.889    891   0.783   6565   0.874  1.046  0.9566  0.9633  0.8999  0.9405
  0.3028   6802   0.821    870   0.752   7672   0.813  0.838  0.9260  0.9363  0.8688  0.9035
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22386
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.6958
Overall R factor                     =     0.1777
Free R factor                        =     0.2093
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9479
Overall weighted R factor            =     0.1581
Free weighted R factor               =     0.1863
Overall weighted R2 factor           =     0.1896
Free weighted R2 factor              =     0.2241
Average correlation coefficient      =     0.9288
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9363
Cruickshanks DPI for coordinate error=     0.1072
DPI based on free R factor           =     0.1036
Overall figure of merit              =     0.8588
ML based su of positional parameters =     0.0650
ML based su of thermal parameters    =     2.0059
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    115219.34       8780.0049       651502.38       651483.13    
 fvalues    115219.34       8780.0049       651502.38       651502.75    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.902 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R03_1-70A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.775     1.644
Bond angles  : others                          3238     1.484     1.580
Torsion angles, period  1. refined              185     6.896     5.000
Torsion angles, period  2. refined               90    36.673    22.778
Torsion angles, period  3. refined              268    14.023    15.000
Torsion angles, period  4. refined                9    12.095    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   296     0.245     0.200
VDW repulsions.others                          1342     0.198     0.200
VDW; torsion: refined_atoms                     728     0.171     0.200
VDW; torsion.others                             751     0.085     0.200
HBOND: refined_atoms                            216     0.196     0.200
HBOND.others                                      1     0.055     0.200
VDW repulsions: symmetry: refined_atoms           7     0.243     0.200
VDW repulsions: symmetry: others                 27     0.163     0.200
HBOND: symmetry: refined_atoms                   20     0.201     0.200
HBOND: symmetry: others                           1     0.047     0.200
M. chain bond B values: refined atoms           746     1.625     1.394
M. chain bond B values: others                  746     1.622     1.394
M. chain angle B values: refined atoms          929     2.572     2.079
M. chain angle B values: others                 930     2.571     2.079
S. chain bond B values: refined atoms           811     3.002     1.794
S. chain bond B values: others                  810     2.995     1.793
S. chain angle B values: refined atoms         1177     4.679     2.524
S. chain angle B values: others                1178     4.677     2.523
Long range B values: refined atoms             1839     7.197    19.482
Long range B values: others                    1747     6.921    18.047
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0402
Partial structure    1: scale =     0.3885, B  =   45.5200
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3017 100.00   453.0   463.0  0.16  0.17     154   467.8   466.5  0.19  0.20
 0.130    5132 100.00   299.1   286.0  0.16  0.14     268   295.7   278.9  0.20  0.17
 0.216    6565  99.97   201.8   185.6  0.17  0.15     307   212.7   197.8  0.20  0.17
 0.303    7669 100.00   104.0   116.0  0.25  0.19     374   107.0   119.4  0.28  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2166   0.935    851   0.841   3017   0.909  0.951  0.9688  0.9747  0.9001  0.9399
  0.1301   4269   0.896    863   0.792   5132   0.878  1.003  0.9566  0.9657  0.9167  0.9450
  0.2165   5674   0.889    891   0.783   6565   0.875  1.046  0.9565  0.9633  0.8999  0.9405
  0.3028   6802   0.821    870   0.752   7672   0.813  0.838  0.9260  0.9363  0.8688  0.9035
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22386
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.6958
Overall R factor                     =     0.1777
Free R factor                        =     0.2093
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9479
Overall weighted R factor            =     0.1581
Free weighted R factor               =     0.1863
Overall weighted R2 factor           =     0.1897
Free weighted R2 factor              =     0.2240
Average correlation coefficient      =     0.9288
Overall correlation coefficient      =     0.9582
Free correlation coefficient         =     0.9363
Cruickshanks DPI for coordinate error=     0.1073
DPI based on free R factor           =     0.1035
Overall figure of merit              =     0.8588
ML based su of positional parameters =     0.0650
ML based su of thermal parameters    =     2.0059
-----------------------------------------------------------------------------
  Time in seconds: CPU =        19.05
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1796   0.2100   0.834      116281.    5872.7   0.0157  1.270   1.803  1.039   0.083
       1   0.1782   0.2093   0.855      115465.    5855.0   0.0128  0.947   1.783  1.032   0.086
       2   0.1771   0.2088   0.858      115213.    5850.1   0.0136  1.006   1.822  1.057   0.089
       3   0.1768   0.2089   0.859      115123.    5848.8   0.0137  1.016   1.839  1.068   0.091
       4   0.1771   0.2090   0.859      115146.    5849.1   0.0131  0.973   1.818  1.056   0.089
       5   0.1776   0.2093   0.859      115207.    5850.5   0.0124  0.927   1.785  1.037   0.087
       6   0.1776   0.2093   0.859      115211.    5850.9   0.0124  0.926   1.782  1.036   0.087
       7   0.1777   0.2093   0.859      115211.    5850.9   0.0124  0.925   1.780  1.035   0.087
       8   0.1777   0.2093   0.859      115214.    5851.0   0.0124  0.924   1.778  1.034   0.087
       9   0.1777   0.2093   0.859      115219.    5851.4   0.0124  0.923   1.776  1.033   0.087
      10   0.1777   0.2093   0.859      115216.    5851.2   0.0124  0.922   1.775  1.032   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1796   0.1777
             R free    0.2100   0.2093
     Rms BondLength    0.0157   0.0124
      Rms BondAngle    1.8034   1.7746
     Rms ChirVolume    0.0829   0.0866
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      51.0s System:    0.1s Elapsed:     0:51