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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: 14:46:07 


 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 1.90     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 11
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R11_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R11_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R11_1-90A.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       0.0693
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9000
  Estimated number of reflections :      21862
  Free R exclusion - flag equals:    11
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.9000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R11_2-00A.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=   2.215 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=   1.845 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=   2.239 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=   2.357 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=   2.470 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=   1.976 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                           11
Number of "free" reflections        813
Number of   all  reflections      16986
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16986

   Current auto weighting coefficient =    7.2495699    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

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

A     10 ARG C   . - A     11 THR N   . mod.= 1.471 id.= 1.337 dev= -0.134 sig.= 0.011
A    125 LEU C   . - A    126 ARG N   . mod.= 1.535 id.= 1.337 dev= -0.198 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.= 0.911 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        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.24394980    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                40.7
Norm of Geom. positional gradient                87.5
Norm of X_ray B-factor gradient                  136.
Norm of Geom. B-factor gradient                 0.208E+05
Product of X_ray and Geom posit. gradients     -0.774E+07
 Cosine of angle between them                      -0.224
Product of X_ray and Geom B-fact gradients     -0.403E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6389E+06 GEOM=     0.2584E+05 TOTAL=     0.6648E+06
 function value    664773.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.828     1.644
Bond angles  : others                          3242     2.348     1.582
Torsion angles, period  1. refined              184     7.217     5.000
Torsion angles, period  2. refined               90    36.687    22.778
Torsion angles, period  3. refined              268    14.360    15.000
Torsion angles, period  4. refined                9    10.526    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   315     0.256     0.200
VDW repulsions.others                          1333     0.230     0.200
VDW; torsion: refined_atoms                     715     0.169     0.200
VDW; torsion.others                             705     0.079     0.200
HBOND: refined_atoms                            238     0.220     0.200
HBOND.others                                      4     0.028     0.200
VDW repulsions: symmetry: refined_atoms           8     0.242     0.200
VDW repulsions: symmetry: others                 28     0.150     0.200
HBOND: symmetry: refined_atoms                   17     0.245     0.200
HBOND: symmetry: others                           1     0.088     0.200
M. chain bond B values: refined atoms           745     1.594     1.175
M. chain bond B values: others                  745     1.593     1.175
M. chain angle B values: refined atoms          926     2.543     1.744
M. chain angle B values: others                 927     2.541     1.744
S. chain bond B values: refined atoms           812     2.407     1.499
S. chain bond B values: others                  811     2.404     1.499
S. chain angle B values: refined atoms         1177     3.837     2.108
S. chain angle B values: others                1178     3.835     2.108
Long range B values: refined atoms             1874     6.790    16.558
Long range B values: others                    1773     6.444    15.166
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =    0.3499
Partial structure    1: scale =     0.3724, B  =   49.1718
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.55 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2202 100.00   481.1   484.7  0.16  0.17     109   492.7   513.3  0.20  0.21
 0.104    3739 100.00   387.3   370.2  0.16  0.15     185   376.1   361.4  0.21  0.19
 0.173    4712  99.96   248.6   243.1  0.15  0.13     230   248.4   246.4  0.20  0.17
 0.242    5515 100.00   189.1   190.0  0.19  0.15     289   185.6   190.2  0.23  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1525   0.920    677   0.824   2202   0.891  0.961  0.9645  0.9708  0.9160  0.9407
  0.1042   3047   0.894    692   0.787   3739   0.874  1.000  0.9516  0.9643  0.9065  0.9447
  0.1733   4012   0.885    700   0.787   4712   0.871  0.986  0.9504  0.9638  0.8760  0.9438
  0.2425   4827   0.858    691   0.757   5518   0.846  0.945  0.9401  0.9489  0.8831  0.9161
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16171
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.7869
Overall R factor                     =     0.1633
Free R factor                        =     0.2109
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9489
Overall weighted R factor            =     0.1508
Free weighted R factor               =     0.1908
Overall weighted R2 factor           =     0.1836
Free weighted R2 factor              =     0.2229
Average correlation coefficient      =     0.9341
Overall correlation coefficient      =     0.9537
Free correlation coefficient         =     0.9253
Cruickshanks DPI for coordinate error=     0.1439
DPI based on free R factor           =     0.1373
Overall figure of merit              =     0.8657
ML based su of positional parameters =     0.0836
ML based su of thermal parameters    =     2.8213
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88134.484       25836.582       664773.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.26703483    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    646265.19    

-------------------------------------------------------------------------------
             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 =     0.0401, B  =   -0.1091
Partial structure    1: scale =     0.3734, B  =   48.9929
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1611
Free R factor                        =     0.2092
Average Fourier shell correlation    =     0.9628
AverageFree Fourier shell correlation=     0.9516
Average correlation coefficient      =     0.9377
Overall figure of merit              =     0.8744
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87680.906       10616.314       646265.19       664773.69    


     CGMAT cycle number =      3

 Weight matrix   0.27018416    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643865.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0746
Partial structure    1: scale =     0.3749, B  =   47.1644
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1594
Free R factor                        =     0.2076
Average Fourier shell correlation    =     0.9635
AverageFree Fourier shell correlation=     0.9523
Average correlation coefficient      =     0.9395
Overall figure of merit              =     0.8754
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87503.977       9499.0850       643865.25       646265.19    


     CGMAT cycle number =      4

 Weight matrix   0.27070463    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    643023.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0733
Partial structure    1: scale =     0.3753, B  =   47.3195
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1587
Free R factor                        =     0.2070
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9525
Average correlation coefficient      =     0.9401
Overall figure of merit              =     0.8757
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87436.297       9147.5313       643023.13       643865.25    


     CGMAT cycle number =      5

 Weight matrix   0.27015272    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642795.75    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0730
Partial structure    1: scale =     0.3758, B  =   47.6617
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1584
Free R factor                        =     0.2072
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9525
Average correlation coefficient      =     0.9405
Overall figure of merit              =     0.8756
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87410.258       9108.9805       642795.75       643023.13    


     CGMAT cycle number =      6

 Weight matrix   0.26936454    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642773.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0761
Partial structure    1: scale =     0.3762, B  =   47.9285
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2072
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9524
Average correlation coefficient      =     0.9406
Overall figure of merit              =     0.8755
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87404.320       9129.3691       642773.13       642795.75    


     CGMAT cycle number =      7

 Weight matrix   0.26830408    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642779.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0746
Partial structure    1: scale =     0.3762, B  =   48.0389
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2072
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9523
Average correlation coefficient      =     0.9407
Overall figure of merit              =     0.8752
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    87403.047       9141.0596       642782.38       642773.13    

 fvalues    87403.047       9141.0596       642754.06       642775.56    
 fvalues    87403.047       9141.0596       642754.06       642775.56    


     CGMAT cycle number =      8

 Weight matrix   0.26800212    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642747.56    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0774
Partial structure    1: scale =     0.3761, B  =   47.9655
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1581
Free R factor                        =     0.2072
Average Fourier shell correlation    =     0.9638
AverageFree Fourier shell correlation=     0.9522
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8751
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87399.719       9137.1855       642747.56       642775.56    


     CGMAT cycle number =      9

 Weight matrix   0.26758167    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642741.75    

-------------------------------------------------------------------------------
             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 =     0.0402, B  =   -0.0741
Partial structure    1: scale =     0.3763, B  =   48.1538
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1580
Free R factor                        =     0.2073
Average Fourier shell correlation    =     0.9637
AverageFree Fourier shell correlation=     0.9521
Average correlation coefficient      =     0.9408
Overall figure of merit              =     0.8750
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87398.828       9137.7930       642741.75       642747.56    


     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.= 0.922 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.26708591    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                36.3
Norm of Geom. positional gradient                36.3
Norm of X_ray B-factor gradient                  119.
Norm of Geom. B-factor gradient                  123.
Product of X_ray and Geom posit. gradients     -0.128E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.471E+08
 Cosine of angle between them                      -0.992


Residuals: XRAY=     0.6336E+06 GEOM=      9138.     TOTAL=     0.6427E+06
 function value    642747.00    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.811     1.644
Bond angles  : others                          3242     1.463     1.582
Torsion angles, period  1. refined              184     6.933     5.000
Torsion angles, period  2. refined               90    36.942    22.778
Torsion angles, period  3. refined              268    14.133    15.000
Torsion angles, period  4. refined                9    10.035    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     0.260     0.200
VDW repulsions.others                          1358     0.206     0.200
VDW; torsion: refined_atoms                     725     0.171     0.200
VDW; torsion.others                             779     0.083     0.200
HBOND: refined_atoms                            233     0.214     0.200
HBOND.others                                      2     0.018     0.200
VDW repulsions: symmetry: refined_atoms           9     0.247     0.200
VDW repulsions: symmetry: others                 30     0.157     0.200
HBOND: symmetry: refined_atoms                   19     0.218     0.200
HBOND: symmetry: others                           1     0.033     0.200
M. chain bond B values: refined atoms           745     1.642     1.203
M. chain bond B values: others                  745     1.641     1.203
M. chain angle B values: refined atoms          926     2.586     1.786
M. chain angle B values: others                 927     2.584     1.785
S. chain bond B values: refined atoms           812     2.716     1.563
S. chain bond B values: others                  811     2.713     1.562
S. chain angle B values: refined atoms         1177     4.256     2.191
S. chain angle B values: others                1178     4.254     2.191
Long range B values: refined atoms             1874     7.275    17.150
Long range B values: others                    1775     6.947    15.743
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0755
Partial structure    1: scale =     0.3765, B  =   48.2260
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2202 100.00   480.9   484.8  0.15  0.17     109   492.5   511.9  0.20  0.21
 0.104    3739 100.00   387.1   369.2  0.16  0.15     185   375.9   358.2  0.21  0.19
 0.173    4712  99.96   248.5   242.9  0.15  0.13     230   248.3   244.1  0.20  0.17
 0.242    5515 100.00   189.0   190.2  0.17  0.13     289   185.5   190.3  0.22  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1525   0.937    677   0.848   2202   0.910  0.962  0.9702  0.9746  0.9244  0.9424
  0.1042   3047   0.895    692   0.792   3739   0.876  1.000  0.9523  0.9645  0.9062  0.9432
  0.1733   4012   0.891    700   0.794   4712   0.876  0.986  0.9522  0.9657  0.8801  0.9455
  0.2425   4827   0.872    691   0.767   5518   0.859  0.950  0.9450  0.9571  0.8887  0.9345
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16171
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.7869
Overall R factor                     =     0.1580
Free R factor                        =     0.2074
Average Fourier shell correlation    =     0.9637
AverageFree Fourier shell correlation=     0.9521
Overall weighted R factor            =     0.1476
Free weighted R factor               =     0.1884
Overall weighted R2 factor           =     0.1811
Free weighted R2 factor              =     0.2202
Average correlation coefficient      =     0.9408
Overall correlation coefficient      =     0.9555
Free correlation coefficient         =     0.9281
Cruickshanks DPI for coordinate error=     0.1392
DPI based on free R factor           =     0.1350
Overall figure of merit              =     0.8749
ML based su of positional parameters =     0.0798
ML based su of thermal parameters    =     2.6878
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    87399.867       9137.6152       642735.75       642741.75    
 fvalues    87399.867       9137.6152       642735.75       642749.06    

    ****                              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.= 0.922 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R11_1-90A.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     1.811     1.644
Bond angles  : others                          3242     1.463     1.582
Torsion angles, period  1. refined              184     6.934     5.000
Torsion angles, period  2. refined               90    36.944    22.778
Torsion angles, period  3. refined              268    14.134    15.000
Torsion angles, period  4. refined                9    10.016    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     0.261     0.200
VDW repulsions.others                          1358     0.206     0.200
VDW; torsion: refined_atoms                     726     0.171     0.200
VDW; torsion.others                             783     0.083     0.200
HBOND: refined_atoms                            230     0.216     0.200
HBOND.others                                      2     0.018     0.200
VDW repulsions: symmetry: refined_atoms           9     0.248     0.200
VDW repulsions: symmetry: others                 30     0.158     0.200
HBOND: symmetry: refined_atoms                   19     0.219     0.200
HBOND: symmetry: others                           1     0.032     0.200
M. chain bond B values: refined atoms           745     1.642     1.203
M. chain bond B values: others                  745     1.641     1.203
M. chain angle B values: refined atoms          926     2.586     1.786
M. chain angle B values: others                 927     2.584     1.786
S. chain bond B values: refined atoms           812     2.719     1.563
S. chain bond B values: others                  811     2.716     1.563
S. chain angle B values: refined atoms         1177     4.260     2.192
S. chain angle B values: others                1178     4.258     2.191
Long range B values: refined atoms             1871     7.237    17.091
Long range B values: others                    1772     6.901    15.678
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0755
Partial structure    1: scale =     0.3765, B  =   48.3565
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2202 100.00   480.8   484.8  0.15  0.17     109   492.4   511.8  0.19  0.20
 0.104    3739 100.00   387.0   369.1  0.16  0.15     185   375.8   358.1  0.21  0.19
 0.173    4712  99.96   248.4   242.9  0.15  0.13     230   248.3   244.1  0.20  0.17
 0.242    5515 100.00   189.0   190.2  0.17  0.13     289   185.5   190.2  0.22  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1525   0.938    677   0.849   2202   0.910  0.962  0.9704  0.9747  0.9248  0.9426
  0.1042   3047   0.895    692   0.792   3739   0.876  1.000  0.9523  0.9645  0.9062  0.9431
  0.1733   4012   0.891    700   0.794   4712   0.876  0.986  0.9522  0.9657  0.8800  0.9455
  0.2425   4827   0.872    691   0.767   5518   0.859  0.950  0.9449  0.9571  0.8885  0.9346
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16171
Percentage observed                  =    99.9823
Percentage of free reflections       =     4.7869
Overall R factor                     =     0.1579
Free R factor                        =     0.2072
Average Fourier shell correlation    =     0.9637
AverageFree Fourier shell correlation=     0.9520
Overall weighted R factor            =     0.1476
Free weighted R factor               =     0.1881
Overall weighted R2 factor           =     0.1810
Free weighted R2 factor              =     0.2200
Average correlation coefficient      =     0.9408
Overall correlation coefficient      =     0.9556
Free correlation coefficient         =     0.9282
Cruickshanks DPI for coordinate error=     0.1391
DPI based on free R factor           =     0.1348
Overall figure of merit              =     0.8749
ML based su of positional parameters =     0.0798
ML based su of thermal parameters    =     2.6878
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.42
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1633   0.2109   0.866       88134.    4563.1   0.0137  1.060   1.828  1.058   0.086
       1   0.1611   0.2092   0.874       87681.    4553.7   0.0119  0.868   1.773  1.022   0.087
       2   0.1594   0.2076   0.875       87504.    4548.3   0.0125  0.915   1.793  1.034   0.088
       3   0.1587   0.2070   0.876       87436.    4546.1   0.0126  0.924   1.802  1.040   0.088
       4   0.1584   0.2072   0.876       87410.    4546.2   0.0126  0.928   1.807  1.043   0.088
       5   0.1583   0.2072   0.876       87404.    4546.5   0.0127  0.929   1.809  1.045   0.087
       6   0.1582   0.2072   0.875       87404.    4547.0   0.0126  0.930   1.811  1.046   0.087
       7   0.1581   0.2072   0.875       87400.    4547.2   0.0126  0.929   1.811  1.046   0.087
       8   0.1580   0.2073   0.875       87399.    4547.3   0.0126  0.929   1.811  1.046   0.087
       9   0.1580   0.2074   0.875       87400.    4547.9   0.0126  0.929   1.811  1.046   0.087
      10   0.1579   0.2072   0.875       87397.    4547.9   0.0126  0.928   1.811  1.046   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1633   0.1579
             R free    0.2109   0.2072
     Rms BondLength    0.0137   0.0126
      Rms BondAngle    1.8279   1.8112
     Rms ChirVolume    0.0859   0.0870
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.4s System:    0.1s Elapsed:     0:47