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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 15:17:18 


 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 1.80     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 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_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R03_1-80A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R03_1-80A.mtz

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

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

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


  Residual                               : Rice Maximum Likelihood for Fs

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

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


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

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  Free R exclusion - flag equals:     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  1.8000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R03_1-90A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.008 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=   2.201 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=   1.830 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=   2.213 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=   2.355 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=   2.416 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=   2.111 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                            3
Number of "free" reflections        956
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.898 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  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.29277244    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                42.6
Norm of Geom. positional gradient                80.3
Norm of X_ray B-factor gradient                  138.
Norm of Geom. B-factor gradient                 0.223E+05
Product of X_ray and Geom posit. gradients     -0.123E+08
 Cosine of angle between them                      -0.372
Product of X_ray and Geom B-fact gradients     -0.460E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7054E+06 GEOM=     0.2708E+05 TOTAL=     0.7325E+06
 function value    732475.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.814     1.644
Bond angles  : others                          3242     2.349     1.582
Torsion angles, period  1. refined              184     6.978     5.000
Torsion angles, period  2. refined               90    37.091    22.778
Torsion angles, period  3. refined              268    14.191    15.000
Torsion angles, period  4. refined                9    11.430    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   318     0.259     0.200
VDW repulsions.others                          1337     0.233     0.200
VDW; torsion: refined_atoms                     717     0.171     0.200
VDW; torsion.others                             699     0.082     0.200
HBOND: refined_atoms                            221     0.212     0.200
HBOND.others                                      2     0.039     0.200
VDW repulsions: symmetry: refined_atoms           9     0.248     0.200
VDW repulsions: symmetry: others                 28     0.179     0.200
HBOND: symmetry: refined_atoms                   21     0.196     0.200
HBOND: symmetry: others                           1     0.089     0.200
M. chain bond B values: refined atoms           745     1.609     1.205
M. chain bond B values: others                  745     1.608     1.205
M. chain angle B values: refined atoms          926     2.557     1.788
M. chain angle B values: others                 927     2.555     1.788
S. chain bond B values: refined atoms           811     2.819     1.576
S. chain bond B values: others                  810     2.814     1.576
S. chain angle B values: refined atoms         1177     4.417     2.205
S. chain angle B values: others                1178     4.416     2.205
Long range B values: refined atoms             1857     7.179    17.050
Long range B values: others                    1763     6.847    15.678
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.8785
Partial structure    1: scale =     0.3776, B  =   50.4931
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2563 100.00   471.3   480.7  0.16  0.17     130   501.6   492.1  0.18  0.19
 0.116    4351 100.00   342.0   328.0  0.16  0.14     228   331.8   316.5  0.21  0.19
 0.193    5545  99.97   226.0   215.2  0.15  0.13     263   226.7   219.2  0.20  0.17
 0.270    6452 100.00   147.4   154.5  0.22  0.17     335   156.3   164.9  0.23  0.18
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1802   0.928    761   0.822   2563   0.896  0.951  0.9687  0.9725  0.9074  0.9418
  0.1161   3578   0.892    773   0.795   4351   0.875  0.998  0.9527  0.9666  0.9013  0.9481
  0.1931   4762   0.889    783   0.781   5545   0.874  1.015  0.9526  0.9646  0.8963  0.9447
  0.2701   5674   0.822    786   0.743   6460   0.812  0.894  0.9396  0.9394  0.8940  0.9036
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18919
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.8101
Overall R factor                     =     0.1680
Free R factor                        =     0.2052
Average Fourier shell correlation    =     0.9575
AverageFree Fourier shell correlation=     0.9503
Overall weighted R factor            =     0.1514
Free weighted R factor               =     0.1850
Overall weighted R2 factor           =     0.1832
Free weighted R2 factor              =     0.2225
Average correlation coefficient      =     0.9311
Overall correlation coefficient      =     0.9568
Free correlation coefficient         =     0.9315
Cruickshanks DPI for coordinate error=     0.1224
DPI based on free R factor           =     0.1170
Overall figure of merit              =     0.8560
ML based su of positional parameters =     0.0750
ML based su of thermal parameters    =     2.4442
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100777.24       27078.717       732475.19      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.32840866    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    712647.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0956
Partial structure    1: scale =     0.3770, B  =   49.6332
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1670
Free R factor                        =     0.2034
Average Fourier shell correlation    =     0.9613
AverageFree Fourier shell correlation=     0.9537
Average correlation coefficient      =     0.9337
Overall figure of merit              =     0.8707
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100308.99       10528.561       712647.50       732475.19    


     CGMAT cycle number =      3

 Weight matrix   0.33550629    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710270.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0647
Partial structure    1: scale =     0.3764, B  =   47.0189
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1656
Free R factor                        =     0.2017
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9545
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8726
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100073.64       9798.9805       710270.56       712647.50    


     CGMAT cycle number =      4

 Weight matrix   0.33787325    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709488.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0375
Partial structure    1: scale =     0.3768, B  =   47.0275
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1653
Free R factor                        =     0.2011
Average Fourier shell correlation    =     0.9625
AverageFree Fourier shell correlation=     0.9547
Average correlation coefficient      =     0.9363
Overall figure of merit              =     0.8732
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    99987.766       9618.3047       709488.81       710270.56    


     CGMAT cycle number =      5

 Weight matrix   0.33875960    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709167.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0560
Partial structure    1: scale =     0.3776, B  =   46.9492
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1651
Free R factor                        =     0.2011
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9548
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8733
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    99942.180       9616.4512       709167.88       709488.81    


     CGMAT cycle number =      6

 Weight matrix   0.30793902    
 Actual weight    6.3632374      is applied to the X-ray term


 function value    645481.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0453
Partial structure    1: scale =     0.3777, B  =   46.6348
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1649
Free R factor                        =     0.2012
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9548
Average correlation coefficient      =     0.9368
Overall figure of merit              =     0.8733
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    99921.922       9654.1660       645481.13       709167.88    


     CGMAT cycle number =      7

 Weight matrix   0.27885446    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    587652.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0808
Partial structure    1: scale =     0.3778, B  =   46.4987
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1655
Free R factor                        =     0.2016
Average Fourier shell correlation    =     0.9624
AverageFree Fourier shell correlation=     0.9546
Average correlation coefficient      =     0.9364
Overall figure of merit              =     0.8730
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    99974.117       9326.1729       587652.56       645481.13    


     CGMAT cycle number =      8

 Weight matrix   0.27745536    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    587707.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0889
Partial structure    1: scale =     0.3777, B  =   46.5322
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1663
Free R factor                        =     0.2017
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9545
Average correlation coefficient      =     0.9358
Overall figure of merit              =     0.8727
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    100050.67       8945.1025       587731.06       587652.56    

 fvalues    100050.67       8945.1025       587712.69       587714.38    
 fvalues    100050.67       8945.1025       587712.69       587714.38    


     CGMAT cycle number =      9

 Weight matrix   0.27709693    
 Actual weight    5.7847610      is applied to the X-ray term


 function value    587716.38    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0822
Partial structure    1: scale =     0.3776, B  =   46.5068
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1664
Free R factor                        =     0.2016
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9545
Average correlation coefficient      =     0.9358
Overall figure of merit              =     0.8727
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02

 fvalues    100056.95       8896.9473       587702.50       587714.38    


     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.= 0.912 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.27680835    
 Actual weight    5.7847610      is applied to the X-ray term
Norm of X_ray positional gradient                35.2
Norm of Geom. positional gradient                35.4
Norm of X_ray B-factor gradient                  113.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.121E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.426E+08
 Cosine of angle between them                      -0.988


Residuals: XRAY=     0.5789E+06 GEOM=      8852.     TOTAL=     0.5877E+06
 function value    587719.25    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.781     1.644
Bond angles  : others                          3242     1.458     1.582
Torsion angles, period  1. refined              184     6.967     5.000
Torsion angles, period  2. refined               90    36.898    22.778
Torsion angles, period  3. refined              268    14.113    15.000
Torsion angles, period  4. refined                9    12.156    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   310     0.261     0.200
VDW repulsions.others                          1364     0.205     0.200
VDW; torsion: refined_atoms                     720     0.170     0.200
VDW; torsion.others                             790     0.084     0.200
HBOND: refined_atoms                            222     0.200     0.200
HBOND.others                                      2     0.045     0.200
VDW repulsions: symmetry: refined_atoms           9     0.235     0.200
VDW repulsions: symmetry: others                 29     0.170     0.200
HBOND: symmetry: refined_atoms                   23     0.191     0.200
HBOND: symmetry: others                           1     0.049     0.200
M. chain bond B values: refined atoms           745     1.577     1.291
M. chain bond B values: others                  745     1.575     1.291
M. chain angle B values: refined atoms          926     2.495     1.919
M. chain angle B values: others                 927     2.493     1.919
S. chain bond B values: refined atoms           811     2.841     1.673
S. chain bond B values: others                  810     2.836     1.673
S. chain angle B values: refined atoms         1177     4.474     2.349
S. chain angle B values: others                1178     4.472     2.348
Long range B values: refined atoms             1852     7.099    18.192
Long range B values: others                    1757     6.761    16.739
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0795
Partial structure    1: scale =     0.3774, B  =   46.4005
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2563 100.00   471.5   481.0  0.16  0.17     130   501.8   492.7  0.18  0.19
 0.116    4351 100.00   342.1   327.5  0.16  0.15     228   331.9   315.1  0.20  0.18
 0.193    5545  99.97   226.1   215.1  0.16  0.13     263   226.8   219.1  0.20  0.17
 0.270    6452 100.00   147.5   153.7  0.20  0.15     335   156.3   163.8  0.23  0.18
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1802   0.941    761   0.840   2563   0.911  0.953  0.9712  0.9752  0.9088  0.9429
  0.1161   3578   0.897    773   0.803   4351   0.880  0.998  0.9554  0.9671  0.9070  0.9454
  0.1931   4762   0.893    783   0.782   5545   0.877  1.015  0.9538  0.9645  0.8993  0.9408
  0.2701   5674   0.857    786   0.781   6460   0.848  0.911  0.9478  0.9516  0.8970  0.9219
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18919
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.8101
Overall R factor                     =     0.1664
Free R factor                        =     0.2018
Average Fourier shell correlation    =     0.9621
AverageFree Fourier shell correlation=     0.9545
Overall weighted R factor            =     0.1520
Free weighted R factor               =     0.1821
Overall weighted R2 factor           =     0.1841
Free weighted R2 factor              =     0.2195
Average correlation coefficient      =     0.9357
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9337
Cruickshanks DPI for coordinate error=     0.1213
DPI based on free R factor           =     0.1150
Overall figure of merit              =     0.8726
ML based su of positional parameters =     0.0700
ML based su of thermal parameters    =     2.2507
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    100067.98       8852.1113       587728.25       587702.50    

 fvalues    100067.98       8852.1113       587720.94       587721.44    
 fvalues    100067.98       8852.1113       587720.94       587721.44    

    ****                              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.= 0.913 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R03_1-80A.mtz 




-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.779     1.644
Bond angles  : others                          3242     1.457     1.582
Torsion angles, period  1. refined              184     6.966     5.000
Torsion angles, period  2. refined               90    36.894    22.778
Torsion angles, period  3. refined              268    14.113    15.000
Torsion angles, period  4. refined                9    12.160    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   309     0.261     0.200
VDW repulsions.others                          1363     0.205     0.200
VDW; torsion: refined_atoms                     720     0.170     0.200
VDW; torsion.others                             791     0.084     0.200
HBOND: refined_atoms                            223     0.200     0.200
HBOND.others                                      2     0.045     0.200
VDW repulsions: symmetry: refined_atoms           9     0.235     0.200
VDW repulsions: symmetry: others                 29     0.170     0.200
HBOND: symmetry: refined_atoms                   23     0.192     0.200
HBOND: symmetry: others                           1     0.049     0.200
M. chain bond B values: refined atoms           745     1.575     1.291
M. chain bond B values: others                  745     1.573     1.291
M. chain angle B values: refined atoms          926     2.492     1.920
M. chain angle B values: others                 927     2.490     1.919
S. chain bond B values: refined atoms           811     2.837     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             1852     7.096    18.189
Long range B values: others                    1757     6.759    16.736
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0783
Partial structure    1: scale =     0.3774, B  =   46.4225
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2563 100.00   471.5   481.0  0.16  0.17     130   501.9   492.7  0.18  0.19
 0.116    4351 100.00   342.2   327.5  0.16  0.15     228   331.9   315.1  0.20  0.18
 0.193    5545  99.97   226.1   215.1  0.16  0.13     263   226.8   219.1  0.20  0.17
 0.270    6452 100.00   147.5   153.7  0.20  0.15     335   156.4   163.8  0.23  0.18
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1802   0.941    761   0.840   2563   0.911  0.953  0.9711  0.9751  0.9084  0.9428
  0.1161   3578   0.897    773   0.803   4351   0.880  0.998  0.9554  0.9671  0.9070  0.9454
  0.1931   4762   0.893    783   0.782   5545   0.877  1.015  0.9538  0.9644  0.8992  0.9408
  0.2701   5674   0.857    786   0.781   6460   0.848  0.911  0.9478  0.9516  0.8970  0.9220
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18919
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.8101
Overall R factor                     =     0.1665
Free R factor                        =     0.2019
Average Fourier shell correlation    =     0.9621
AverageFree Fourier shell correlation=     0.9544
Overall weighted R factor            =     0.1520
Free weighted R factor               =     0.1822
Overall weighted R2 factor           =     0.1842
Free weighted R2 factor              =     0.2196
Average correlation coefficient      =     0.9357
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9336
Cruickshanks DPI for coordinate error=     0.1213
DPI based on free R factor           =     0.1151
Overall figure of merit              =     0.8725
ML based su of positional parameters =     0.0700
ML based su of thermal parameters    =     2.2507
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.44
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1680   0.2052   0.856      100777.    5224.0   0.0129  0.942   1.814  1.047   0.086
       1   0.1670   0.2034   0.871      100309.    5208.0   0.0127  0.932   1.798  1.038   0.086
       2   0.1656   0.2017   0.873      100074.    5200.3   0.0134  0.986   1.829  1.055   0.088
       3   0.1653   0.2011   0.873       99988.    5197.0   0.0136  0.997   1.845  1.064   0.088
       4   0.1651   0.2011   0.873       99942.    5195.8   0.0136  1.001   1.854  1.069   0.088
       5   0.1649   0.2012   0.873       99922.    5196.1   0.0136  1.003   1.859  1.071   0.088
       6   0.1655   0.2016   0.873       99974.    5198.1   0.0130  0.957   1.831  1.055   0.086
       7   0.1663   0.2017   0.873      100050.    5199.5   0.0123  0.909   1.792  1.032   0.083
       8   0.1664   0.2016   0.873      100059.    5199.8   0.0123  0.907   1.786  1.029   0.083
       9   0.1664   0.2018   0.873      100068.    5200.5   0.0123  0.905   1.781  1.026   0.083
      10   0.1665   0.2019   0.872      100075.    5201.1   0.0122  0.904   1.779  1.025   0.083
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1680   0.1665
             R free    0.2052   0.2019
     Rms BondLength    0.0129   0.0122
      Rms BondAngle    1.8144   1.7793
     Rms ChirVolume    0.0855   0.0829
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      49.6s System:    0.1s Elapsed:     0:50