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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: 15:59:32 


 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 17
  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_R17_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R17_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_R17_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:    17
  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_R17_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=   2.011 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=   2.227 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=   1.833 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=   2.197 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=   2.356 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.410 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.151 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                           17
Number of "free" reflections        981
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.= 0.904 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   0.24847358    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                37.6
Norm of Geom. positional gradient                78.7
Norm of X_ray B-factor gradient                  122.
Norm of Geom. B-factor gradient                 0.218E+05
Product of X_ray and Geom posit. gradients     -0.102E+08
 Cosine of angle between them                      -0.355
Product of X_ray and Geom B-fact gradients     -0.381E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.7084E+06 GEOM=     0.2624E+05 TOTAL=     0.7346E+06
 function value    734620.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.788     1.644
Bond angles  : others                          3242     2.342     1.582
Torsion angles, period  1. refined              184     6.990     5.000
Torsion angles, period  2. refined               90    37.018    22.778
Torsion angles, period  3. refined              268    14.224    15.000
Torsion angles, period  4. refined                9    10.849    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   304     0.262     0.200
VDW repulsions.others                          1347     0.231     0.200
VDW; torsion: refined_atoms                     721     0.171     0.200
VDW; torsion.others                             707     0.081     0.200
HBOND: refined_atoms                            228     0.210     0.200
HBOND.others                                      1     0.052     0.200
VDW repulsions: symmetry: refined_atoms           9     0.221     0.200
VDW repulsions: symmetry: others                 23     0.180     0.200
HBOND: symmetry: refined_atoms                   23     0.203     0.200
HBOND: symmetry: others                           1     0.025     0.200
M. chain bond B values: refined atoms           745     1.549     1.209
M. chain bond B values: others                  745     1.548     1.209
M. chain angle B values: refined atoms          926     2.473     1.796
M. chain angle B values: others                 927     2.472     1.795
S. chain bond B values: refined atoms           811     2.608     1.557
S. chain bond B values: others                  810     2.606     1.557
S. chain angle B values: refined atoms         1177     4.101     2.187
S. chain angle B values: others                1178     4.099     2.186
Long range B values: refined atoms             1855     7.041    17.124
Long range B values: others                    1760     6.714    15.742
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.8528
Partial structure    1: scale =     0.3792, B  =   51.0497
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2560 100.00   472.0   481.3  0.16  0.17     133   491.4   484.8  0.19  0.20
 0.116    4342 100.00   340.9   326.8  0.16  0.14     237   355.4   336.9  0.19  0.18
 0.193    5538  99.97   226.1   215.1  0.16  0.13     270   227.7   211.6  0.22  0.18
 0.270    6447 100.00   148.2   155.2  0.22  0.16     340   143.2   151.2  0.27  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1799   0.914    761   0.831   2560   0.889  0.951  0.9639  0.9693  0.9126  0.9395
  0.1161   3562   0.895    780   0.796   4342   0.877  1.000  0.9601  0.9667  0.9170  0.9485
  0.1931   4772   0.870    766   0.755   5538   0.854  1.008  0.9439  0.9585  0.8776  0.9419
  0.2701   5680   0.808    774   0.722   6454   0.797  0.888  0.9185  0.9344  0.8627  0.9049
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18894
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9358
Overall R factor                     =     0.1690
Free R factor                        =     0.2102
Average Fourier shell correlation    =     0.9536
AverageFree Fourier shell correlation=     0.9417
Overall weighted R factor            =     0.1521
Free weighted R factor               =     0.1874
Overall weighted R2 factor           =     0.1837
Free weighted R2 factor              =     0.2210
Average correlation coefficient      =     0.9305
Overall correlation coefficient      =     0.9560
Free correlation coefficient         =     0.9333
Cruickshanks DPI for coordinate error=     0.1233
DPI based on free R factor           =     0.1199
Overall figure of merit              =     0.8447
ML based su of positional parameters =     0.0814
ML based su of thermal parameters    =     2.6618
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    101204.09       26236.145       734620.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.26347721    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    715768.69    

-------------------------------------------------------------------------------
             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  =   -0.0861
Partial structure    1: scale =     0.3790, B  =   50.1474
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                     =     0.1682
Free R factor                        =     0.2093
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9442
Average correlation coefficient      =     0.9326
Overall figure of merit              =     0.8520
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100841.87       9919.8838       715768.69       734620.38    


     CGMAT cycle number =      3

 Weight matrix   0.26613820    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    713979.00    

-------------------------------------------------------------------------------
             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  =   -0.0525
Partial structure    1: scale =     0.3787, B  =   47.5517
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                     =     0.1671
Free R factor                        =     0.2090
Average Fourier shell correlation    =     0.9568
AverageFree Fourier shell correlation=     0.9448
Average correlation coefficient      =     0.9340
Overall figure of merit              =     0.8531
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100709.33       9057.9043       713979.00       715768.69    


     CGMAT cycle number =      4

 Weight matrix   0.26723149    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    713359.06    

-------------------------------------------------------------------------------
             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  =   -0.0424
Partial structure    1: scale =     0.3787, B  =   47.4656
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                     =     0.1668
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9570
AverageFree Fourier shell correlation=     0.9450
Average correlation coefficient      =     0.9345
Overall figure of merit              =     0.8534
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100658.10       8796.4805       713359.06       713979.00    


     CGMAT cycle number =      5

 Weight matrix   0.26772493    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    713207.63    

-------------------------------------------------------------------------------
             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  =   -0.0375
Partial structure    1: scale =     0.3788, B  =   47.4221
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                     =     0.1667
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9571
AverageFree Fourier shell correlation=     0.9451
Average correlation coefficient      =     0.9347
Overall figure of merit              =     0.8535
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100639.68       8774.0107       713207.63       713359.06    


     CGMAT cycle number =      6

 Weight matrix   0.26891658    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    713100.88    

-------------------------------------------------------------------------------
             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  =   -0.0357
Partial structure    1: scale =     0.3790, B  =   47.3658
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                     =     0.1666
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9572
AverageFree Fourier shell correlation=     0.9452
Average correlation coefficient      =     0.9348
Overall figure of merit              =     0.8539
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100622.38       8788.3135       713100.88       713207.63    


     CGMAT cycle number =      7

 Weight matrix   0.26925388    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    713053.69    

-------------------------------------------------------------------------------
             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  =   -0.0545
Partial structure    1: scale =     0.3795, B  =   47.4109
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                     =     0.1666
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9573
AverageFree Fourier shell correlation=     0.9452
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8540
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100615.16       8791.7539       713053.69       713100.88    


     CGMAT cycle number =      8

 Weight matrix   0.26953045    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    713024.75    

-------------------------------------------------------------------------------
             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  =   -0.0528
Partial structure    1: scale =     0.3799, B  =   47.3269
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                     =     0.1666
Free R factor                        =     0.2085
Average Fourier shell correlation    =     0.9573
AverageFree Fourier shell correlation=     0.9453
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8540
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    100608.85       8806.9619       713024.75       713053.69    


     CGMAT cycle number =      9

 Weight matrix   0.26935694    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    712951.25    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0363
Partial structure    1: scale =     0.3838, B  =   47.9343
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                     =     0.1666
Free R factor                        =     0.2085
Average Fourier shell correlation    =     0.9573
AverageFree Fourier shell correlation=     0.9452
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8540
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    100598.30       8807.2813       712951.25       713024.75    


     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.= 0.921 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  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   0.26888460    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                35.5
Norm of Geom. positional gradient                35.5
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                  115.
Product of X_ray and Geom posit. gradients     -0.122E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.422E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.7042E+06 GEOM=      8803.     TOTAL=     0.7130E+06
 function value    712991.94    

-------------------------------------------------------------------------------
             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     1.800     1.644
Bond angles  : others                          3242     1.464     1.582
Torsion angles, period  1. refined              184     6.954     5.000
Torsion angles, period  2. refined               90    37.006    22.778
Torsion angles, period  3. refined              268    14.132    15.000
Torsion angles, period  4. refined                9    11.151    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                   302     0.263     0.200
VDW repulsions.others                          1362     0.203     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             791     0.084     0.200
HBOND: refined_atoms                            229     0.198     0.200
HBOND.others                                      1     0.072     0.200
VDW repulsions: symmetry: refined_atoms           8     0.220     0.200
VDW repulsions: symmetry: others                 22     0.168     0.200
HBOND: symmetry: refined_atoms                   20     0.223     0.200
M. chain bond B values: refined atoms           745     1.595     1.291
M. chain bond B values: others                  745     1.594     1.291
M. chain angle B values: refined atoms          926     2.515     1.919
M. chain angle B values: others                 927     2.514     1.919
S. chain bond B values: refined atoms           811     2.787     1.662
S. chain bond B values: others                  810     2.784     1.661
S. chain angle B values: refined atoms         1177     4.375     2.336
S. chain angle B values: others                1178     4.373     2.335
Long range B values: refined atoms             1855     7.076    18.230
Long range B values: others                    1758     6.760    16.742
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0430
Partial structure    1: scale =     0.3840, B  =   47.9966
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2560 100.00   472.2   480.9  0.16  0.17     133   491.6   486.4  0.18  0.19
 0.116    4342 100.00   341.1   325.9  0.16  0.14     237   355.5   336.0  0.19  0.18
 0.193    5538  99.97   226.2   215.1  0.16  0.14     270   227.8   211.8  0.21  0.18
 0.270    6447 100.00   148.2   154.6  0.20  0.15     340   143.3   150.6  0.27  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1799   0.928    761   0.849   2560   0.904  0.953  0.9677  0.9723  0.9154  0.9396
  0.1161   3562   0.896    780   0.800   4342   0.879  1.000  0.9605  0.9674  0.9159  0.9487
  0.1931   4772   0.875    766   0.760   5538   0.859  1.008  0.9464  0.9594  0.8817  0.9400
  0.2701   5680   0.823    774   0.738   6454   0.812  0.895  0.9248  0.9427  0.8687  0.9193
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18894
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9358
Overall R factor                     =     0.1666
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9573
AverageFree Fourier shell correlation=     0.9452
Overall weighted R factor            =     0.1515
Free weighted R factor               =     0.1857
Overall weighted R2 factor           =     0.1832
Free weighted R2 factor              =     0.2171
Average correlation coefficient      =     0.9349
Overall correlation coefficient      =     0.9568
Free correlation coefficient         =     0.9348
Cruickshanks DPI for coordinate error=     0.1216
DPI based on free R factor           =     0.1190
Overall figure of merit              =     0.8539
ML based su of positional parameters =     0.0781
ML based su of thermal parameters    =     2.5476
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    100602.57       8802.9141       712973.81       712951.25    
 fvalues    100602.57       8802.9141       712973.81       712976.81    

    ****                              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.= 0.921 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_R17_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     1.799     1.644
Bond angles  : others                          3242     1.464     1.582
Torsion angles, period  1. refined              184     6.950     5.000
Torsion angles, period  2. refined               90    37.007    22.778
Torsion angles, period  3. refined              268    14.111    15.000
Torsion angles, period  4. refined                9    11.143    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                   302     0.263     0.200
VDW repulsions.others                          1359     0.203     0.200
VDW; torsion: refined_atoms                     719     0.172     0.200
VDW; torsion.others                             795     0.083     0.200
HBOND: refined_atoms                            227     0.199     0.200
HBOND.others                                      1     0.072     0.200
VDW repulsions: symmetry: refined_atoms           9     0.207     0.200
VDW repulsions: symmetry: others                 23     0.164     0.200
HBOND: symmetry: refined_atoms                   20     0.224     0.200
M. chain bond B values: refined atoms           745     1.596     1.291
M. chain bond B values: others                  745     1.595     1.291
M. chain angle B values: refined atoms          926     2.517     1.919
M. chain angle B values: others                 927     2.515     1.918
S. chain bond B values: refined atoms           811     2.789     1.662
S. chain bond B values: others                  810     2.786     1.661
S. chain angle B values: refined atoms         1177     4.378     2.336
S. chain angle B values: others                1178     4.376     2.335
Long range B values: refined atoms             1853     7.073    18.219
Long range B values: others                    1756     6.757    16.729
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0444
Partial structure    1: scale =     0.3840, B  =   47.9099
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2560 100.00   472.2   480.9  0.16  0.17     133   491.6   486.3  0.18  0.19
 0.116    4342 100.00   341.0   325.9  0.16  0.14     237   355.5   336.1  0.19  0.18
 0.193    5538  99.97   226.2   215.1  0.16  0.14     270   227.8   211.8  0.21  0.18
 0.270    6447 100.00   148.2   154.7  0.20  0.15     340   143.3   150.7  0.27  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1799   0.928    761   0.849   2560   0.905  0.953  0.9679  0.9723  0.9159  0.9397
  0.1161   3562   0.896    780   0.800   4342   0.879  1.000  0.9605  0.9674  0.9158  0.9487
  0.1931   4772   0.875    766   0.760   5538   0.859  1.008  0.9464  0.9594  0.8816  0.9399
  0.2701   5680   0.823    774   0.738   6454   0.813  0.895  0.9248  0.9428  0.8687  0.9194
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18894
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9358
Overall R factor                     =     0.1667
Free R factor                        =     0.2085
Average Fourier shell correlation    =     0.9573
AverageFree Fourier shell correlation=     0.9452
Overall weighted R factor            =     0.1515
Free weighted R factor               =     0.1854
Overall weighted R2 factor           =     0.1831
Free weighted R2 factor              =     0.2168
Average correlation coefficient      =     0.9349
Overall correlation coefficient      =     0.9568
Free correlation coefficient         =     0.9349
Cruickshanks DPI for coordinate error=     0.1216
DPI based on free R factor           =     0.1190
Overall figure of merit              =     0.8540
ML based su of positional parameters =     0.0781
ML based su of thermal parameters    =     2.5476
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.73
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1690   0.2102   0.845      101204.    5417.5   0.0121  0.898   1.788  1.028   0.083
       1   0.1682   0.2093   0.852      100842.    5410.7   0.0120  0.881   1.764  1.012   0.083
       2   0.1671   0.2090   0.853      100709.    5407.3   0.0123  0.910   1.782  1.022   0.084
       3   0.1668   0.2088   0.853      100658.    5405.3   0.0124  0.915   1.790  1.026   0.084
       4   0.1667   0.2088   0.854      100640.    5404.5   0.0124  0.917   1.795  1.028   0.084
       5   0.1666   0.2086   0.854      100622.    5403.9   0.0124  0.917   1.797  1.029   0.083
       6   0.1666   0.2086   0.854      100615.    5403.7   0.0124  0.919   1.799  1.030   0.083
       7   0.1666   0.2085   0.854      100609.    5403.6   0.0124  0.919   1.800  1.030   0.083
       8   0.1666   0.2085   0.854      100598.    5403.4   0.0124  0.919   1.800  1.030   0.083
       9   0.1666   0.2086   0.854      100605.    5403.7   0.0124  0.919   1.800  1.030   0.083
      10   0.1667   0.2085   0.854      100602.    5403.4   0.0124  0.918   1.799  1.030   0.083
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1690   0.1667
             R free    0.2102   0.2085
     Rms BondLength    0.0121   0.0124
      Rms BondAngle    1.7881   1.7993
     Rms ChirVolume    0.0832   0.0832
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.9s System:    0.1s Elapsed:     0:47