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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: 15:08:13 


 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 0
  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_R00_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R00_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_R00_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:     0
  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_R00_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=   2.009 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=   2.207 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=   1.866 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=   2.212 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=   2.400 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=   2.429 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=   2.117 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                            0
Number of "free" reflections       1001
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.= 0.932 id.= 3.000 dev= -2.07 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   0.23309332    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                36.6
Norm of Geom. positional gradient                77.5
Norm of X_ray B-factor gradient                  122.
Norm of Geom. B-factor gradient                 0.221E+05
Product of X_ray and Geom posit. gradients     -0.839E+07
 Cosine of angle between them                      -0.306
Product of X_ray and Geom B-fact gradients     -0.362E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.7101E+06 GEOM=     0.2589E+05 TOTAL=     0.7360E+06
 function value    736004.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.722     1.644
Bond angles  : others                          3242     2.336     1.582
Torsion angles, period  1. refined              184     6.979     5.000
Torsion angles, period  2. refined               90    36.925    22.778
Torsion angles, period  3. refined              268    14.142    15.000
Torsion angles, period  4. refined                9    11.057    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                   299     0.262     0.200
VDW repulsions.others                          1339     0.227     0.200
VDW; torsion: refined_atoms                     711     0.171     0.200
VDW; torsion.others                             705     0.080     0.200
HBOND: refined_atoms                            224     0.207     0.200
VDW repulsions: symmetry: refined_atoms           9     0.222     0.200
VDW repulsions: symmetry: others                 24     0.197     0.200
HBOND: symmetry: refined_atoms                   19     0.221     0.200
M. chain bond B values: refined atoms           745     1.529     1.216
M. chain bond B values: others                  745     1.528     1.216
M. chain angle B values: refined atoms          926     2.456     1.806
M. chain angle B values: others                 927     2.455     1.805
S. chain bond B values: refined atoms           811     2.483     1.552
S. chain bond B values: others                  810     2.480     1.552
S. chain angle B values: refined atoms         1177     3.925     2.183
S. chain angle B values: others                1178     3.923     2.182
Long range B values: refined atoms             1844     6.604    16.982
Long range B values: others                    1749     6.326    15.652
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =    0.8317
Partial structure    1: scale =     0.3839, B  =   49.4541
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2575 100.00   473.9   480.5  0.16  0.17     118   467.3   478.1  0.21  0.23
 0.116    4340 100.00   342.2   328.4  0.16  0.15     239   339.4   312.6  0.22  0.20
 0.193    5512  99.97   225.9   215.1  0.16  0.14     296   236.9   226.2  0.21  0.18
 0.270    6440 100.00   147.8   154.2  0.21  0.16     347   153.4   158.7  0.26  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1808   0.909    767   0.807   2575   0.878  0.954  0.9585  0.9682  0.9034  0.9397
  0.1161   3566   0.873    774   0.771   4340   0.855  0.991  0.9437  0.9603  0.8872  0.9448
  0.1931   4740   0.868    772   0.751   5512   0.851  1.007  0.9462  0.9570  0.8922  0.9391
  0.2701   5670   0.811    777   0.722   6447   0.800  0.889  0.9262  0.9361  0.8560  0.9068
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18874
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0365
Overall R factor                     =     0.1706
Free R factor                        =     0.2240
Average Fourier shell correlation    =     0.9522
AverageFree Fourier shell correlation=     0.9401
Overall weighted R factor            =     0.1539
Free weighted R factor               =     0.2039
Overall weighted R2 factor           =     0.1849
Free weighted R2 factor              =     0.2457
Average correlation coefficient      =     0.9295
Overall correlation coefficient      =     0.9553
Free correlation coefficient         =     0.9175
Cruickshanks DPI for coordinate error=     0.1246
DPI based on free R factor           =     0.1280
Overall figure of merit              =     0.8383
ML based su of positional parameters =     0.0840
ML based su of thermal parameters    =     2.7044
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    101451.68       25886.770       736004.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.26614007    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    715517.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =   -0.0461
Partial structure    1: scale =     0.3841, B  =   48.6374
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                     =     0.1696
Free R factor                        =     0.2211
Average Fourier shell correlation    =     0.9565
AverageFree Fourier shell correlation=     0.9448
Average correlation coefficient      =     0.9321
Overall figure of merit              =     0.8537
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100860.45       9538.4678       715517.31       736004.00    


     CGMAT cycle number =      3

 Weight matrix   0.27305433    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    712916.69    

-------------------------------------------------------------------------------
             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  =    0.0068
Partial structure    1: scale =     0.3842, B  =   46.3147
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                     =     0.1681
Free R factor                        =     0.2192
Average Fourier shell correlation    =     0.9576
AverageFree Fourier shell correlation=     0.9461
Average correlation coefficient      =     0.9342
Overall figure of merit              =     0.8559
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100589.85       8831.9043       712916.69       715517.31    


     CGMAT cycle number =      4

 Weight matrix   0.27605551    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711987.88    

-------------------------------------------------------------------------------
             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  =    0.0195
Partial structure    1: scale =     0.3843, B  =   46.2937
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1677
Free R factor                        =     0.2185
Average Fourier shell correlation    =     0.9581
AverageFree Fourier shell correlation=     0.9468
Average correlation coefficient      =     0.9349
Overall figure of merit              =     0.8569
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100484.35       8641.5186       711987.88       712916.69    


     CGMAT cycle number =      5

 Weight matrix   0.27759039    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711631.31    

-------------------------------------------------------------------------------
             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  =    0.0245
Partial structure    1: scale =     0.3842, B  =   46.3685
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                     =     0.1675
Free R factor                        =     0.2181
Average Fourier shell correlation    =     0.9583
AverageFree Fourier shell correlation=     0.9471
Average correlation coefficient      =     0.9353
Overall figure of merit              =     0.8574
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100431.30       8656.2471       711631.31       711987.88    


     CGMAT cycle number =      6

 Weight matrix   0.27920172    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711442.38    

-------------------------------------------------------------------------------
             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  =    0.0308
Partial structure    1: scale =     0.3841, B  =   46.2051
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                     =     0.1674
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9585
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9354
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100398.66       8695.8115       711442.38       711631.31    


     CGMAT cycle number =      7

 Weight matrix   0.27947912    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711362.44    

-------------------------------------------------------------------------------
             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  =   -0.0013
Partial structure    1: scale =     0.3839, B  =   45.9872
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                     =     0.1673
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9585
AverageFree Fourier shell correlation=     0.9474
Average correlation coefficient      =     0.9356
Overall figure of merit              =     0.8580
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100386.80       8698.8291       711362.44       711442.38    


     CGMAT cycle number =      8

 Weight matrix   0.27955142    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711349.13    

-------------------------------------------------------------------------------
             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  =    0.0004
Partial structure    1: scale =     0.3839, B  =   45.9869
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                     =     0.1673
Free R factor                        =     0.2179
Average Fourier shell correlation    =     0.9585
AverageFree Fourier shell correlation=     0.9474
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8580
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    100382.11       8718.3691       711349.13       711362.44    


     CGMAT cycle number =      9

 Weight matrix   0.27938244    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711359.75    

-------------------------------------------------------------------------------
             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  =    0.0036
Partial structure    1: scale =     0.3842, B  =   46.0685
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                     =     0.1673
Free R factor                        =     0.2181
Average Fourier shell correlation    =     0.9585
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    100384.28       8714.7051       711327.06       711349.13    
 fvalues    100384.28       8714.7051       711327.06       711360.63    


     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.= 0.942 id.= 3.000 dev= -2.06 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   0.27974755    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                36.1
Norm of Geom. positional gradient                36.0
Norm of X_ray B-factor gradient                  120.
Norm of Geom. B-factor gradient                  120.
Product of X_ray and Geom posit. gradients     -0.126E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.466E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7026E+06 GEOM=      8717.     TOTAL=     0.7113E+06
 function value    711329.06    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.793     1.644
Bond angles  : others                          3242     1.469     1.582
Torsion angles, period  1. refined              184     6.970     5.000
Torsion angles, period  2. refined               90    36.605    22.778
Torsion angles, period  3. refined              268    14.015    15.000
Torsion angles, period  4. refined                9    11.900    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   305     0.261     0.200
VDW repulsions.others                          1367     0.199     0.200
VDW; torsion: refined_atoms                     716     0.172     0.200
VDW; torsion.others                             788     0.084     0.200
HBOND: refined_atoms                            220     0.195     0.200
HBOND.others                                      1     0.031     0.200
VDW repulsions: symmetry: refined_atoms           8     0.211     0.200
VDW repulsions: symmetry: others                 23     0.180     0.200
HBOND: symmetry: refined_atoms                   21     0.206     0.200
M. chain bond B values: refined atoms           745     1.614     1.290
M. chain bond B values: others                  745     1.613     1.290
M. chain angle B values: refined atoms          926     2.538     1.917
M. chain angle B values: others                 927     2.537     1.917
S. chain bond B values: refined atoms           811     2.735     1.658
S. chain bond B values: others                  810     2.731     1.658
S. chain angle B values: refined atoms         1177     4.292     2.331
S. chain angle B values: others                1178     4.290     2.330
Long range B values: refined atoms             1849     6.778    17.900
Long range B values: others                    1759     6.482    16.514
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0001
Partial structure    1: scale =     0.3844, B  =   46.0994
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2575 100.00   473.1   480.9  0.16  0.17     118   466.5   477.0  0.21  0.22
 0.116    4340 100.00   341.7   327.1  0.16  0.15     239   338.9   311.2  0.22  0.20
 0.193    5512  99.97   225.5   214.4  0.16  0.14     296   236.5   225.7  0.21  0.17
 0.270    6440 100.00   147.6   153.8  0.19  0.15     347   153.1   159.2  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1808   0.925    767   0.824   2575   0.895  0.954  0.9633  0.9715  0.9079  0.9391
  0.1161   3566   0.880    774   0.781   4340   0.862  0.991  0.9479  0.9622  0.8947  0.9444
  0.1931   4740   0.875    772   0.761   5512   0.859  1.007  0.9501  0.9589  0.9001  0.9386
  0.2701   5670   0.850    777   0.766   6447   0.839  0.905  0.9393  0.9506  0.8719  0.9261
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18874
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0365
Overall R factor                     =     0.1673
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9586
AverageFree Fourier shell correlation=     0.9474
Overall weighted R factor            =     0.1534
Free weighted R factor               =     0.1988
Overall weighted R2 factor           =     0.1859
Free weighted R2 factor              =     0.2366
Average correlation coefficient      =     0.9358
Overall correlation coefficient      =     0.9562
Free correlation coefficient         =     0.9227
Cruickshanks DPI for coordinate error=     0.1223
DPI based on free R factor           =     0.1245
Overall figure of merit              =     0.8580
ML based su of positional parameters =     0.0766
ML based su of thermal parameters    =     2.4331
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    100379.49       8716.6553       711329.06       711360.63    

    ****                              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.= 0.942 id.= 3.000 dev= -2.06 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_R00_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     1.794     1.644
Bond angles  : others                          3242     1.469     1.582
Torsion angles, period  1. refined              184     6.967     5.000
Torsion angles, period  2. refined               90    36.589    22.778
Torsion angles, period  3. refined              268    14.024    15.000
Torsion angles, period  4. refined                9    11.913    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.262     0.200
VDW repulsions.others                          1377     0.198     0.200
VDW; torsion: refined_atoms                     716     0.172     0.200
VDW; torsion.others                             793     0.084     0.200
HBOND: refined_atoms                            221     0.194     0.200
HBOND.others                                      1     0.033     0.200
VDW repulsions: symmetry: refined_atoms           8     0.211     0.200
VDW repulsions: symmetry: others                 23     0.181     0.200
HBOND: symmetry: refined_atoms                   21     0.205     0.200
M. chain bond B values: refined atoms           745     1.614     1.290
M. chain bond B values: others                  745     1.612     1.290
M. chain angle B values: refined atoms          926     2.537     1.916
M. chain angle B values: others                 927     2.536     1.916
S. chain bond B values: refined atoms           811     2.737     1.658
S. chain bond B values: others                  810     2.732     1.658
S. chain angle B values: refined atoms         1177     4.294     2.330
S. chain angle B values: others                1178     4.293     2.330
Long range B values: refined atoms             1849     6.763    17.914
Long range B values: others                    1757     6.437    16.486
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.0003
Partial structure    1: scale =     0.3844, B  =   46.0956
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2575 100.00   473.1   480.9  0.16  0.17     118   466.5   476.9  0.21  0.22
 0.116    4340 100.00   341.7   327.1  0.16  0.15     239   338.9   311.3  0.22  0.20
 0.193    5512  99.97   225.5   214.4  0.16  0.14     296   236.5   225.7  0.21  0.17
 0.270    6440 100.00   147.6   153.8  0.19  0.15     347   153.1   159.2  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1808   0.925    767   0.824   2575   0.895  0.954  0.9633  0.9715  0.9080  0.9392
  0.1161   3566   0.880    774   0.781   4340   0.862  0.991  0.9480  0.9623  0.8949  0.9444
  0.1931   4740   0.875    772   0.761   5512   0.859  1.007  0.9501  0.9589  0.9001  0.9386
  0.2701   5670   0.850    777   0.766   6447   0.840  0.905  0.9394  0.9506  0.8720  0.9262
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18874
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0365
Overall R factor                     =     0.1673
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9586
AverageFree Fourier shell correlation=     0.9474
Overall weighted R factor            =     0.1533
Free weighted R factor               =     0.1987
Overall weighted R2 factor           =     0.1859
Free weighted R2 factor              =     0.2363
Average correlation coefficient      =     0.9358
Overall correlation coefficient      =     0.9562
Free correlation coefficient         =     0.9228
Cruickshanks DPI for coordinate error=     0.1223
DPI based on free R factor           =     0.1245
Overall figure of merit              =     0.8581
ML based su of positional parameters =     0.0766
ML based su of thermal parameters    =     2.4331
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.62
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1706   0.2240   0.838      101452.    5555.1   0.0113  0.834   1.722  0.995   0.083
       1   0.1696   0.2211   0.854      100860.    5536.3   0.0111  0.818   1.709  0.986   0.084
       2   0.1681   0.2192   0.856      100590.    5525.7   0.0119  0.874   1.746  1.006   0.085
       3   0.1677   0.2185   0.857      100484.    5520.8   0.0120  0.886   1.765  1.016   0.085
       4   0.1675   0.2181   0.857      100431.    5518.2   0.0120  0.892   1.776  1.021   0.085
       5   0.1674   0.2178   0.858      100399.    5516.7   0.0121  0.895   1.783  1.025   0.085
       6   0.1673   0.2178   0.858      100387.    5516.1   0.0121  0.897   1.787  1.027   0.085
       7   0.1673   0.2179   0.858      100382.    5516.1   0.0121  0.898   1.790  1.028   0.085
       8   0.1673   0.2181   0.858      100384.    5516.4   0.0121  0.898   1.792  1.029   0.085
       9   0.1673   0.2180   0.858      100379.    5516.2   0.0121  0.898   1.793  1.030   0.085
      10   0.1673   0.2180   0.858      100376.    5515.9   0.0121  0.898   1.794  1.030   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1706   0.1673
             R free    0.2240   0.2180
     Rms BondLength    0.0113   0.0121
      Rms BondAngle    1.7222   1.7945
     Rms ChirVolume    0.0830   0.0854
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.8s System:    2.0s Elapsed:     0:49