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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 17:02:47 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.70     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 15
  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_R15_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R15_1-70A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R15_1-70A.mtz

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

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

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


  Residual                               : Rice Maximum Likelihood for Fs

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

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


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

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0865
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7000
  Estimated number of reflections :      29131
  Free R exclusion - flag equals:    15
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.7000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R15_1-80A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.045 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=   2.194 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=   1.838 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=   2.186 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=   2.394 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=   2.411 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=   2.076 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                           15
Number of "free" reflections       1201
Number of   all  reflections      23491
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23491

   Current auto weighting coefficient =    6.7496872    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              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.= 0.903 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.29752350    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                40.4
Norm of Geom. positional gradient                80.1
Norm of X_ray B-factor gradient                  134.
Norm of Geom. B-factor gradient                 0.219E+05
Product of X_ray and Geom posit. gradients     -0.124E+08
 Cosine of angle between them                      -0.395
Product of X_ray and Geom B-fact gradients     -0.435E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7823E+06 GEOM=     0.2669E+05 TOTAL=     0.8090E+06
 function value    809009.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.814     1.644
Bond angles  : others                          3242     2.347     1.582
Torsion angles, period  1. refined              184     7.020     5.000
Torsion angles, period  2. refined               90    36.464    22.778
Torsion angles, period  3. refined              268    14.012    15.000
Torsion angles, period  4. refined                9    11.920    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   304     0.266     0.200
VDW repulsions.others                          1354     0.230     0.200
VDW; torsion: refined_atoms                     722     0.171     0.200
VDW; torsion.others                             715     0.082     0.200
HBOND: refined_atoms                            232     0.199     0.200
HBOND.others                                      1     0.077     0.200
VDW repulsions: symmetry: refined_atoms           9     0.228     0.200
VDW repulsions: symmetry: others                 23     0.194     0.200
HBOND: symmetry: refined_atoms                   25     0.211     0.200
M. chain bond B values: refined atoms           745     1.651     1.293
M. chain bond B values: others                  745     1.650     1.293
M. chain angle B values: refined atoms          926     2.607     1.921
M. chain angle B values: others                 927     2.606     1.921
S. chain bond B values: refined atoms           811     2.867     1.675
S. chain bond B values: others                  810     2.863     1.675
S. chain angle B values: refined atoms         1177     4.496     2.350
S. chain angle B values: others                1178     4.494     2.349
Long range B values: refined atoms             1861     7.236    18.334
Long range B values: others                    1760     6.803    16.813
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.0827
Partial structure    1: scale =     0.3887, B  =   49.2026
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3022 100.00   451.9   460.1  0.16  0.17     149   488.1   500.9  0.19  0.20
 0.130    5121 100.00   298.2   285.2  0.16  0.15     279   312.0   295.4  0.20  0.18
 0.216    6506  99.97   202.4   185.9  0.17  0.15     366   200.5   188.3  0.21  0.18
 0.303    7637 100.00   104.4   117.2  0.26  0.20     406   100.0   112.9  0.30  0.24
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2165   0.909    857   0.811   3022   0.881  0.945  0.9692  0.9694  0.9272  0.9387
  0.1301   4249   0.879    872   0.776   5121   0.862  1.001  0.9524  0.9612  0.9105  0.9447
  0.2165   5624   0.880    882   0.772   6506   0.865  1.045  0.9462  0.9597  0.8932  0.9394
  0.3028   6774   0.779    865   0.710   7639   0.771  0.820  0.9019  0.9227  0.8361  0.8944
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22288
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1130
Overall R factor                     =     0.1799
Free R factor                        =     0.2133
Average Fourier shell correlation    =     0.9487
AverageFree Fourier shell correlation=     0.9355
Overall weighted R factor            =     0.1584
Free weighted R factor               =     0.1929
Overall weighted R2 factor           =     0.1883
Free weighted R2 factor              =     0.2298
Average correlation coefficient      =     0.9251
Overall correlation coefficient      =     0.9572
Free correlation coefficient         =     0.9424
Cruickshanks DPI for coordinate error=     0.1091
DPI based on free R factor           =     0.1059
Overall figure of merit              =     0.8345
ML based su of positional parameters =     0.0730
ML based su of thermal parameters    =     2.2541
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    115904.28       26692.143       809009.75      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35101813    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    787594.06    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0549
Partial structure    1: scale =     0.3884, B  =   48.4537
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1796
Free R factor                        =     0.2118
Average Fourier shell correlation    =     0.9545
AverageFree Fourier shell correlation=     0.9419
Average correlation coefficient      =     0.9268
Overall figure of merit              =     0.8554
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115193.46       10074.222       787594.06       809009.75    


     CGMAT cycle number =      3

 Weight matrix   0.35904154    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785458.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0203
Partial structure    1: scale =     0.3882, B  =   44.6921
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1786
Free R factor                        =     0.2107
Average Fourier shell correlation    =     0.9556
AverageFree Fourier shell correlation=     0.9430
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8578
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    114958.16       9526.3574       785458.00       787594.06    


     CGMAT cycle number =      4

 Weight matrix   0.36137113    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784762.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0148
Partial structure    1: scale =     0.3882, B  =   44.3593
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1783
Free R factor                        =     0.2101
Average Fourier shell correlation    =     0.9559
AverageFree Fourier shell correlation=     0.9433
Average correlation coefficient      =     0.9293
Overall figure of merit              =     0.8583
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    114872.69       9407.5566       784762.25       785458.00    


     CGMAT cycle number =      5

 Weight matrix   0.36291766    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784514.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0199
Partial structure    1: scale =     0.3883, B  =   44.2599
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1782
Free R factor                        =     0.2097
Average Fourier shell correlation    =     0.9561
AverageFree Fourier shell correlation=     0.9435
Average correlation coefficient      =     0.9296
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114832.54       9430.6992       784514.38       784762.25    


     CGMAT cycle number =      6

 Weight matrix   0.36488315    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784336.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0166
Partial structure    1: scale =     0.3885, B  =   44.3428
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1781
Free R factor                        =     0.2092
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9437
Average correlation coefficient      =     0.9298
Overall figure of merit              =     0.8590
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114799.66       9475.0156       784336.81       784514.38    


     CGMAT cycle number =      7

 Weight matrix   0.36689368    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784214.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0247
Partial structure    1: scale =     0.3888, B  =   44.3159
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1780
Free R factor                        =     0.2090
Average Fourier shell correlation    =     0.9564
AverageFree Fourier shell correlation=     0.9440
Average correlation coefficient      =     0.9299
Overall figure of merit              =     0.8595
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    114776.91       9506.2207       784214.50       784336.81    


     CGMAT cycle number =      8

 Weight matrix   0.33573991    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    713666.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0052
Partial structure    1: scale =     0.3889, B  =   44.3238
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1779
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9442
Average correlation coefficient      =     0.9300
Overall figure of merit              =     0.8602
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    114754.42       9524.3965       713666.63       784214.50    


     CGMAT cycle number =      9

 Weight matrix   0.30490544    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649687.38    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0089
Partial structure    1: scale =     0.3892, B  =   44.3096
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1784
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9564
AverageFree Fourier shell correlation=     0.9442
Average correlation coefficient      =     0.9296
Overall figure of merit              =     0.8602
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    114810.95       9242.7412       649687.38       713666.63    


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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.30491996    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                36.9
Norm of Geom. positional gradient                37.2
Norm of X_ray B-factor gradient                  117.
Norm of Geom. B-factor gradient                  119.
Product of X_ray and Geom posit. gradients     -0.133E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.447E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.6408E+06 GEOM=      8893.     TOTAL=     0.6497E+06
 function value    649697.94    

-------------------------------------------------------------------------------
             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     1.777     1.644
Bond angles  : others                          3242     1.503     1.582
Torsion angles, period  1. refined              184     6.956     5.000
Torsion angles, period  2. refined               90    36.007    22.778
Torsion angles, period  3. refined              268    13.711    15.000
Torsion angles, period  4. refined                9    11.936    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   305     0.267     0.200
VDW repulsions.others                          1367     0.203     0.200
VDW; torsion: refined_atoms                     730     0.172     0.200
VDW; torsion.others                             791     0.084     0.200
HBOND: refined_atoms                            226     0.194     0.200
HBOND.others                                      1     0.112     0.200
VDW repulsions: symmetry: refined_atoms           7     0.244     0.200
VDW repulsions: symmetry: others                 21     0.192     0.200
HBOND: symmetry: refined_atoms                   24     0.202     0.200
M. chain bond B values: refined atoms           745     1.649     1.387
M. chain bond B values: others                  745     1.647     1.387
M. chain angle B values: refined atoms          926     2.624     2.065
M. chain angle B values: others                 927     2.623     2.065
S. chain bond B values: refined atoms           811     2.917     1.778
S. chain bond B values: others                  810     2.910     1.778
S. chain angle B values: refined atoms         1177     4.550     2.503
S. chain angle B values: others                1178     4.548     2.502
Long range B values: refined atoms             1861     7.385    19.779
Long range B values: others                    1768     6.984    18.331
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =    0.0116
Partial structure    1: scale =     0.3893, B  =   44.1699
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3022 100.00   453.0   461.2  0.16  0.17     149   489.2   502.2  0.18  0.20
 0.130    5121 100.00   298.9   285.1  0.16  0.15     279   312.7   294.9  0.20  0.18
 0.216    6506  99.97   202.9   186.3  0.17  0.15     366   200.9   187.9  0.20  0.18
 0.303    7637 100.00   104.6   116.8  0.25  0.19     406   100.2   113.0  0.29  0.23
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2165   0.930    857   0.844   3022   0.905  0.948  0.9733  0.9734  0.9304  0.9379
  0.1301   4249   0.884    872   0.782   5121   0.867  1.001  0.9548  0.9621  0.9142  0.9430
  0.2165   5624   0.889    882   0.782   6506   0.875  1.045  0.9504  0.9618  0.9009  0.9384
  0.3028   6774   0.834    865   0.761   7639   0.826  0.839  0.9207  0.9408  0.8440  0.9082
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22288
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1130
Overall R factor                     =     0.1790
Free R factor                        =     0.2087
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9442
Overall weighted R factor            =     0.1593
Free weighted R factor               =     0.1894
Overall weighted R2 factor           =     0.1898
Free weighted R2 factor              =     0.2260
Average correlation coefficient      =     0.9291
Overall correlation coefficient      =     0.9572
Free correlation coefficient         =     0.9449
Cruickshanks DPI for coordinate error=     0.1085
DPI based on free R factor           =     0.1036
Overall figure of merit              =     0.8603
ML based su of positional parameters =     0.0655
ML based su of thermal parameters    =     1.9880
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    114873.48       8893.2568       649686.69       649687.38    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.922 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R15_1-70A.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     1.765     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.959     5.000
Torsion angles, period  2. refined               90    35.970    22.778
Torsion angles, period  3. refined              268    13.679    15.000
Torsion angles, period  4. refined                9    11.899    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.267     0.200
VDW repulsions.others                          1369     0.202     0.200
VDW; torsion: refined_atoms                     730     0.171     0.200
VDW; torsion.others                             792     0.084     0.200
HBOND: refined_atoms                            225     0.194     0.200
HBOND.others                                      1     0.110     0.200
VDW repulsions: symmetry: refined_atoms           7     0.243     0.200
VDW repulsions: symmetry: others                 21     0.192     0.200
HBOND: symmetry: refined_atoms                   25     0.198     0.200
M. chain bond B values: refined atoms           745     1.639     1.387
M. chain bond B values: others                  745     1.637     1.387
M. chain angle B values: refined atoms          926     2.610     2.065
M. chain angle B values: others                 927     2.609     2.065
S. chain bond B values: refined atoms           811     2.893     1.775
S. chain bond B values: others                  810     2.886     1.774
S. chain angle B values: refined atoms         1177     4.512     2.499
S. chain angle B values: others                1178     4.510     2.499
Long range B values: refined atoms             1859     7.338    19.750
Long range B values: others                    1767     6.940    18.313
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =    0.0167
Partial structure    1: scale =     0.3893, B  =   44.1920
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3022 100.00   453.0   461.2  0.16  0.17     149   489.3   502.2  0.18  0.20
 0.130    5121 100.00   298.9   285.2  0.16  0.15     279   312.7   294.9  0.20  0.18
 0.216    6506  99.97   202.9   186.3  0.17  0.15     366   200.9   187.9  0.20  0.18
 0.303    7637 100.00   104.6   116.8  0.25  0.19     406   100.2   113.1  0.29  0.23
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2165   0.930    857   0.844   3022   0.906  0.948  0.9733  0.9734  0.9304  0.9377
  0.1301   4249   0.884    872   0.782   5121   0.867  1.001  0.9547  0.9621  0.9141  0.9429
  0.2165   5624   0.889    882   0.783   6506   0.875  1.045  0.9504  0.9617  0.9009  0.9382
  0.3028   6774   0.834    865   0.761   7639   0.826  0.839  0.9208  0.9408  0.8441  0.9081
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22288
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1130
Overall R factor                     =     0.1791
Free R factor                        =     0.2087
Average Fourier shell correlation    =     0.9562
AverageFree Fourier shell correlation=     0.9442
Overall weighted R factor            =     0.1595
Free weighted R factor               =     0.1893
Overall weighted R2 factor           =     0.1900
Free weighted R2 factor              =     0.2259
Average correlation coefficient      =     0.9289
Overall correlation coefficient      =     0.9571
Free correlation coefficient         =     0.9449
Cruickshanks DPI for coordinate error=     0.1086
DPI based on free R factor           =     0.1036
Overall figure of merit              =     0.8604
ML based su of positional parameters =     0.0655
ML based su of thermal parameters    =     1.9880
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.97
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1799   0.2133   0.834      115904.    6401.6   0.0129  0.952   1.814  1.050   0.088
       1   0.1796   0.2118   0.855      115193.    6375.2   0.0123  0.914   1.770  1.026   0.087
       2   0.1786   0.2107   0.858      114958.    6367.2   0.0132  0.982   1.804  1.048   0.090
       3   0.1783   0.2101   0.858      114873.    6363.6   0.0133  0.994   1.818  1.058   0.091
       4   0.1782   0.2097   0.859      114833.    6361.3   0.0134  0.997   1.825  1.063   0.091
       5   0.1781   0.2092   0.859      114800.    6359.4   0.0134  0.999   1.830  1.067   0.091
       6   0.1780   0.2090   0.860      114777.    6357.0   0.0134  1.001   1.833  1.069   0.092
       7   0.1779   0.2086   0.860      114754.    6355.2   0.0134  1.004   1.837  1.071   0.092
       8   0.1784   0.2086   0.860      114811.    6355.8   0.0129  0.962   1.812  1.056   0.090
       9   0.1790   0.2087   0.860      114876.    6356.1   0.0123  0.919   1.777  1.035   0.088
      10   0.1791   0.2087   0.860      114889.    6355.7   0.0122  0.914   1.765  1.029   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1799   0.1791
             R free    0.2133   0.2087
     Rms BondLength    0.0129   0.0122
      Rms BondAngle    1.8142   1.7654
     Rms ChirVolume    0.0879   0.0873
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.2s System:    0.2s Elapsed:     0:47