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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: 20:33:49 


 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 1.42     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 2
  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_R02_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R02_1-42A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R02_1-42A.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       0.1240
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4200
  Estimated number of reflections :      51186
  Free R exclusion - flag equals:     2
  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  1.4200

  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_R02_1-50A.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=   2.065 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=   2.193 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=   1.828 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=   2.210 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=   2.395 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=   2.407 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=   2.095 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  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  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:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                            2
Number of "free" reflections       1995
Number of   all  reflections      39817
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          39817

   Current auto weighting coefficient =    6.0498405    

 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.= 0.897 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        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.25805607    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                38.8
Norm of Geom. positional gradient                80.2
Norm of X_ray B-factor gradient                  104.
Norm of Geom. B-factor gradient                  95.5
Product of X_ray and Geom posit. gradients     -0.141E+08
 Cosine of angle between them                      -0.468
Product of X_ray and Geom B-fact gradients     -0.292E+08
 Cosine of angle between them                      -0.910


Residuals: XRAY=     0.1065E+07 GEOM=     0.1272E+05 TOTAL=     0.1078E+07
 function value    1077645.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.774     1.644
Bond angles  : others                          3238     2.351     1.580
Torsion angles, period  1. refined              185     6.826     5.000
Torsion angles, period  2. refined               90    35.715    22.778
Torsion angles, period  3. refined              268    13.209    15.000
Torsion angles, period  4. refined                9    11.941    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   301     0.247     0.200
VDW repulsions.others                          1328     0.221     0.200
VDW; torsion: refined_atoms                     727     0.173     0.200
VDW; torsion.others                             723     0.080     0.200
HBOND: refined_atoms                            209     0.186     0.200
HBOND.others                                      2     0.069     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 22     0.199     0.200
HBOND: symmetry: refined_atoms                   17     0.196     0.200
M. chain bond B values: refined atoms           746     1.731     1.623
M. chain bond B values: others                  746     1.726     1.623
M. chain angle B values: refined atoms          929     2.695     2.425
M. chain angle B values: others                 930     2.694     2.425
S. chain bond B values: refined atoms           811     3.154     2.033
S. chain bond B values: others                  810     3.150     2.033
S. chain angle B values: refined atoms         1177     4.893     2.877
S. chain angle B values: others                1178     4.891     2.876
Long range B values: refined atoms             1837     7.266    22.106
Long range B values: others                    1750     7.012    20.657
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.7952
Partial structure    1: scale =     0.3945, B  =   38.2226
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5058 100.00   380.9   390.4  0.17  0.18     271   361.5   376.0  0.21  0.21
 0.186    8677  99.98   205.8   181.9  0.19  0.17     466   207.3   185.8  0.23  0.20
 0.310   11077 100.00    91.9    88.4  0.23  0.20     570    92.8    91.5  0.25  0.22
 0.434   12816  98.63    38.7    48.0  0.47  0.46     679    38.6    47.4  0.46  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3829   0.911   1229   0.809   5058   0.886  0.948  0.9611  0.9700  0.9088  0.9360
  0.1863   7440   0.865   1237   0.768   8677   0.851  1.094  0.9475  0.9560  0.9047  0.9338
  0.3102   9828   0.802   1249   0.724  11077   0.793  0.950  0.9271  0.9357  0.8761  0.9147
  0.4340  11569   0.362   1247   0.320  12816   0.358  0.356  0.5989  0.6100  0.6339  0.6442
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37628
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0134
Overall R factor                     =     0.2190
Free R factor                        =     0.2487
Average Fourier shell correlation    =     0.8340
AverageFree Fourier shell correlation=     0.8243
Overall weighted R factor            =     0.1827
Free weighted R factor               =     0.2129
Overall weighted R2 factor           =     0.2102
Free weighted R2 factor              =     0.2446
Average correlation coefficient      =     0.8298
Overall correlation coefficient      =     0.9598
Free correlation coefficient         =     0.9460
Cruickshanks DPI for coordinate error=     0.0780
DPI based on free R factor           =     0.0795
Overall figure of merit              =     0.6710
ML based su of positional parameters =     0.0742
ML based su of thermal parameters    =     2.1573
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176025.34       12720.276       1077645.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31455234    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1066530.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0706
Partial structure    1: scale =     0.3943, B  =   38.4800
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2188
Free R factor                        =     0.2482
Average Fourier shell correlation    =     0.8472
AverageFree Fourier shell correlation=     0.8365
Average correlation coefficient      =     0.8295
Overall figure of merit              =     0.6874
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    174966.16       8012.9277       1066530.3       1077645.5    


     CGMAT cycle number =      3

 Weight matrix   0.31972939    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065954.6    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0002
Partial structure    1: scale =     0.3943, B  =   38.4824
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2179
Free R factor                        =     0.2480
Average Fourier shell correlation    =     0.8489
AverageFree Fourier shell correlation=     0.8377
Average correlation coefficient      =     0.8306
Overall figure of merit              =     0.6884
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    174779.09       8568.9863       1065954.6       1066530.3    


     CGMAT cycle number =      4

 Weight matrix   0.32358700    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1065854.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0001
Partial structure    1: scale =     0.3943, B  =   38.4853
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2178
Free R factor                        =     0.2481
Average Fourier shell correlation    =     0.8507
AverageFree Fourier shell correlation=     0.8397
Average correlation coefficient      =     0.8310
Overall figure of merit              =     0.6942
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174740.73       8700.3564       1065854.0       1065954.6    


     CGMAT cycle number =      5

 Weight matrix   0.29994330    
 Actual weight    5.4998550      is applied to the X-ray term


 function value    969216.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0001
Partial structure    1: scale =     0.3945, B  =   38.5438
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2177
Free R factor                        =     0.2481
Average Fourier shell correlation    =     0.8559
AverageFree Fourier shell correlation=     0.8453
Average correlation coefficient      =     0.8312
Overall figure of merit              =     0.7022
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    174632.41       8763.0938       969216.00       1065854.0    


     CGMAT cycle number =      6

 Weight matrix   0.27016374    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    882088.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0000
Partial structure    1: scale =     0.3945, B  =   38.5440
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2180
Free R factor                        =     0.2482
Average Fourier shell correlation    =     0.8532
AverageFree Fourier shell correlation=     0.8424
Average correlation coefficient      =     0.8311
Overall figure of merit              =     0.6982
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    174722.47       8499.0762       882088.31       969216.00    


     CGMAT cycle number =      7

 Weight matrix   0.26759404    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    882382.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0051
Partial structure    1: scale =     0.3946, B  =   38.4764
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2184
Free R factor                        =     0.2482
Average Fourier shell correlation    =     0.8512
AverageFree Fourier shell correlation=     0.8403
Average correlation coefficient      =     0.8306
Overall figure of merit              =     0.6952
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    174795.20       8167.6406       882489.56       882088.31    

 fvalues    174795.20       8167.6406       882348.69       882120.56    
 fvalues    174795.20       8167.6406       882348.69       882120.56    


     CGMAT cycle number =      8

 Weight matrix   0.26830325    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    882355.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0055
Partial structure    1: scale =     0.3946, B  =   38.4474
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2185
Free R factor                        =     0.2483
Average Fourier shell correlation    =     0.8522
AverageFree Fourier shell correlation=     0.8414
Average correlation coefficient      =     0.8305
Overall figure of merit              =     0.6968
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    174876.64       8147.2515       882188.25       882120.56    
 fvalues    174876.64       8147.2515       882188.25       882507.38    


     CGMAT cycle number =      9

 Weight matrix   0.27007055    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    882183.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0001
Partial structure    1: scale =     0.3946, B  =   38.4472
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2185
Free R factor                        =     0.2484
Average Fourier shell correlation    =     0.8543
AverageFree Fourier shell correlation=     0.8437
Average correlation coefficient      =     0.8305
Overall figure of merit              =     0.7001
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    174816.48       8124.4463       882183.75       882507.38    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.916 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        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.26811481    
 Actual weight    4.9998679      is applied to the X-ray term
Norm of X_ray positional gradient                37.5
Norm of Geom. positional gradient                37.7
Norm of X_ray B-factor gradient                  93.5
Norm of Geom. B-factor gradient                  94.6
Product of X_ray and Geom posit. gradients     -0.137E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.286E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8743E+06 GEOM=      8102.     TOTAL=     0.8824E+06
 function value    882380.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.765     1.644
Bond angles  : others                          3238     1.493     1.580
Torsion angles, period  1. refined              185     6.825     5.000
Torsion angles, period  2. refined               90    35.653    22.778
Torsion angles, period  3. refined              268    13.170    15.000
Torsion angles, period  4. refined                9    12.184    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   295     0.249     0.200
VDW repulsions.others                          1335     0.196     0.200
VDW; torsion: refined_atoms                     729     0.172     0.200
VDW; torsion.others                             772     0.084     0.200
HBOND: refined_atoms                            208     0.187     0.200
HBOND.others                                      2     0.051     0.200
VDW repulsions: symmetry: refined_atoms           8     0.195     0.200
VDW repulsions: symmetry: others                 25     0.177     0.200
HBOND: symmetry: refined_atoms                   17     0.195     0.200
M. chain bond B values: refined atoms           746     1.765     1.698
M. chain bond B values: others                  746     1.759     1.699
M. chain angle B values: refined atoms          929     2.730     2.539
M. chain angle B values: others                 930     2.728     2.539
S. chain bond B values: refined atoms           811     3.199     2.115
S. chain bond B values: others                  810     3.195     2.114
S. chain angle B values: refined atoms         1177     4.956     2.997
S. chain angle B values: others                1178     4.954     2.997
Long range B values: refined atoms             1832     7.258    23.032
Long range B values: others                    1745     7.011    21.567
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0000
Partial structure    1: scale =     0.3946, B  =   38.4472
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5058 100.00   381.4   390.9  0.17  0.18     271   362.0   376.7  0.21  0.21
 0.186    8677  99.98   206.1   182.3  0.19  0.17     466   207.6   186.5  0.23  0.20
 0.310   11077 100.00    92.0    88.6  0.23  0.20     570    92.9    91.7  0.25  0.21
 0.434   12816  98.63    38.7    48.1  0.47  0.46     679    38.7    47.5  0.46  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3829   0.925   1229   0.835   5058   0.903  0.951  0.9656  0.9735  0.9091  0.9359
  0.1863   7440   0.885   1237   0.788   8677   0.871  1.096  0.9523  0.9608  0.9056  0.9344
  0.3102   9828   0.824   1249   0.748  11077   0.815  0.956  0.9338  0.9426  0.8769  0.9154
  0.4340  11569   0.398   1247   0.358  12816   0.394  0.372  0.6377  0.6522  0.6345  0.6450
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37628
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0134
Overall R factor                     =     0.2185
Free R factor                        =     0.2484
Average Fourier shell correlation    =     0.8521
AverageFree Fourier shell correlation=     0.8413
Overall weighted R factor            =     0.1825
Free weighted R factor               =     0.2125
Overall weighted R2 factor           =     0.2103
Free weighted R2 factor              =     0.2446
Average correlation coefficient      =     0.8305
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9463
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0794
Overall figure of merit              =     0.6966
ML based su of positional parameters =     0.0661
ML based su of thermal parameters    =     1.9154
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    174887.56       8101.9795       882641.81       882183.75    

 fvalues    174887.56       8101.9795       882617.25       882516.69    
 fvalues    174887.56       8101.9795       882617.25       882516.69    

    ****                              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.= 0.916 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
          28          24          36  0.70425701      2.37302221E-02  0.70425248    
          36           8          36  0.70425701      2.37302221E-02  0.70425248    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R02_1-42A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.764     1.644
Bond angles  : others                          3238     1.493     1.580
Torsion angles, period  1. refined              185     6.825     5.000
Torsion angles, period  2. refined               90    35.653    22.778
Torsion angles, period  3. refined              268    13.168    15.000
Torsion angles, period  4. refined                9    12.182    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   295     0.249     0.200
VDW repulsions.others                          1335     0.196     0.200
VDW; torsion: refined_atoms                     729     0.172     0.200
VDW; torsion.others                             772     0.084     0.200
HBOND: refined_atoms                            208     0.187     0.200
HBOND.others                                      2     0.051     0.200
VDW repulsions: symmetry: refined_atoms           8     0.195     0.200
VDW repulsions: symmetry: others                 25     0.177     0.200
HBOND: symmetry: refined_atoms                   17     0.195     0.200
M. chain bond B values: refined atoms           746     1.764     1.698
M. chain bond B values: others                  746     1.759     1.699
M. chain angle B values: refined atoms          929     2.729     2.539
M. chain angle B values: others                 930     2.728     2.539
S. chain bond B values: refined atoms           811     3.198     2.115
S. chain bond B values: others                  810     3.194     2.114
S. chain angle B values: refined atoms         1177     4.954     2.997
S. chain angle B values: others                1178     4.952     2.997
Long range B values: refined atoms             1832     7.258    23.032
Long range B values: others                    1745     7.010    21.566
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.0014
Partial structure    1: scale =     0.3944, B  =   38.4470
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5058 100.00   381.4   390.9  0.17  0.18     271   362.0   376.7  0.21  0.21
 0.186    8677  99.98   206.1   182.3  0.19  0.17     466   207.6   186.5  0.23  0.20
 0.310   11077 100.00    92.0    88.6  0.23  0.20     570    92.9    91.7  0.25  0.21
 0.434   12816  98.63    38.7    48.1  0.47  0.46     679    38.7    47.5  0.46  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3829   0.925   1229   0.835   5058   0.903  0.951  0.9656  0.9735  0.9091  0.9359
  0.1863   7440   0.885   1237   0.788   8677   0.871  1.096  0.9523  0.9608  0.9056  0.9344
  0.3102   9828   0.824   1249   0.748  11077   0.815  0.956  0.9338  0.9426  0.8769  0.9154
  0.4340  11569   0.390   1247   0.350  12816   0.386  0.367  0.6316  0.6466  0.6345  0.6450
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37628
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0134
Overall R factor                     =     0.2185
Free R factor                        =     0.2484
Average Fourier shell correlation    =     0.8501
AverageFree Fourier shell correlation=     0.8392
Overall weighted R factor            =     0.1825
Free weighted R factor               =     0.2126
Overall weighted R2 factor           =     0.2103
Free weighted R2 factor              =     0.2446
Average correlation coefficient      =     0.8304
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9462
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0794
Overall figure of merit              =     0.6936
ML based su of positional parameters =     0.0661
ML based su of thermal parameters    =     1.9154
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.14
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2190   0.2487   0.671      176025.    9448.7   0.0124  0.929   1.774  1.032   0.087
       1   0.2188   0.2482   0.687      174966.    9414.8   0.0123  0.919   1.755  1.021   0.088
       2   0.2179   0.2480   0.688      174779.    9409.9   0.0133  0.997   1.811  1.054   0.091
       3   0.2178   0.2481   0.694      174741.    9408.0   0.0134  1.005   1.831  1.065   0.091
       4   0.2177   0.2481   0.702      174632.    9402.4   0.0134  1.010   1.841  1.071   0.092
       5   0.2180   0.2482   0.698      174722.    9405.1   0.0128  0.968   1.813  1.054   0.090
       6   0.2184   0.2482   0.695      174848.    9409.0   0.0122  0.922   1.774  1.031   0.088
       7   0.2185   0.2483   0.697      174846.    9408.8   0.0122  0.921   1.772  1.030   0.087
       8   0.2185   0.2484   0.700      174816.    9407.0   0.0122  0.919   1.768  1.028   0.087
       9   0.2185   0.2484   0.697      174860.    9409.5   0.0122  0.918   1.765  1.026   0.087
      10   0.2185   0.2484   0.694      174911.    9412.0   0.0122  0.918   1.764  1.026   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2190   0.2185
             R free    0.2487   0.2484
     Rms BondLength    0.0124   0.0122
      Rms BondAngle    1.7742   1.7642
     Rms ChirVolume    0.0871   0.0872
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      61.2s System:    0.2s Elapsed:     1:02