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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: 16:37:23 


 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 8
  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_R08_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R08_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_R08_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:     8
  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_R08_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=   2.050 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.201 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.851 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=   2.182 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=   2.404 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=   2.405 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=   2.084 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                            8
Number of "free" reflections       1172
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.= 0.912 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  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   0.30992219    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                41.3
Norm of Geom. positional gradient                80.5
Norm of X_ray B-factor gradient                  135.
Norm of Geom. B-factor gradient                  121.
Product of X_ray and Geom posit. gradients     -0.131E+08
 Cosine of angle between them                      -0.405
Product of X_ray and Geom B-fact gradients     -0.431E+08
 Cosine of angle between them                      -0.815


Residuals: XRAY=     0.7823E+06 GEOM=     0.1357E+05 TOTAL=     0.7959E+06
 function value    795893.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.818     1.644
Bond angles  : others                          3238     2.362     1.580
Torsion angles, period  1. refined              185     7.021     5.000
Torsion angles, period  2. refined               90    36.569    22.778
Torsion angles, period  3. refined              268    13.965    15.000
Torsion angles, period  4. refined                9    11.727    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   295     0.245     0.200
VDW repulsions.others                          1308     0.223     0.200
VDW; torsion: refined_atoms                     719     0.171     0.200
VDW; torsion.others                             717     0.081     0.200
HBOND: refined_atoms                            219     0.198     0.200
VDW repulsions: symmetry: refined_atoms          10     0.210     0.200
VDW repulsions: symmetry: others                 24     0.190     0.200
HBOND: symmetry: refined_atoms                   25     0.174     0.200
M. chain bond B values: refined atoms           746     1.675     1.291
M. chain bond B values: others                  746     1.674     1.292
M. chain angle B values: refined atoms          929     2.626     1.923
M. chain angle B values: others                 930     2.625     1.923
S. chain bond B values: refined atoms           811     2.933     1.674
S. chain bond B values: others                  810     2.929     1.673
S. chain angle B values: refined atoms         1177     4.554     2.347
S. chain angle B values: others                1178     4.552     2.346
Long range B values: refined atoms             1838     6.994    17.887
Long range B values: others                    1747     6.727    16.559
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.0737
Partial structure    1: scale =     0.3824, B  =   44.1305
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3013 100.00   454.5   463.7  0.16  0.17     158   456.4   460.3  0.20  0.21
 0.130    5129 100.00   299.6   286.2  0.16  0.14     271   298.0   287.7  0.21  0.19
 0.216    6534  99.97   202.8   186.5  0.17  0.15     338   201.1   184.6  0.22  0.19
 0.303    7638 100.00   104.4   117.3  0.26  0.20     405   105.1   116.4  0.28  0.21
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2161   0.918    852   0.826   3013   0.892  0.948  0.9648  0.9711  0.9182  0.9396
  0.1301   4258   0.889    871   0.783   5129   0.871  1.003  0.9516  0.9643  0.9027  0.9458
  0.2165   5645   0.876    889   0.761   6534   0.860  1.044  0.9431  0.9590  0.8727  0.9403
  0.3028   6774   0.781    867   0.711   7641   0.773  0.821  0.9193  0.9236  0.8757  0.8923
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22317
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9896
Overall R factor                     =     0.1793
Free R factor                        =     0.2198
Average Fourier shell correlation    =     0.9498
AverageFree Fourier shell correlation=     0.9398
Overall weighted R factor            =     0.1583
Free weighted R factor               =     0.1983
Overall weighted R2 factor           =     0.1892
Free weighted R2 factor              =     0.2330
Average correlation coefficient      =     0.9250
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9361
Cruickshanks DPI for coordinate error=     0.1086
DPI based on free R factor           =     0.1090
Overall figure of merit              =     0.8370
ML based su of positional parameters =     0.0715
ML based su of thermal parameters    =     2.2162
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    115905.68       13566.308       795893.38      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37226039    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786326.06    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0809
Partial structure    1: scale =     0.3827, B  =   44.3558
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                     =     0.1788
Free R factor                        =     0.2187
Average Fourier shell correlation    =     0.9558
AverageFree Fourier shell correlation=     0.9454
Average correlation coefficient      =     0.9269
Overall figure of merit              =     0.8606
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115242.05       8478.2598       786326.06       795893.38    


     CGMAT cycle number =      3

 Weight matrix   0.37991133    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784879.06    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0168
Partial structure    1: scale =     0.3828, B  =   44.1859
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                     =     0.1778
Free R factor                        =     0.2174
Average Fourier shell correlation    =     0.9568
AverageFree Fourier shell correlation=     0.9460
Average correlation coefficient      =     0.9291
Overall figure of merit              =     0.8626
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    114934.02       9110.4395       784879.06       786326.06    


     CGMAT cycle number =      4

 Weight matrix   0.38182408    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784336.50    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0022
Partial structure    1: scale =     0.3878, B  =   44.9960
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                     =     0.1776
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9570
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9297
Overall figure of merit              =     0.8629
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    114823.47       9313.9766       784336.50       784879.06    


     CGMAT cycle number =      5

 Weight matrix   0.34761339    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    713680.69    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0206
Partial structure    1: scale =     0.3880, B  =   44.9186
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                     =     0.1774
Free R factor                        =     0.2175
Average Fourier shell correlation    =     0.9571
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9300
Overall figure of merit              =     0.8631
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114779.73       9383.1348       713680.69       784336.50    


     CGMAT cycle number =      6

 Weight matrix   0.31568825    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649579.13    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0211
Partial structure    1: scale =     0.3881, B  =   44.7694
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                     =     0.1778
Free R factor                        =     0.2176
Average Fourier shell correlation    =     0.9570
AverageFree Fourier shell correlation=     0.9463
Average correlation coefficient      =     0.9297
Overall figure of merit              =     0.8631
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114814.06       9117.1270       649579.13       713680.69    


     CGMAT cycle number =      7

 Weight matrix   0.31540236    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649625.13    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0295
Partial structure    1: scale =     0.3882, B  =   44.7410
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                     =     0.1785
Free R factor                        =     0.2177
Average Fourier shell correlation    =     0.9568
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8631
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    114885.86       8764.8877       649652.44       649579.13    

 fvalues    114885.86       8764.8877       649640.63       649627.38    
 fvalues    114885.86       8764.8877       649640.63       649627.38    


     CGMAT cycle number =      8

 Weight matrix   0.31536078    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649628.44    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0315
Partial structure    1: scale =     0.3882, B  =   44.7096
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                     =     0.1785
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9568
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8631
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    114891.09       8737.0234       649640.88       649627.38    

 fvalues    114891.09       8737.0234       649640.69       649628.69    
 fvalues    114891.09       8737.0234       649640.69       649628.69    


     CGMAT cycle number =      9

 Weight matrix   0.31537363    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649626.63    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0316
Partial structure    1: scale =     0.3882, B  =   44.7165
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                     =     0.1785
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9568
AverageFree Fourier shell correlation=     0.9462
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8631
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    114892.11       8729.2842       649626.63       649628.69    


     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.= 0.914 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  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   0.31521425    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                37.9
Norm of Geom. positional gradient                38.1
Norm of X_ray B-factor gradient                  117.
Norm of Geom. B-factor gradient                  120.
Product of X_ray and Geom posit. gradients     -0.139E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.451E+08
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.6409E+06 GEOM=      8717.     TOTAL=     0.6496E+06
 function value    649632.31    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.765     1.644
Bond angles  : others                          3238     1.500     1.580
Torsion angles, period  1. refined              185     6.912     5.000
Torsion angles, period  2. refined               90    36.165    22.778
Torsion angles, period  3. refined              268    13.640    15.000
Torsion angles, period  4. refined                9    11.524    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   293     0.247     0.200
VDW repulsions.others                          1336     0.196     0.200
VDW; torsion: refined_atoms                     727     0.171     0.200
VDW; torsion.others                             767     0.084     0.200
HBOND: refined_atoms                            215     0.194     0.200
HBOND.others                                      1     0.069     0.200
VDW repulsions: symmetry: refined_atoms          10     0.187     0.200
VDW repulsions: symmetry: others                 21     0.194     0.200
HBOND: symmetry: refined_atoms                   20     0.195     0.200
M. chain bond B values: refined atoms           746     1.647     1.394
M. chain bond B values: others                  746     1.644     1.394
M. chain angle B values: refined atoms          929     2.621     2.081
M. chain angle B values: others                 930     2.619     2.081
S. chain bond B values: refined atoms           811     2.962     1.785
S. chain bond B values: others                  810     2.953     1.784
S. chain angle B values: refined atoms         1177     4.575     2.512
S. chain angle B values: others                1178     4.573     2.511
Long range B values: refined atoms             1838     6.996    19.369
Long range B values: others                    1747     6.682    17.957
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0308
Partial structure    1: scale =     0.3883, B  =   44.7012
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3013 100.00   454.0   463.9  0.16  0.17     158   455.9   461.0  0.19  0.20
 0.130    5129 100.00   299.3   285.3  0.16  0.15     271   297.7   287.0  0.21  0.19
 0.216    6534  99.97   202.6   186.1  0.17  0.15     338   200.9   184.9  0.22  0.19
 0.303    7638 100.00   104.2   116.2  0.25  0.19     405   105.0   115.4  0.27  0.21
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2161   0.931    852   0.848   3013   0.908  0.948  0.9692  0.9741  0.9145  0.9384
  0.1301   4258   0.892    871   0.784   5129   0.873  1.003  0.9531  0.9645  0.9059  0.9445
  0.2165   5645   0.883    889   0.770   6534   0.868  1.044  0.9458  0.9603  0.8748  0.9378
  0.3028   6774   0.843    867   0.771   7641   0.835  0.848  0.9327  0.9417  0.8793  0.9078
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22317
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9896
Overall R factor                     =     0.1785
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9568
AverageFree Fourier shell correlation=     0.9461
Overall weighted R factor            =     0.1595
Free weighted R factor               =     0.1964
Overall weighted R2 factor           =     0.1915
Free weighted R2 factor              =     0.2290
Average correlation coefficient      =     0.9292
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9364
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.1080
Overall figure of merit              =     0.8630
ML based su of positional parameters =     0.0644
ML based su of thermal parameters    =     1.9449
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    114895.55       8717.2695       649623.88       649626.63    
 fvalues    114895.55       8717.2695       649623.88       649633.81    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.914 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R08_1-70A.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     1.499     1.580
Torsion angles, period  1. refined              185     6.911     5.000
Torsion angles, period  2. refined               90    36.159    22.778
Torsion angles, period  3. refined              268    13.630    15.000
Torsion angles, period  4. refined                9    11.518    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   293     0.247     0.200
VDW repulsions.others                          1337     0.195     0.200
VDW; torsion: refined_atoms                     727     0.171     0.200
VDW; torsion.others                             768     0.084     0.200
HBOND: refined_atoms                            215     0.194     0.200
HBOND.others                                      1     0.069     0.200
VDW repulsions: symmetry: refined_atoms          10     0.186     0.200
VDW repulsions: symmetry: others                 21     0.193     0.200
HBOND: symmetry: refined_atoms                   20     0.195     0.200
M. chain bond B values: refined atoms           746     1.645     1.394
M. chain bond B values: others                  746     1.643     1.394
M. chain angle B values: refined atoms          929     2.619     2.081
M. chain angle B values: others                 930     2.617     2.081
S. chain bond B values: refined atoms           811     2.959     1.785
S. chain bond B values: others                  810     2.950     1.784
S. chain angle B values: refined atoms         1177     4.570     2.511
S. chain angle B values: others                1178     4.568     2.511
Long range B values: refined atoms             1838     6.992    19.368
Long range B values: others                    1747     6.678    17.956
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0211
Partial structure    1: scale =     0.3883, B  =   44.6923
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3013 100.00   454.0   463.9  0.16  0.17     158   455.9   461.0  0.19  0.20
 0.130    5129 100.00   299.3   285.2  0.16  0.15     271   297.7   287.0  0.21  0.19
 0.216    6534  99.97   202.6   186.0  0.17  0.15     338   200.9   184.8  0.22  0.19
 0.303    7638 100.00   104.3   116.1  0.25  0.19     405   105.0   115.3  0.27  0.21
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2161   0.931    852   0.848   3013   0.908  0.948  0.9692  0.9741  0.9144  0.9384
  0.1301   4258   0.892    871   0.784   5129   0.873  1.003  0.9531  0.9645  0.9059  0.9444
  0.2165   5645   0.883    889   0.769   6534   0.868  1.044  0.9458  0.9603  0.8747  0.9378
  0.3028   6774   0.843    867   0.771   7641   0.834  0.848  0.9327  0.9417  0.8794  0.9079
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22317
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9896
Overall R factor                     =     0.1785
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9568
AverageFree Fourier shell correlation=     0.9461
Overall weighted R factor            =     0.1596
Free weighted R factor               =     0.1965
Overall weighted R2 factor           =     0.1916
Free weighted R2 factor              =     0.2290
Average correlation coefficient      =     0.9292
Overall correlation coefficient      =     0.9576
Free correlation coefficient         =     0.9364
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.1080
Overall figure of merit              =     0.8630
ML based su of positional parameters =     0.0644
ML based su of thermal parameters    =     1.9449
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.20
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1793   0.2198   0.837      115906.    6240.4   0.0128  0.946   1.818  1.045   0.088
       1   0.1788   0.2187   0.861      115242.    6214.0   0.0125  0.925   1.784  1.028   0.088
       2   0.1778   0.2174   0.863      114934.    6207.6   0.0134  0.996   1.813  1.051   0.092
       3   0.1776   0.2175   0.863      114823.    6205.1   0.0135  1.004   1.827  1.061   0.093
       4   0.1774   0.2175   0.863      114780.    6203.8   0.0135  1.005   1.834  1.067   0.094
       5   0.1778   0.2176   0.863      114814.    6203.9   0.0129  0.961   1.808  1.052   0.092
       6   0.1785   0.2177   0.863      114885.    6205.8   0.0122  0.916   1.771  1.031   0.089
       7   0.1785   0.2178   0.863      114891.    6206.0   0.0122  0.914   1.767  1.029   0.089
       8   0.1785   0.2178   0.863      114892.    6205.8   0.0122  0.914   1.767  1.028   0.089
       9   0.1785   0.2178   0.863      114895.    6206.0   0.0122  0.913   1.765  1.028   0.089
      10   0.1785   0.2178   0.863      114901.    6206.1   0.0122  0.913   1.764  1.027   0.089
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1793   0.1785
             R free    0.2198   0.2178
     Rms BondLength    0.0128   0.0122
      Rms BondAngle    1.8184   1.7635
     Rms ChirVolume    0.0880   0.0888
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      55.4s System:    0.1s Elapsed:     0:56