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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: 17:29:09 


 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 1.60     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_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R02_1-60A.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_1-60A.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       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  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  1.6000

  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_1-70A.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=   2.059 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=   1.841 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=   2.214 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.400 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.415 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=   2.081 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       1399
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 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.= 0.915 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.31025776    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                41.2
Norm of Geom. positional gradient                79.1
Norm of X_ray B-factor gradient                  126.
Norm of Geom. B-factor gradient                  111.
Product of X_ray and Geom posit. gradients     -0.133E+08
 Cosine of angle between them                      -0.422
Product of X_ray and Geom B-fact gradients     -0.384E+08
 Cosine of angle between them                      -0.856


Residuals: XRAY=     0.8725E+06 GEOM=     0.1310E+05 TOTAL=     0.8856E+06
 function value    885594.56    

-------------------------------------------------------------------------------
             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     1.768     1.644
Bond angles  : others                          3238     2.348     1.580
Torsion angles, period  1. refined              185     6.867     5.000
Torsion angles, period  2. refined               90    35.929    22.778
Torsion angles, period  3. refined              268    13.694    15.000
Torsion angles, period  4. refined                9    11.685    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                   299     0.249     0.200
VDW repulsions.others                          1325     0.222     0.200
VDW; torsion: refined_atoms                     728     0.173     0.200
VDW; torsion.others                             717     0.081     0.200
HBOND: refined_atoms                            209     0.192     0.200
HBOND.others                                      2     0.052     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 23     0.187     0.200
HBOND: symmetry: refined_atoms                   22     0.182     0.200
M. chain bond B values: refined atoms           746     1.618     1.395
M. chain bond B values: others                  746     1.614     1.396
M. chain angle B values: refined atoms          929     2.561     2.082
M. chain angle B values: others                 930     2.560     2.082
S. chain bond B values: refined atoms           811     2.963     1.791
S. chain bond B values: others                  810     2.957     1.791
S. chain angle B values: refined atoms         1177     4.651     2.517
S. chain angle B values: others                1178     4.650     2.517
Long range B values: refined atoms             1833     7.170    19.247
Long range B values: others                    1747     6.879    17.872
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    1.2252
Partial structure    1: scale =     0.3879, B  =   42.0807
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3586 100.00   433.6   442.6  0.16  0.17     196   416.4   428.6  0.19  0.20
 0.147    6107  99.97   259.3   244.4  0.17  0.15     337   251.6   238.9  0.23  0.20
 0.244    7831 100.00   167.5   151.4  0.19  0.17     387   165.8   154.2  0.22  0.19
 0.342    9111 100.00    71.2    85.5  0.33  0.26     479    75.0    90.0  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2621   0.923    965   0.828   3586   0.898  0.949  0.9664  0.9731  0.9162  0.9382
  0.1468   5135   0.877    972   0.780   6107   0.861  1.019  0.9443  0.9592  0.8821  0.9376
  0.2444   6845   0.870    986   0.767   7831   0.857  1.056  0.9443  0.9557  0.8925  0.9375
  0.3419   8138   0.678    978   0.595   9116   0.669  0.709  0.8760  0.8673  0.8406  0.8508
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26639
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.9897
Overall R factor                     =     0.1933
Free R factor                        =     0.2309
Average Fourier shell correlation    =     0.9286
AverageFree Fourier shell correlation=     0.9240
Overall weighted R factor            =     0.1670
Free weighted R factor               =     0.2016
Overall weighted R2 factor           =     0.1966
Free weighted R2 factor              =     0.2383
Average correlation coefficient      =     0.9079
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9382
Cruickshanks DPI for coordinate error=     0.0971
DPI based on free R factor           =     0.0987
Overall figure of merit              =     0.7992
ML based su of positional parameters =     0.0702
ML based su of thermal parameters    =     2.1148
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134236.77       13102.225       885594.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37874907    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    873908.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0613
Partial structure    1: scale =     0.3878, B  =   42.4291
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1927
Free R factor                        =     0.2297
Average Fourier shell correlation    =     0.9400
AverageFree Fourier shell correlation=     0.9344
Average correlation coefficient      =     0.9097
Overall figure of merit              =     0.8318
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133182.28       8270.1211       873908.69       885594.56    


     CGMAT cycle number =      3

 Weight matrix   0.39416707    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872499.94    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0038
Partial structure    1: scale =     0.3880, B  =   42.4498
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1916
Free R factor                        =     0.2290
Average Fourier shell correlation    =     0.9424
AverageFree Fourier shell correlation=     0.9363
Average correlation coefficient      =     0.9118
Overall figure of merit              =     0.8384
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132878.69       8834.6846       872499.94       873908.69    


     CGMAT cycle number =      4

 Weight matrix   0.36165982    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    793624.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.014     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0020
Partial structure    1: scale =     0.3880, B  =   42.4339
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1914
Free R factor                        =     0.2287
Average Fourier shell correlation    =     0.9429
AverageFree Fourier shell correlation=     0.9367
Average correlation coefficient      =     0.9128
Overall figure of merit              =     0.8395
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132779.31       9061.6953       793624.75       872499.94    


     CGMAT cycle number =      5

 Weight matrix   0.32907149    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722225.06    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0087
Partial structure    1: scale =     0.3883, B  =   42.5587
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1917
Free R factor                        =     0.2286
Average Fourier shell correlation    =     0.9429
AverageFree Fourier shell correlation=     0.9367
Average correlation coefficient      =     0.9127
Overall figure of merit              =     0.8396
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132797.95       8885.8213       722225.06       793624.75    


     CGMAT cycle number =      6

 Weight matrix   0.32839075    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722237.50    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0007
Partial structure    1: scale =     0.3882, B  =   42.4825
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1922
Free R factor                        =     0.2286
Average Fourier shell correlation    =     0.9427
AverageFree Fourier shell correlation=     0.9366
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8396
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    132862.94       8582.8398       722266.00       722225.06    
 fvalues    132862.94       8582.8398       722266.00       722271.19    


     CGMAT cycle number =      7

 Weight matrix   0.32854292    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722258.50    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0004
Partial structure    1: scale =     0.3881, B  =   42.4261
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2286
Average Fourier shell correlation    =     0.9428
AverageFree Fourier shell correlation=     0.9366
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8396
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    132875.00       8505.3916       722258.50       722271.19    


     CGMAT cycle number =      8

 Weight matrix   0.32820168    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722269.06    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0013
Partial structure    1: scale =     0.3881, B  =   42.4166
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2286
Average Fourier shell correlation    =     0.9428
AverageFree Fourier shell correlation=     0.9366
Average correlation coefficient      =     0.9123
Overall figure of merit              =     0.8396
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    132883.64       8469.4297       722260.88       722258.50    
 fvalues    132883.64       8469.4297       722260.88       722269.00    


     CGMAT cycle number =      9

 Weight matrix   0.32798135    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722265.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0012
Partial structure    1: scale =     0.3884, B  =   42.4236
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1924
Free R factor                        =     0.2286
Average Fourier shell correlation    =     0.9428
AverageFree Fourier shell correlation=     0.9366
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8396
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    132887.34       8445.5566       722265.00       722269.00    


     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.= 0.913 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.32779834    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                38.1
Norm of Geom. positional gradient                38.2
Norm of X_ray B-factor gradient                  107.
Norm of Geom. B-factor gradient                  107.
Product of X_ray and Geom posit. gradients     -0.141E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.372E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7138E+06 GEOM=      8438.     TOTAL=     0.7223E+06
 function value    722267.25    

-------------------------------------------------------------------------------
             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     1.776     1.644
Bond angles  : others                          3238     1.504     1.580
Torsion angles, period  1. refined              185     6.830     5.000
Torsion angles, period  2. refined               90    35.770    22.778
Torsion angles, period  3. refined              268    13.290    15.000
Torsion angles, period  4. refined                9    11.565    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   298     0.248     0.200
VDW repulsions.others                          1356     0.194     0.200
VDW; torsion: refined_atoms                     733     0.173     0.200
VDW; torsion.others                             788     0.084     0.200
HBOND: refined_atoms                            210     0.188     0.200
HBOND.others                                      1     0.096     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 25     0.182     0.200
HBOND: symmetry: refined_atoms                   20     0.187     0.200
M. chain bond B values: refined atoms           746     1.679     1.513
M. chain bond B values: others                  746     1.675     1.514
M. chain angle B values: refined atoms          929     2.643     2.261
M. chain angle B values: others                 930     2.642     2.261
S. chain bond B values: refined atoms           811     3.049     1.911
S. chain bond B values: others                  810     3.045     1.911
S. chain angle B values: refined atoms         1177     4.747     2.697
S. chain angle B values: others                1178     4.745     2.697
Long range B values: refined atoms             1839     7.176    20.777
Long range B values: others                    1751     6.887    19.341
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0024
Partial structure    1: scale =     0.3886, B  =   42.4034
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3586 100.00   433.8   442.9  0.16  0.17     196   416.6   429.7  0.19  0.20
 0.147    6107  99.97   259.5   244.4  0.17  0.15     337   251.8   238.8  0.23  0.20
 0.244    7831 100.00   167.6   151.5  0.19  0.17     387   165.9   154.1  0.22  0.19
 0.342    9111 100.00    71.3    85.2  0.32  0.26     479    75.0    89.8  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2621   0.936    965   0.851   3586   0.913  0.951  0.9697  0.9755  0.9170  0.9374
  0.1468   5135   0.884    972   0.792   6107   0.870  1.019  0.9475  0.9613  0.8868  0.9387
  0.2444   6845   0.884    986   0.782   7831   0.871  1.058  0.9500  0.9601  0.8966  0.9367
  0.3419   8138   0.773    978   0.687   9116   0.763  0.752  0.9044  0.9026  0.8433  0.8640
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26639
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.9897
Overall R factor                     =     0.1924
Free R factor                        =     0.2286
Average Fourier shell correlation    =     0.9428
AverageFree Fourier shell correlation=     0.9366
Overall weighted R factor            =     0.1673
Free weighted R factor               =     0.1996
Overall weighted R2 factor           =     0.1971
Free weighted R2 factor              =     0.2343
Average correlation coefficient      =     0.9124
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9397
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0977
Overall figure of merit              =     0.8396
ML based su of positional parameters =     0.0620
ML based su of thermal parameters    =     1.8301
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    132890.30       8437.5527       722267.94       722265.00    
 fvalues    132890.30       8437.5527       722267.94       722272.88    

    ****                              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.= 0.913 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_R02_1-60A.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     1.776     1.644
Bond angles  : others                          3238     1.504     1.580
Torsion angles, period  1. refined              185     6.829     5.000
Torsion angles, period  2. refined               90    35.761    22.778
Torsion angles, period  3. refined              268    13.275    15.000
Torsion angles, period  4. refined                9    11.574    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   299     0.248     0.200
VDW repulsions.others                          1358     0.194     0.200
VDW; torsion: refined_atoms                     733     0.172     0.200
VDW; torsion.others                             786     0.084     0.200
HBOND: refined_atoms                            209     0.189     0.200
HBOND.others                                      1     0.098     0.200
VDW repulsions: symmetry: refined_atoms           8     0.201     0.200
VDW repulsions: symmetry: others                 25     0.182     0.200
HBOND: symmetry: refined_atoms                   20     0.187     0.200
M. chain bond B values: refined atoms           746     1.679     1.513
M. chain bond B values: others                  746     1.674     1.514
M. chain angle B values: refined atoms          929     2.643     2.261
M. chain angle B values: others                 930     2.641     2.261
S. chain bond B values: refined atoms           811     3.046     1.911
S. chain bond B values: others                  810     3.042     1.910
S. chain angle B values: refined atoms         1177     4.743     2.697
S. chain angle B values: others                1178     4.741     2.696
Long range B values: refined atoms             1839     7.164    20.789
Long range B values: others                    1751     6.875    19.354
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0011
Partial structure    1: scale =     0.3886, B  =   42.4465
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3586 100.00   433.9   442.9  0.16  0.17     196   416.6   429.6  0.19  0.20
 0.147    6107  99.97   259.5   244.4  0.17  0.15     337   251.8   238.8  0.23  0.20
 0.244    7831 100.00   167.6   151.5  0.19  0.17     387   165.9   154.1  0.22  0.19
 0.342    9111 100.00    71.3    85.2  0.32  0.26     479    75.0    89.8  0.34  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2621   0.936    965   0.851   3586   0.913  0.951  0.9697  0.9754  0.9171  0.9374
  0.1468   5135   0.885    972   0.792   6107   0.870  1.019  0.9476  0.9613  0.8868  0.9387
  0.2444   6845   0.884    986   0.782   7831   0.871  1.058  0.9500  0.9600  0.8965  0.9366
  0.3419   8138   0.773    978   0.687   9116   0.763  0.752  0.9044  0.9026  0.8433  0.8641
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26639
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.9897
Overall R factor                     =     0.1925
Free R factor                        =     0.2285
Average Fourier shell correlation    =     0.9428
AverageFree Fourier shell correlation=     0.9365
Overall weighted R factor            =     0.1674
Free weighted R factor               =     0.1996
Overall weighted R2 factor           =     0.1971
Free weighted R2 factor              =     0.2344
Average correlation coefficient      =     0.9124
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9397
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0977
Overall figure of merit              =     0.8395
ML based su of positional parameters =     0.0620
ML based su of thermal parameters    =     1.8301
-----------------------------------------------------------------------------
  Time in seconds: CPU =        20.25
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1933   0.2309   0.799      134237.    7229.5   0.0125  0.928   1.768  1.028   0.087
       1   0.1927   0.2297   0.832      133182.    7188.7   0.0126  0.935   1.763  1.027   0.087
       2   0.1916   0.2290   0.838      132879.    7177.5   0.0134  1.000   1.811  1.055   0.089
       3   0.1914   0.2287   0.840      132779.    7173.4   0.0136  1.016   1.837  1.071   0.090
       4   0.1917   0.2286   0.840      132798.    7172.9   0.0131  0.979   1.822  1.061   0.088
       5   0.1922   0.2286   0.840      132857.    7173.8   0.0125  0.936   1.791  1.043   0.086
       6   0.1924   0.2286   0.840      132875.    7174.2   0.0125  0.932   1.782  1.037   0.086
       7   0.1924   0.2286   0.840      132884.    7174.6   0.0125  0.930   1.779  1.035   0.086
       8   0.1924   0.2286   0.840      132887.    7174.8   0.0125  0.929   1.777  1.034   0.086
       9   0.1924   0.2286   0.840      132889.    7175.0   0.0125  0.929   1.776  1.034   0.086
      10   0.1925   0.2285   0.840      132891.    7175.1   0.0124  0.928   1.776  1.034   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1933   0.1925
             R free    0.2309   0.2285
     Rms BondLength    0.0125   0.0124
      Rms BondAngle    1.7684   1.7758
     Rms ChirVolume    0.0867   0.0859
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      52.4s System:    0.2s Elapsed:     0:53