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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: 18:15:32 


 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 13
  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_R13_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R13_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_R13_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:    13
  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_R13_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=   2.054 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=   2.210 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=   1.842 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=   2.209 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=   2.389 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=   2.398 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=   2.075 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                           13
Number of "free" reflections       1357
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.= 0.910 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   0.32009894    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                42.4
Norm of Geom. positional gradient                79.8
Norm of X_ray B-factor gradient                  127.
Norm of Geom. B-factor gradient                  114.
Product of X_ray and Geom posit. gradients     -0.140E+08
 Cosine of angle between them                      -0.427
Product of X_ray and Geom B-fact gradients     -0.408E+08
 Cosine of angle between them                      -0.871


Residuals: XRAY=     0.8729E+06 GEOM=     0.1330E+05 TOTAL=     0.8863E+06
 function value    886252.69    

-------------------------------------------------------------------------------
             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     1.784     1.644
Bond angles  : others                          3238     2.346     1.580
Torsion angles, period  1. refined              185     6.987     5.000
Torsion angles, period  2. refined               90    36.510    22.778
Torsion angles, period  3. refined              268    14.045    15.000
Torsion angles, period  4. refined                9    10.736    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   307     0.243     0.200
VDW repulsions.others                          1327     0.223     0.200
VDW; torsion: refined_atoms                     726     0.172     0.200
VDW; torsion.others                             727     0.080     0.200
HBOND: refined_atoms                            219     0.197     0.200
HBOND.others                                      1     0.100     0.200
VDW repulsions: symmetry: refined_atoms          10     0.180     0.200
VDW repulsions: symmetry: others                 27     0.177     0.200
HBOND: symmetry: refined_atoms                   24     0.189     0.200
M. chain bond B values: refined atoms           746     1.701     1.395
M. chain bond B values: others                  746     1.699     1.395
M. chain angle B values: refined atoms          929     2.672     2.080
M. chain angle B values: others                 930     2.671     2.080
S. chain bond B values: refined atoms           811     3.008     1.801
S. chain bond B values: others                  810     3.001     1.801
S. chain angle B values: refined atoms         1177     4.716     2.531
S. chain angle B values: others                1178     4.714     2.531
Long range B values: refined atoms             1851     7.585    19.591
Long range B values: others                    1756     7.126    18.069
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    1.2186
Partial structure    1: scale =     0.3864, B  =   43.3285
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3598 100.00   432.6   442.5  0.16  0.17     184   427.5   432.7  0.18  0.18
 0.147    6103  99.97   258.7   243.9  0.17  0.15     341   259.4   239.4  0.20  0.18
 0.244    7826 100.00   167.4   151.5  0.19  0.17     392   165.0   149.4  0.23  0.19
 0.342    9151 100.00    71.2    85.7  0.34  0.27     439    74.8    89.2  0.33  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2629   0.924    969   0.840   3598   0.902  0.951  0.9702  0.9731  0.9269  0.9378
  0.1468   5121   0.895    982   0.800   6103   0.879  1.026  0.9577  0.9641  0.9254  0.9403
  0.2444   6834   0.867    992   0.761   7826   0.853  1.054  0.9457  0.9548  0.9129  0.9356
  0.3419   8156   0.678    999   0.600   9155   0.669  0.705  0.8715  0.8671  0.8338  0.8501
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26681
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.8399
Overall R factor                     =     0.1933
Free R factor                        =     0.2149
Average Fourier shell correlation    =     0.9293
AverageFree Fourier shell correlation=     0.9280
Overall weighted R factor            =     0.1664
Free weighted R factor               =     0.1855
Overall weighted R2 factor           =     0.1956
Free weighted R2 factor              =     0.2114
Average correlation coefficient      =     0.9077
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9479
Cruickshanks DPI for coordinate error=     0.0969
DPI based on free R factor           =     0.0917
Overall figure of merit              =     0.8027
ML based su of positional parameters =     0.0691
ML based su of thermal parameters    =     2.1009
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134306.98       13304.009       886252.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.39977345    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874065.31    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0536
Partial structure    1: scale =     0.3880, B  =   44.4455
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                     =     0.1928
Free R factor                        =     0.2135
Average Fourier shell correlation    =     0.9418
AverageFree Fourier shell correlation=     0.9390
Average correlation coefficient      =     0.9094
Overall figure of merit              =     0.8381
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133178.55       8451.0850       874065.31       886252.69    


     CGMAT cycle number =      3

 Weight matrix   0.41485399    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872719.06    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0093
Partial structure    1: scale =     0.3883, B  =   44.4153
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                        =     0.2126
Average Fourier shell correlation    =     0.9444
AverageFree Fourier shell correlation=     0.9410
Average correlation coefficient      =     0.9117
Overall figure of merit              =     0.8450
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132872.63       9093.2080       872719.06       874065.31    


     CGMAT cycle number =      4

 Weight matrix   0.37882218    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    793907.94    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =    0.0013
Partial structure    1: scale =     0.3886, B  =   44.3855
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                     =     0.1913
Free R factor                        =     0.2126
Average Fourier shell correlation    =     0.9449
AverageFree Fourier shell correlation=     0.9413
Average correlation coefficient      =     0.9127
Overall figure of merit              =     0.8460
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132780.19       9339.6953       793907.94       872719.06    


     CGMAT cycle number =      5

 Weight matrix   0.34349501    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722535.06    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =    0.0065
Partial structure    1: scale =     0.3888, B  =   44.2215
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                        =     0.2125
Average Fourier shell correlation    =     0.9449
AverageFree Fourier shell correlation=     0.9413
Average correlation coefficient      =     0.9127
Overall figure of merit              =     0.8460
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132805.55       9155.0273       722535.06       793907.94    


     CGMAT cycle number =      6

 Weight matrix   0.34214911    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722543.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    0.0051
Partial structure    1: scale =     0.3888, B  =   44.1959
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                     =     0.1921
Free R factor                        =     0.2127
Average Fourier shell correlation    =     0.9448
AverageFree Fourier shell correlation=     0.9412
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8458
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    132870.36       8840.9746       722588.88       722535.06    

 fvalues    132870.36       8840.9746       722564.94       722569.19    
 fvalues    132870.36       8840.9746       722564.94       722569.19    


     CGMAT cycle number =      7

 Weight matrix   0.34149557    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722569.38    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =    0.0077
Partial structure    1: scale =     0.3891, B  =   44.0764
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                        =     0.2128
Average Fourier shell correlation    =     0.9447
AverageFree Fourier shell correlation=     0.9411
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8457
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05

 fvalues    132877.39       8795.7256       722561.75       722569.19    


     CGMAT cycle number =      8

 Weight matrix   0.34115550    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722565.63    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =    0.0071
Partial structure    1: scale =     0.3891, B  =   44.0278
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                     =     0.1923
Free R factor                        =     0.2129
Average Fourier shell correlation    =     0.9447
AverageFree Fourier shell correlation=     0.9411
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8456
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    132886.53       8749.0117       722581.38       722561.75    

 fvalues    132886.53       8749.0117       722568.63       722564.06    
 fvalues    132886.53       8749.0117       722568.63       722564.06    


     CGMAT cycle number =      9

 Weight matrix   0.34084409    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    722581.19    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =    0.0100
Partial structure    1: scale =     0.3890, B  =   44.0667
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                     =     0.1923
Free R factor                        =     0.2129
Average Fourier shell correlation    =     0.9447
AverageFree Fourier shell correlation=     0.9411
Average correlation coefficient      =     0.9124
Overall figure of merit              =     0.8456
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    132888.56       8741.6377       722582.19       722564.06    

 fvalues    132888.56       8741.6377       722575.50       722567.63    
 fvalues    132888.56       8741.6377       722575.50       722567.63    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.915 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   0.34095472    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                39.3
Norm of Geom. positional gradient                39.5
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  111.
Product of X_ray and Geom posit. gradients     -0.150E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.399E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.7138E+06 GEOM=      8739.     TOTAL=     0.7226E+06
 function value    722568.50    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.805     1.644
Bond angles  : others                          3238     1.508     1.580
Torsion angles, period  1. refined              185     6.930     5.000
Torsion angles, period  2. refined               90    36.056    22.778
Torsion angles, period  3. refined              268    13.697    15.000
Torsion angles, period  4. refined                9    10.700    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                   308     0.244     0.200
VDW repulsions.others                          1366     0.196     0.200
VDW; torsion: refined_atoms                     724     0.174     0.200
VDW; torsion.others                             787     0.084     0.200
HBOND: refined_atoms                            225     0.199     0.200
HBOND.others                                      1     0.113     0.200
VDW repulsions: symmetry: refined_atoms           9     0.191     0.200
VDW repulsions: symmetry: others                 27     0.174     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           746     1.747     1.509
M. chain bond B values: others                  746     1.744     1.509
M. chain angle B values: refined atoms          929     2.737     2.255
M. chain angle B values: others                 930     2.736     2.254
S. chain bond B values: refined atoms           811     3.112     1.921
S. chain bond B values: others                  810     3.106     1.921
S. chain angle B values: refined atoms         1177     4.829     2.710
S. chain angle B values: others                1178     4.827     2.709
Long range B values: refined atoms             1860     7.717    21.252
Long range B values: others                    1762     7.232    19.692
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    0.0089
Partial structure    1: scale =     0.3890, B  =   44.0880
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3598 100.00   432.6   442.5  0.17  0.17     184   427.6   432.3  0.18  0.18
 0.147    6103  99.97   258.7   243.6  0.17  0.15     341   259.4   239.4  0.19  0.18
 0.244    7826 100.00   167.4   151.5  0.19  0.17     392   165.0   149.6  0.22  0.19
 0.342    9151 100.00    71.2    85.4  0.32  0.26     439    74.8    89.3  0.33  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2629   0.934    969   0.854   3598   0.913  0.951  0.9721  0.9753  0.9264  0.9368
  0.1468   5121   0.901    982   0.807   6103   0.885  1.026  0.9597  0.9659  0.9278  0.9419
  0.2444   6834   0.880    992   0.776   7826   0.867  1.054  0.9505  0.9587  0.9137  0.9341
  0.3419   8156   0.783    999   0.706   9155   0.775  0.752  0.9053  0.9067  0.8380  0.8647
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26681
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.8399
Overall R factor                     =     0.1923
Free R factor                        =     0.2129
Average Fourier shell correlation    =     0.9447
AverageFree Fourier shell correlation=     0.9411
Overall weighted R factor            =     0.1664
Free weighted R factor               =     0.1843
Overall weighted R2 factor           =     0.1965
Free weighted R2 factor              =     0.2102
Average correlation coefficient      =     0.9124
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9486
Cruickshanks DPI for coordinate error=     0.0964
DPI based on free R factor           =     0.0908
Overall figure of merit              =     0.8456
ML based su of positional parameters =     0.0608
ML based su of thermal parameters    =     1.8041
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    132889.36       8738.8281       722557.06       722567.63    
 fvalues    132889.36       8738.8281       722557.06       722569.06    

    ****                              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

 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_R13_1-60A.mtz 




-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2106     1.804     1.644
Bond angles  : others                          3238     1.508     1.580
Torsion angles, period  1. refined              185     6.929     5.000
Torsion angles, period  2. refined               90    36.048    22.778
Torsion angles, period  3. refined              268    13.693    15.000
Torsion angles, period  4. refined                9    10.698    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                   308     0.244     0.200
VDW repulsions.others                          1364     0.196     0.200
VDW; torsion: refined_atoms                     724     0.174     0.200
VDW; torsion.others                             788     0.084     0.200
HBOND: refined_atoms                            225     0.199     0.200
HBOND.others                                      1     0.114     0.200
VDW repulsions: symmetry: refined_atoms           9     0.191     0.200
VDW repulsions: symmetry: others                 27     0.174     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           746     1.746     1.509
M. chain bond B values: others                  746     1.743     1.509
M. chain angle B values: refined atoms          929     2.736     2.255
M. chain angle B values: others                 930     2.735     2.254
S. chain bond B values: refined atoms           811     3.111     1.921
S. chain bond B values: others                  810     3.105     1.921
S. chain angle B values: refined atoms         1177     4.827     2.709
S. chain angle B values: others                1178     4.825     2.709
Long range B values: refined atoms             1860     7.715    21.251
Long range B values: others                    1762     7.230    19.691
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    0.0067
Partial structure    1: scale =     0.3890, B  =   44.0977
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.40 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3598 100.00   432.6   442.5  0.17  0.17     184   427.6   432.3  0.18  0.18
 0.147    6103  99.97   258.7   243.6  0.17  0.15     341   259.4   239.4  0.19  0.18
 0.244    7826 100.00   167.4   151.6  0.19  0.17     392   165.0   149.6  0.22  0.19
 0.342    9151 100.00    71.2    85.4  0.32  0.26     439    74.8    89.3  0.33  0.27
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2629   0.934    969   0.854   3598   0.912  0.951  0.9721  0.9753  0.9264  0.9368
  0.1468   5121   0.901    982   0.807   6103   0.885  1.026  0.9597  0.9659  0.9278  0.9419
  0.2444   6834   0.880    992   0.776   7826   0.867  1.054  0.9505  0.9587  0.9137  0.9341
  0.3419   8156   0.783    999   0.706   9155   0.775  0.752  0.9054  0.9067  0.8381  0.8647
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26681
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.8399
Overall R factor                     =     0.1923
Free R factor                        =     0.2129
Average Fourier shell correlation    =     0.9447
AverageFree Fourier shell correlation=     0.9411
Overall weighted R factor            =     0.1664
Free weighted R factor               =     0.1843
Overall weighted R2 factor           =     0.1965
Free weighted R2 factor              =     0.2102
Average correlation coefficient      =     0.9124
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9486
Cruickshanks DPI for coordinate error=     0.0964
DPI based on free R factor           =     0.0908
Overall figure of merit              =     0.8456
ML based su of positional parameters =     0.0608
ML based su of thermal parameters    =     1.8041
-----------------------------------------------------------------------------
  Time in seconds: CPU =        23.59
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1933   0.2149   0.803      134307.    6962.3   0.0124  0.931   1.784  1.033   0.087
       1   0.1928   0.2135   0.838      133179.    6924.9   0.0126  0.944   1.781  1.032   0.086
       2   0.1916   0.2126   0.845      132873.    6914.9   0.0137  1.022   1.834  1.064   0.089
       3   0.1913   0.2126   0.846      132780.    6912.5   0.0138  1.039   1.862  1.081   0.090
       4   0.1916   0.2125   0.846      132806.    6913.2   0.0133  0.998   1.847  1.072   0.088
       5   0.1921   0.2127   0.846      132866.    6915.0   0.0127  0.952   1.815  1.053   0.086
       6   0.1922   0.2128   0.846      132879.    6915.7   0.0126  0.949   1.810  1.050   0.086
       7   0.1923   0.2129   0.846      132887.    6916.4   0.0126  0.946   1.805  1.047   0.086
       8   0.1923   0.2129   0.846      132891.    6916.6   0.0126  0.946   1.805  1.047   0.086
       9   0.1923   0.2129   0.846      132889.    6916.5   0.0126  0.946   1.805  1.046   0.086
      10   0.1923   0.2129   0.846      132889.    6916.5   0.0126  0.946   1.804  1.046   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1933   0.1923
             R free    0.2149   0.2129
     Rms BondLength    0.0124   0.0126
      Rms BondAngle    1.7845   1.8042
     Rms ChirVolume    0.0870   0.0856
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      55.6s System:    0.1s Elapsed:     0:56