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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 19:48:39 


 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 1.50     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_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R13_1-50A.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_1-50A.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       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  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  1.5000

  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_1-60A.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=   2.060 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=   2.202 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=   1.831 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=   2.205 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=   2.390 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=   2.395 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.084 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3945
  Number of missing atoms           :       1
  Number of rebuilt atoms           :    1480
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2949         0      2949
               Angles:      5344         0      5344
              Chirals:       196         0       196
               Planes:       453         0       453
             Torsions:      1556         0      1556
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                           13
Number of "free" reflections       1641
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 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.= 0.900 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.29975140    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                40.4
Norm of Geom. positional gradient                80.5
Norm of X_ray B-factor gradient                  116.
Norm of Geom. B-factor gradient                  106.
Product of X_ray and Geom posit. gradients     -0.148E+08
 Cosine of angle between them                      -0.469
Product of X_ray and Geom B-fact gradients     -0.356E+08
 Cosine of angle between them                      -0.892


Residuals: XRAY=     0.9772E+06 GEOM=     0.1317E+05 TOTAL=     0.9904E+06
 function value    990394.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.804     1.644
Bond angles  : others                          3238     2.351     1.580
Torsion angles, period  1. refined              185     6.929     5.000
Torsion angles, period  2. refined               90    36.044    22.778
Torsion angles, period  3. refined              268    13.690    15.000
Torsion angles, period  4. refined                9    10.685    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.015     0.020
VDW repulsions: refined_atoms                   308     0.244     0.200
VDW repulsions.others                          1345     0.222     0.200
VDW; torsion: refined_atoms                     725     0.174     0.200
VDW; torsion.others                             730     0.081     0.200
HBOND: refined_atoms                            225     0.199     0.200
HBOND.others                                      2     0.063     0.200
VDW repulsions: symmetry: refined_atoms           9     0.191     0.200
VDW repulsions: symmetry: others                 27     0.176     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             1861     7.713    21.253
Long range B values: others                    1763     7.230    19.696
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0457, B  =    1.1766
Partial structure    1: scale =     0.3938, B  =   40.5285
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4326 100.00   405.7   415.5  0.17  0.17     221   405.2   410.4  0.18  0.18
 0.167    7399  99.97   227.7   208.0  0.18  0.16     399   232.2   207.6  0.21  0.19
 0.278    9435 100.00   123.9   114.1  0.21  0.19     475   122.8   113.9  0.24  0.21
 0.389   11096 100.00    50.2    62.5  0.41  0.36     545    49.9    61.8  0.42  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3220   0.924   1106   0.831   4326   0.900  0.950  0.9705  0.9729  0.9302  0.9364
  0.1670   6275   0.882   1124   0.782   7399   0.866  1.062  0.9526  0.9603  0.9119  0.9354
  0.2780   8312   0.837   1123   0.757   9435   0.828  1.018  0.9359  0.9460  0.8979  0.9271
  0.3890   9973   0.552   1134   0.489  11107   0.546  0.561  0.7520  0.7661  0.7445  0.7725
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32267
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8396
Overall R factor                     =     0.2076
Free R factor                        =     0.2262
Average Fourier shell correlation    =     0.8910
AverageFree Fourier shell correlation=     0.8834
Overall weighted R factor            =     0.1750
Free weighted R factor               =     0.1917
Overall weighted R2 factor           =     0.2035
Free weighted R2 factor              =     0.2142
Average correlation coefficient      =     0.8771
Overall correlation coefficient      =     0.9592
Free correlation coefficient         =     0.9513
Cruickshanks DPI for coordinate error=     0.0859
DPI based on free R factor           =     0.0823
Overall figure of merit              =     0.7492
ML based su of positional parameters =     0.0700
ML based su of thermal parameters    =     2.0705
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156363.59       13173.639       990394.31      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.37776142    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    978450.19    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0679
Partial structure    1: scale =     0.3938, B  =   40.4552
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2073
Free R factor                        =     0.2249
Average Fourier shell correlation    =     0.9079
AverageFree Fourier shell correlation=     0.8986
Average correlation coefficient      =     0.8774
Overall figure of merit              =     0.7784
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155234.88       8283.5547       978450.19       990394.31    


     CGMAT cycle number =      3

 Weight matrix   0.39573354    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    976800.75    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0009
Partial structure    1: scale =     0.3938, B  =   40.4382
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2063
Free R factor                        =     0.2244
Average Fourier shell correlation    =     0.9144
AverageFree Fourier shell correlation=     0.9055
Average correlation coefficient      =     0.8795
Overall figure of merit              =     0.7942
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    154868.98       8920.8848       976800.75       978450.19    


     CGMAT cycle number =      4

 Weight matrix   0.35714760    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    888979.06    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0213
Partial structure    1: scale =     0.3936, B  =   40.1416
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2060
Free R factor                        =     0.2241
Average Fourier shell correlation    =     0.9129
AverageFree Fourier shell correlation=     0.9031
Average correlation coefficient      =     0.8805
Overall figure of merit              =     0.7883
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    154863.81       9117.6816       888979.06       976800.75    


     CGMAT cycle number =      5

 Weight matrix   0.32678503    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    808710.63    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0208
Partial structure    1: scale =     0.3937, B  =   40.0526
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2063
Free R factor                        =     0.2242
Average Fourier shell correlation    =     0.9142
AverageFree Fourier shell correlation=     0.9048
Average correlation coefficient      =     0.8804
Overall figure of merit              =     0.7926
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    154849.39       8911.2119       808710.63       888979.06    


     CGMAT cycle number =      6

 Weight matrix   0.32276294    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809106.38    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0196
Partial structure    1: scale =     0.3937, B  =   40.0634
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2066
Free R factor                        =     0.2243
Average Fourier shell correlation    =     0.9123
AverageFree Fourier shell correlation=     0.9023
Average correlation coefficient      =     0.8801
Overall figure of merit              =     0.7865
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03

 fvalues    154891.14       8601.4492       808616.56       808710.63    


     CGMAT cycle number =      7

 Weight matrix   0.32343984    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809026.19    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0192
Partial structure    1: scale =     0.3934, B  =   39.9376
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2067
Free R factor                        =     0.2244
Average Fourier shell correlation    =     0.9128
AverageFree Fourier shell correlation=     0.9030
Average correlation coefficient      =     0.8800
Overall figure of merit              =     0.7883
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    154939.22       8522.2441       809241.06       808616.56    

 fvalues    154939.22       8522.2441       809185.25       808785.69    
 fvalues    154939.22       8522.2441       809185.25       808785.69    


     CGMAT cycle number =      8

 Weight matrix   0.32243872    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809139.31    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =    0.0167
Partial structure    1: scale =     0.3929, B  =   39.8396
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2067
Free R factor                        =     0.2245
Average Fourier shell correlation    =     0.9122
AverageFree Fourier shell correlation=     0.9023
Average correlation coefficient      =     0.8800
Overall figure of merit              =     0.7865
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02

 fvalues    154912.67       8510.8906       808637.19       808785.69    


     CGMAT cycle number =      9

 Weight matrix   0.32311690    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    809058.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0211
Partial structure    1: scale =     0.3926, B  =   39.9238
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2067
Free R factor                        =     0.2244
Average Fourier shell correlation    =     0.9127
AverageFree Fourier shell correlation=     0.9030
Average correlation coefficient      =     0.8800
Overall figure of merit              =     0.7882
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    154949.72       8499.0400       809180.19       808637.19    

 fvalues    154949.72       8499.0400       809200.00       808816.69    
 fvalues    154949.72       8499.0400       809200.00       808816.69    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.32186192    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                39.4
Norm of Geom. positional gradient                39.6
Norm of X_ray B-factor gradient                  104.
Norm of Geom. B-factor gradient                  103.
Product of X_ray and Geom posit. gradients     -0.151E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.345E+08
 Cosine of angle between them                      -0.995


Residuals: XRAY=     0.8007E+06 GEOM=      8497.     TOTAL=     0.8092E+06
 function value    809199.50    

-------------------------------------------------------------------------------
             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     1.797     1.644
Bond angles  : others                          3238     1.499     1.580
Torsion angles, period  1. refined              185     6.914     5.000
Torsion angles, period  2. refined               90    35.795    22.778
Torsion angles, period  3. refined              268    13.547    15.000
Torsion angles, period  4. refined                9    10.807    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   300     0.247     0.200
VDW repulsions.others                          1354     0.196     0.200
VDW; torsion: refined_atoms                     724     0.173     0.200
VDW; torsion.others                             780     0.084     0.200
HBOND: refined_atoms                            224     0.199     0.200
HBOND.others                                      1     0.112     0.200
VDW repulsions: symmetry: refined_atoms           9     0.190     0.200
VDW repulsions: symmetry: others                 27     0.179     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           746     1.795     1.620
M. chain bond B values: others                  746     1.792     1.620
M. chain angle B values: refined atoms          929     2.785     2.420
M. chain angle B values: others                 930     2.783     2.420
S. chain bond B values: refined atoms           811     3.191     2.039
S. chain bond B values: others                  810     3.185     2.039
S. chain angle B values: refined atoms         1177     4.934     2.885
S. chain angle B values: others                1178     4.931     2.885
Long range B values: refined atoms             1849     7.693    22.520
Long range B values: others                    1750     7.215    20.882
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0221
Partial structure    1: scale =     0.3925, B  =   39.9344
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4326 100.00   406.3   416.0  0.17  0.17     221   405.9   411.1  0.18  0.18
 0.167    7399  99.97   228.1   208.3  0.18  0.16     399   232.5   208.0  0.21  0.19
 0.278    9435 100.00   124.1   114.5  0.21  0.19     475   123.0   114.4  0.24  0.21
 0.389   11096 100.00    50.2    62.5  0.41  0.36     545    50.0    61.7  0.42  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3220   0.935   1106   0.849   4326   0.913  0.951  0.9731  0.9755  0.9316  0.9368
  0.1670   6275   0.896   1124   0.798   7399   0.881  1.062  0.9569  0.9639  0.9147  0.9358
  0.2780   8312   0.853   1123   0.774   9435   0.844  1.018  0.9426  0.9522  0.9001  0.9281
  0.3890   9973   0.631   1134   0.573  11107   0.625  0.595  0.7985  0.8191  0.7442  0.7799
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32267
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8396
Overall R factor                     =     0.2067
Free R factor                        =     0.2244
Average Fourier shell correlation    =     0.9122
AverageFree Fourier shell correlation=     0.9022
Overall weighted R factor            =     0.1745
Free weighted R factor               =     0.1900
Overall weighted R2 factor           =     0.2027
Free weighted R2 factor              =     0.2119
Average correlation coefficient      =     0.8800
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9523
Cruickshanks DPI for coordinate error=     0.0856
DPI based on free R factor           =     0.0816
Overall figure of merit              =     0.7863
ML based su of positional parameters =     0.0613
ML based su of thermal parameters    =     1.7905
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    154921.59       8496.6016       808669.00       808816.69    

    ****                              VDW outliers                              ****

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

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

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R13_1-50A.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     1.797     1.644
Bond angles  : others                          3238     1.499     1.580
Torsion angles, period  1. refined              185     6.914     5.000
Torsion angles, period  2. refined               90    35.789    22.778
Torsion angles, period  3. refined              268    13.544    15.000
Torsion angles, period  4. refined                9    10.803    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   300     0.247     0.200
VDW repulsions.others                          1355     0.196     0.200
VDW; torsion: refined_atoms                     724     0.173     0.200
VDW; torsion.others                             781     0.084     0.200
HBOND: refined_atoms                            224     0.199     0.200
HBOND.others                                      1     0.112     0.200
VDW repulsions: symmetry: refined_atoms           9     0.190     0.200
VDW repulsions: symmetry: others                 27     0.179     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           746     1.794     1.619
M. chain bond B values: others                  746     1.791     1.619
M. chain angle B values: refined atoms          929     2.784     2.420
M. chain angle B values: others                 930     2.783     2.420
S. chain bond B values: refined atoms           811     3.190     2.039
S. chain bond B values: others                  810     3.184     2.039
S. chain angle B values: refined atoms         1177     4.932     2.885
S. chain angle B values: others                1178     4.930     2.884
Long range B values: refined atoms             1849     7.692    22.519
Long range B values: others                    1750     7.213    20.880
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    0.0210
Partial structure    1: scale =     0.3925, B  =   39.9291
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4326 100.00   406.3   416.0  0.17  0.17     221   405.9   411.2  0.18  0.18
 0.167    7399  99.97   228.1   208.3  0.18  0.16     399   232.5   208.0  0.21  0.19
 0.278    9435 100.00   124.1   114.5  0.21  0.19     475   123.0   114.4  0.24  0.21
 0.389   11096 100.00    50.2    62.5  0.41  0.36     545    50.0    61.8  0.42  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3220   0.935   1106   0.849   4326   0.913  0.951  0.9731  0.9755  0.9316  0.9368
  0.1670   6275   0.896   1124   0.798   7399   0.881  1.062  0.9569  0.9639  0.9147  0.9358
  0.2780   8312   0.853   1123   0.774   9435   0.844  1.018  0.9426  0.9522  0.9001  0.9281
  0.3890   9973   0.637   1134   0.578  11107   0.630  0.599  0.8007  0.8207  0.7441  0.7798
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32267
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8396
Overall R factor                     =     0.2067
Free R factor                        =     0.2244
Average Fourier shell correlation    =     0.9127
AverageFree Fourier shell correlation=     0.9030
Overall weighted R factor            =     0.1745
Free weighted R factor               =     0.1901
Overall weighted R2 factor           =     0.2027
Free weighted R2 factor              =     0.2119
Average correlation coefficient      =     0.8800
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9523
Cruickshanks DPI for coordinate error=     0.0856
DPI based on free R factor           =     0.0816
Overall figure of merit              =     0.7882
ML based su of positional parameters =     0.0613
ML based su of thermal parameters    =     1.7905
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.21
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2076   0.2262   0.749      156364.    8084.5   0.0126  0.947   1.804  1.046   0.086
       1   0.2073   0.2249   0.778      155235.    8051.0   0.0125  0.941   1.786  1.035   0.087
       2   0.2063   0.2244   0.794      154869.    8037.0   0.0136  1.025   1.840  1.067   0.090
       3   0.2060   0.2241   0.788      154864.    8038.0   0.0138  1.038   1.863  1.080   0.091
       4   0.2063   0.2242   0.793      154849.    8035.5   0.0132  0.996   1.844  1.069   0.089
       5   0.2066   0.2243   0.786      154986.    8040.4   0.0126  0.950   1.810  1.049   0.087
       6   0.2067   0.2244   0.788      154986.    8040.3   0.0125  0.945   1.800  1.043   0.087
       7   0.2067   0.2245   0.786      155010.    8041.8   0.0125  0.945   1.799  1.043   0.087
       8   0.2067   0.2244   0.788      154996.    8040.8   0.0125  0.944   1.798  1.042   0.087
       9   0.2067   0.2244   0.786      155024.    8042.3   0.0125  0.944   1.797  1.042   0.087
      10   0.2067   0.2244   0.788      155002.    8041.1   0.0125  0.943   1.797  1.042   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2076   0.2067
             R free    0.2262   0.2244
     Rms BondLength    0.0126   0.0125
      Rms BondAngle    1.8040   1.7969
     Rms ChirVolume    0.0859   0.0867
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      64.1s System:    0.2s Elapsed:     1:04