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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: 21:51:07 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.42     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 16
  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_R16_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R16_1-42A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R16_1-42A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.1240
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4200
  Estimated number of reflections :      51186
  Free R exclusion - flag equals:    16
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    41.9635  1.4200

  Damping factors:     1.0000  1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :CDO_complete_R16_1-50A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.052 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=   2.187 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=   1.829 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=   2.204 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=   2.391 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=   2.397 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=   2.059 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  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  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:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


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


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

FreeR flag                           16
Number of "free" reflections       1965
Number of   all  reflections      39817
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          39817

   Current auto weighting coefficient =    6.0498405    

 mode : HKRF


######  TLS Group Definitions ######



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.894 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.26088807    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                39.1
Norm of Geom. positional gradient                79.4
Norm of X_ray B-factor gradient                  104.
Norm of Geom. B-factor gradient                 0.238E+05
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.457
Product of X_ray and Geom B-fact gradients     -0.305E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1065E+07 GEOM=     0.2686E+05 TOTAL=     0.1092E+07
 function value    1091727.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.746     1.644
Bond angles  : others                          3242     2.339     1.582
Torsion angles, period  1. refined              184     6.874     5.000
Torsion angles, period  2. refined               90    35.754    22.778
Torsion angles, period  3. refined              268    13.004    15.000
Torsion angles, period  4. refined                9    11.865    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   296     0.269     0.200
VDW repulsions.others                          1336     0.231     0.200
VDW; torsion: refined_atoms                     714     0.173     0.200
VDW; torsion.others                             716     0.080     0.200
HBOND: refined_atoms                            217     0.194     0.200
HBOND.others                                      2     0.075     0.200
VDW repulsions: symmetry: refined_atoms           8     0.197     0.200
VDW repulsions: symmetry: others                 22     0.180     0.200
HBOND: symmetry: refined_atoms                   22     0.192     0.200
M. chain bond B values: refined atoms           745     1.743     1.625
M. chain bond B values: others                  745     1.740     1.625
M. chain angle B values: refined atoms          926     2.709     2.425
M. chain angle B values: others                 927     2.708     2.425
S. chain bond B values: refined atoms           811     3.038     2.028
S. chain bond B values: others                  810     3.031     2.027
S. chain angle B values: refined atoms         1177     4.698     2.875
S. chain angle B values: others                1178     4.696     2.875
Long range B values: refined atoms             1833     6.952    22.251
Long range B values: others                    1742     6.644    20.694
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.7921
Partial structure    1: scale =     0.3956, B  =   46.1309
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5056 100.00   379.5   389.6  0.18  0.18     273   372.8   384.7  0.20  0.21
 0.186    8666  99.98   205.9   182.1  0.19  0.17     477   198.5   177.4  0.22  0.20
 0.310   11096 100.00    91.8    88.4  0.23  0.20     551    90.5    88.5  0.28  0.24
 0.434   12844  98.63    38.5    47.9  0.47  0.46     651    40.1    48.1  0.44  0.42
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3825   0.912   1231   0.804   5056   0.886  0.947  0.9626  0.9693  0.9174  0.9335
  0.1863   7417   0.875   1249   0.774   8666   0.860  1.098  0.9455  0.9600  0.8888  0.9386
  0.3102   9841   0.782   1255   0.710  11096   0.774  0.940  0.9115  0.9290  0.8510  0.9122
  0.4340  11593   0.408   1251   0.361  12844   0.403  0.386  0.6593  0.6302  0.6764  0.6408
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37662
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9276
Overall R factor                     =     0.2194
Free R factor                        =     0.2453
Average Fourier shell correlation    =     0.8397
AverageFree Fourier shell correlation=     0.8428
Overall weighted R factor            =     0.1833
Free weighted R factor               =     0.2114
Overall weighted R2 factor           =     0.2133
Free weighted R2 factor              =     0.2393
Average correlation coefficient      =     0.8286
Overall correlation coefficient      =     0.9594
Free correlation coefficient         =     0.9477
Cruickshanks DPI for coordinate error=     0.0781
DPI based on free R factor           =     0.0784
Overall figure of merit              =     0.6824
ML based su of positional parameters =     0.0738
ML based su of thermal parameters    =     2.1616
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176015.91       26859.260       1091727.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30813399    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1069805.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0579
Partial structure    1: scale =     0.3955, B  =   45.4429
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2191
Free R factor                        =     0.2446
Average Fourier shell correlation    =     0.8453
AverageFree Fourier shell correlation=     0.8471
Average correlation coefficient      =     0.8287
Overall figure of merit              =     0.6929
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175162.64       10099.808       1069805.8       1091727.4    


     CGMAT cycle number =      3

 Weight matrix   0.30964679    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068059.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0113
Partial structure    1: scale =     0.3954, B  =   41.9132
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2182
Free R factor                        =     0.2442
Average Fourier shell correlation    =     0.8442
AverageFree Fourier shell correlation=     0.8453
Average correlation coefficient      =     0.8298
Overall figure of merit              =     0.6904
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    175032.59       9139.7207       1068059.0       1069805.8    


     CGMAT cycle number =      4

 Weight matrix   0.31261098    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067131.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0116
Partial structure    1: scale =     0.3954, B  =   38.8410
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2180
Free R factor                        =     0.2441
Average Fourier shell correlation    =     0.8466
AverageFree Fourier shell correlation=     0.8478
Average correlation coefficient      =     0.8301
Overall figure of merit              =     0.6944
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    174940.69       8768.3027       1067131.5       1068059.0    


     CGMAT cycle number =      5

 Weight matrix   0.30996770    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067400.1    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0046
Partial structure    1: scale =     0.3955, B  =   38.8777
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2180
Free R factor                        =     0.2440
Average Fourier shell correlation    =     0.8438
AverageFree Fourier shell correlation=     0.8448
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.6900
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03

 fvalues    174940.38       8717.5137       1067078.9       1067131.5    


     CGMAT cycle number =      6

 Weight matrix   0.30942610    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067418.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0000
Partial structure    1: scale =     0.3956, B  =   38.8923
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2179
Free R factor                        =     0.2440
Average Fourier shell correlation    =     0.8435
AverageFree Fourier shell correlation=     0.8444
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.6895
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03

 fvalues    174938.47       8725.3789       1067075.3       1067078.9    


     CGMAT cycle number =      7

 Weight matrix   0.30908722    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067432.6    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0001
Partial structure    1: scale =     0.3956, B  =   38.8923
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2179
Free R factor                        =     0.2440
Average Fourier shell correlation    =     0.8435
AverageFree Fourier shell correlation=     0.8443
Average correlation coefficient      =     0.8302
Overall figure of merit              =     0.6894
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    174941.64       8728.0527       1067434.3       1067075.3    

 fvalues    174941.64       8728.0527       1067412.8       1067097.0    
 fvalues    174941.64       8728.0527       1067412.8       1067097.0    


     CGMAT cycle number =      8

 Weight matrix   0.30941880    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067423.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0069
Partial structure    1: scale =     0.3956, B  =   38.9131
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2179
Free R factor                        =     0.2440
Average Fourier shell correlation    =     0.8438
AverageFree Fourier shell correlation=     0.8447
Average correlation coefficient      =     0.8302
Overall figure of merit              =     0.6899
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    174946.39       8725.2246       1067473.9       1067097.0    

 fvalues    174946.39       8725.2246       1067481.1       1067123.0    
 fvalues    174946.39       8725.2246       1067481.1       1067123.0    


     CGMAT cycle number =      9

 Weight matrix   0.30898929    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067485.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0053
Partial structure    1: scale =     0.3956, B  =   38.9185
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2179
Free R factor                        =     0.2440
Average Fourier shell correlation    =     0.8435
AverageFree Fourier shell correlation=     0.8444
Average correlation coefficient      =     0.8302
Overall figure of merit              =     0.6895
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    174950.05       8725.0146       1067499.9       1067123.0    

 fvalues    174950.05       8725.0146       1067494.4       1067144.9    
 fvalues    174950.05       8725.0146       1067494.4       1067144.9    


     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.= 0.911 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  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.30883786    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                42.8
Norm of Geom. positional gradient                42.9
Norm of X_ray B-factor gradient                  101.
Norm of Geom. B-factor gradient                  101.
Product of X_ray and Geom posit. gradients     -0.178E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.330E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.1059E+07 GEOM=      8725.     TOTAL=     0.1067E+07
 function value    1067497.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.820     1.644
Bond angles  : others                          3242     1.502     1.582
Torsion angles, period  1. refined              184     6.863     5.000
Torsion angles, period  2. refined               90    35.687    22.778
Torsion angles, period  3. refined              268    12.987    15.000
Torsion angles, period  4. refined                9    12.071    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.271     0.200
VDW repulsions.others                          1360     0.206     0.200
VDW; torsion: refined_atoms                     716     0.174     0.200
VDW; torsion.others                             769     0.084     0.200
HBOND: refined_atoms                            218     0.197     0.200
HBOND.others                                      1     0.132     0.200
VDW repulsions: symmetry: refined_atoms           8     0.198     0.200
VDW repulsions: symmetry: others                 22     0.167     0.200
HBOND: symmetry: refined_atoms                   20     0.200     0.200
M. chain bond B values: refined atoms           745     1.874     1.699
M. chain bond B values: others                  745     1.870     1.699
M. chain angle B values: refined atoms          926     2.848     2.535
M. chain angle B values: others                 927     2.847     2.535
S. chain bond B values: refined atoms           811     3.299     2.126
S. chain bond B values: others                  810     3.292     2.126
S. chain angle B values: refined atoms         1177     5.051     3.012
S. chain angle B values: others                1178     5.049     3.012
Long range B values: refined atoms             1838     7.186    23.274
Long range B values: others                    1746     6.914    21.713
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0037
Partial structure    1: scale =     0.3956, B  =   38.9166
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5056 100.00   379.7   389.7  0.18  0.18     273   373.0   384.7  0.20  0.21
 0.186    8666  99.98   206.0   182.3  0.19  0.16     477   198.6   177.4  0.22  0.20
 0.310   11096 100.00    91.8    88.5  0.23  0.20     551    90.5    88.6  0.27  0.24
 0.434   12844  98.63    38.6    47.9  0.47  0.46     651    40.1    48.1  0.44  0.42
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3825   0.921   1231   0.821   5056   0.896  0.949  0.9654  0.9719  0.9180  0.9342
  0.1863   7417   0.894   1249   0.794   8666   0.879  1.099  0.9511  0.9650  0.8902  0.9405
  0.3102   9841   0.809   1255   0.737  11096   0.801  0.950  0.9202  0.9373  0.8517  0.9138
  0.4340  11593   0.387   1251   0.345  12844   0.383  0.368  0.6511  0.6299  0.6743  0.6426
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37662
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9276
Overall R factor                     =     0.2179
Free R factor                        =     0.2440
Average Fourier shell correlation    =     0.8434
AverageFree Fourier shell correlation=     0.8443
Overall weighted R factor            =     0.1820
Free weighted R factor               =     0.2098
Overall weighted R2 factor           =     0.2122
Free weighted R2 factor              =     0.2384
Average correlation coefficient      =     0.8302
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9481
Cruickshanks DPI for coordinate error=     0.0776
DPI based on free R factor           =     0.0779
Overall figure of merit              =     0.6894
ML based su of positional parameters =     0.0678
ML based su of thermal parameters    =     1.9831
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    174953.81       8724.9180       1067469.3       1067144.9    

 fvalues    174953.81       8724.9180       1067465.4       1067167.5    
 fvalues    174953.81       8724.9180       1067465.4       1067167.5    

    ****                              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.= 0.911 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
          28          24          36  0.70425701      2.37302221E-02  0.70425248    
          36           8          36  0.70425701      2.37302221E-02  0.70425248    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R16_1-42A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.820     1.644
Bond angles  : others                          3242     1.502     1.582
Torsion angles, period  1. refined              184     6.863     5.000
Torsion angles, period  2. refined               90    35.687    22.778
Torsion angles, period  3. refined              268    12.987    15.000
Torsion angles, period  4. refined                9    12.071    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.271     0.200
VDW repulsions.others                          1360     0.206     0.200
VDW; torsion: refined_atoms                     716     0.174     0.200
VDW; torsion.others                             769     0.084     0.200
HBOND: refined_atoms                            218     0.197     0.200
HBOND.others                                      1     0.132     0.200
VDW repulsions: symmetry: refined_atoms           8     0.198     0.200
VDW repulsions: symmetry: others                 22     0.167     0.200
HBOND: symmetry: refined_atoms                   20     0.200     0.200
M. chain bond B values: refined atoms           745     1.874     1.699
M. chain bond B values: others                  745     1.870     1.699
M. chain angle B values: refined atoms          926     2.848     2.535
M. chain angle B values: others                 927     2.847     2.535
S. chain bond B values: refined atoms           811     3.299     2.126
S. chain bond B values: others                  810     3.292     2.125
S. chain angle B values: refined atoms         1177     5.051     3.012
S. chain angle B values: others                1178     5.049     3.012
Long range B values: refined atoms             1838     7.186    23.274
Long range B values: others                    1746     6.914    21.713
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0083
Partial structure    1: scale =     0.3956, B  =   38.9153
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.33 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5056 100.00   379.7   389.7  0.18  0.18     273   373.0   384.7  0.20  0.21
 0.186    8666  99.98   206.0   182.4  0.19  0.16     477   198.6   177.5  0.22  0.20
 0.310   11096 100.00    91.8    88.6  0.23  0.20     551    90.5    88.7  0.28  0.24
 0.434   12844  98.63    38.6    47.9  0.47  0.46     651    40.1    48.1  0.44  0.42
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3825   0.921   1231   0.821   5056   0.896  0.949  0.9654  0.9719  0.9180  0.9342
  0.1863   7417   0.894   1249   0.794   8666   0.879  1.099  0.9511  0.9650  0.8902  0.9406
  0.3102   9841   0.809   1255   0.737  11096   0.801  0.950  0.9202  0.9373  0.8517  0.9138
  0.4340  11593   0.389   1251   0.347  12844   0.385  0.369  0.6521  0.6308  0.6742  0.6425
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37662
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.9276
Overall R factor                     =     0.2179
Free R factor                        =     0.2440
Average Fourier shell correlation    =     0.8438
AverageFree Fourier shell correlation=     0.8447
Overall weighted R factor            =     0.1820
Free weighted R factor               =     0.2098
Overall weighted R2 factor           =     0.2121
Free weighted R2 factor              =     0.2384
Average correlation coefficient      =     0.8302
Overall correlation coefficient      =     0.9600
Free correlation coefficient         =     0.9481
Cruickshanks DPI for coordinate error=     0.0776
DPI based on free R factor           =     0.0779
Overall figure of merit              =     0.6899
ML based su of positional parameters =     0.0678
ML based su of thermal parameters    =     1.9831
-----------------------------------------------------------------------------
  Time in seconds: CPU =        38.93
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2194   0.2453   0.682      176016.    9343.1   0.0119  0.903   1.746  1.014   0.087
       1   0.2191   0.2446   0.693      175163.    9324.7   0.0121  0.913   1.741  1.011   0.088
       2   0.2182   0.2442   0.690      175033.    9323.9   0.0129  0.980   1.787  1.039   0.090
       3   0.2180   0.2441   0.694      174941.    9320.5   0.0129  0.983   1.804  1.048   0.091
       4   0.2180   0.2440   0.690      174993.    9322.9   0.0130  0.986   1.812  1.053   0.091
       5   0.2179   0.2440   0.690      174995.    9323.1   0.0130  0.987   1.817  1.055   0.091
       6   0.2179   0.2440   0.689      174997.    9323.4   0.0130  0.987   1.819  1.056   0.091
       7   0.2179   0.2440   0.690      174996.    9323.7   0.0130  0.986   1.820  1.057   0.091
       8   0.2179   0.2440   0.689      175006.    9324.1   0.0130  0.986   1.820  1.057   0.091
       9   0.2179   0.2440   0.689      175008.    9324.2   0.0130  0.986   1.820  1.057   0.091
      10   0.2179   0.2440   0.690      175002.    9324.0   0.0130  0.986   1.820  1.057   0.091
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2194   0.2179
             R free    0.2453   0.2440
     Rms BondLength    0.0119   0.0130
      Rms BondAngle    1.7455   1.8199
     Rms ChirVolume    0.0868   0.0913
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      71.7s System:    0.4s Elapsed:     1:12