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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 17:33:21 


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


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

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

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

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

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

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

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

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

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.60     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 3
  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_R03_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R03_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R03_1-60A.mtz

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

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

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


  Residual                               : Rice Maximum Likelihood for Fs

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

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


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

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:     3
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.6000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R03_1-70A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.035 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=   2.204 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=   1.819 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=   2.215 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=   2.372 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=   2.390 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=   2.102 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                            3
Number of "free" reflections       1342
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.883 id.= 3.000 dev= -2.12 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.31682506    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                42.3
Norm of Geom. positional gradient                79.9
Norm of X_ray B-factor gradient                  126.
Norm of Geom. B-factor gradient                  111.
Product of X_ray and Geom posit. gradients     -0.143E+08
 Cosine of angle between them                      -0.437
Product of X_ray and Geom B-fact gradients     -0.394E+08
 Cosine of angle between them                      -0.878


Residuals: XRAY=     0.8738E+06 GEOM=     0.1320E+05 TOTAL=     0.8870E+06
 function value    887016.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.774     1.644
Bond angles  : others                          3238     2.346     1.580
Torsion angles, period  1. refined              185     6.899     5.000
Torsion angles, period  2. refined               90    36.672    22.778
Torsion angles, period  3. refined              268    14.025    15.000
Torsion angles, period  4. refined                9    12.093    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.014     0.020
VDW repulsions: refined_atoms                   297     0.244     0.200
VDW repulsions.others                          1323     0.223     0.200
VDW; torsion: refined_atoms                     728     0.171     0.200
VDW; torsion.others                             698     0.082     0.200
HBOND: refined_atoms                            216     0.196     0.200
HBOND.others                                      1     0.022     0.200
VDW repulsions: symmetry: refined_atoms           7     0.243     0.200
VDW repulsions: symmetry: others                 26     0.172     0.200
HBOND: symmetry: refined_atoms                   20     0.201     0.200
HBOND: symmetry: others                           1     0.032     0.200
M. chain bond B values: refined atoms           746     1.625     1.394
M. chain bond B values: others                  746     1.622     1.394
M. chain angle B values: refined atoms          929     2.573     2.079
M. chain angle B values: others                 930     2.571     2.079
S. chain bond B values: refined atoms           811     3.002     1.794
S. chain bond B values: others                  810     2.995     1.793
S. chain angle B values: refined atoms         1177     4.679     2.524
S. chain angle B values: others                1178     4.677     2.523
Long range B values: refined atoms             1840     7.195    19.483
Long range B values: others                    1748     6.919    18.050
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    1.2128
Partial structure    1: scale =     0.3846, B  =   43.2081
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3604 100.00   431.0   441.4  0.17  0.17     178   453.1   451.9  0.19  0.20
 0.147    6122  99.97   258.7   243.9  0.16  0.15     322   255.2   241.6  0.20  0.18
 0.244    7828 100.00   167.0   151.0  0.19  0.17     390   171.0   154.8  0.22  0.20
 0.342    9139 100.00    71.2    85.6  0.33  0.26     451    73.0    88.6  0.35  0.29
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2637   0.915    967   0.802   3604   0.885  0.947  0.9655  0.9701  0.8986  0.9382
  0.1468   5139   0.895    983   0.802   6122   0.880  1.026  0.9528  0.9648  0.9071  0.9419
  0.2444   6829   0.857    999   0.754   7828   0.844  1.052  0.9458  0.9531  0.9021  0.9361
  0.3419   8154   0.678    989   0.598   9143   0.669  0.707  0.8591  0.8706  0.8264  0.8507
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26696
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.7864
Overall R factor                     =     0.1928
Free R factor                        =     0.2221
Average Fourier shell correlation    =     0.9298
AverageFree Fourier shell correlation=     0.9209
Overall weighted R factor            =     0.1666
Free weighted R factor               =     0.1935
Overall weighted R2 factor           =     0.1972
Free weighted R2 factor              =     0.2311
Average correlation coefficient      =     0.9085
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9395
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0947
Overall figure of merit              =     0.7977
ML based su of positional parameters =     0.0694
ML based su of thermal parameters    =     2.1130
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134440.41       13201.030       887016.94      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.38133761    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    875390.19    

-------------------------------------------------------------------------------
             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 =     0.0442, B  =   -0.0611
Partial structure    1: scale =     0.3853, B  =   43.3824
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1921
Free R factor                        =     0.2214
Average Fourier shell correlation    =     0.9401
AverageFree Fourier shell correlation=     0.9316
Average correlation coefficient      =     0.9104
Overall figure of merit              =     0.8264
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133391.13       8394.2695       875390.19       887016.94    


     CGMAT cycle number =      3

 Weight matrix   0.39326179    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    874163.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0273
Partial structure    1: scale =     0.3850, B  =   43.1139
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1912
Free R factor                        =     0.2207
Average Fourier shell correlation    =     0.9425
AverageFree Fourier shell correlation=     0.9339
Average correlation coefficient      =     0.9125
Overall figure of merit              =     0.8322
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    133114.27       8967.1797       874163.63       875390.19    


     CGMAT cycle number =      4

 Weight matrix   0.35939062    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    795209.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0129
Partial structure    1: scale =     0.3852, B  =   43.1540
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1910
Free R factor                        =     0.2205
Average Fourier shell correlation    =     0.9431
AverageFree Fourier shell correlation=     0.9344
Average correlation coefficient      =     0.9135
Overall figure of merit              =     0.8334
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    133027.56       9179.3848       795209.31       874163.63    


     CGMAT cycle number =      5

 Weight matrix   0.32689700    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723704.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0104
Partial structure    1: scale =     0.3850, B  =   42.8684
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1913
Free R factor                        =     0.2207
Average Fourier shell correlation    =     0.9431
AverageFree Fourier shell correlation=     0.9344
Average correlation coefficient      =     0.9135
Overall figure of merit              =     0.8335
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    133055.25       8983.3418       723704.69       795209.31    


     CGMAT cycle number =      6

 Weight matrix   0.32613254    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723740.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0158
Partial structure    1: scale =     0.3852, B  =   42.9342
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2207
Average Fourier shell correlation    =     0.9430
AverageFree Fourier shell correlation=     0.9344
Average correlation coefficient      =     0.9132
Overall figure of merit              =     0.8334
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    133123.52       8668.0264       723766.13       723704.69    

 fvalues    133123.52       8668.0264       723771.63       723756.06    
 fvalues    133123.52       8668.0264       723771.63       723756.06    


     CGMAT cycle number =      7

 Weight matrix   0.32588944    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723764.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0141
Partial structure    1: scale =     0.3852, B  =   42.8915
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2207
Average Fourier shell correlation    =     0.9430
AverageFree Fourier shell correlation=     0.9343
Average correlation coefficient      =     0.9132
Overall figure of merit              =     0.8334
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    133127.97       8647.6865       723762.00       723756.06    

 fvalues    133127.97       8647.6865       723780.75       723759.69    
 fvalues    133127.97       8647.6865       723780.75       723759.69    


     CGMAT cycle number =      8

 Weight matrix   0.32570541    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723776.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0120
Partial structure    1: scale =     0.3853, B  =   42.8964
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2207
Average Fourier shell correlation    =     0.9429
AverageFree Fourier shell correlation=     0.9343
Average correlation coefficient      =     0.9132
Overall figure of merit              =     0.8333
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    133133.73       8638.6777       723777.81       723759.69    
 fvalues    133133.73       8638.6777       723777.81       723781.63    


     CGMAT cycle number =      9

 Weight matrix   0.32575417    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    723772.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0126
Partial structure    1: scale =     0.3853, B  =   42.8863
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2208
Average Fourier shell correlation    =     0.9429
AverageFree Fourier shell correlation=     0.9343
Average correlation coefficient      =     0.9132
Overall figure of merit              =     0.8333
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    133133.88       8628.3584       723772.13       723781.63    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.900 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        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.32576573    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                38.9
Norm of Geom. positional gradient                39.2
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.147E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.373E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.7151E+06 GEOM=      8616.     TOTAL=     0.7238E+06
 function value    723763.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.778     1.644
Bond angles  : others                          3238     1.498     1.580
Torsion angles, period  1. refined              185     6.846     5.000
Torsion angles, period  2. refined               90    36.251    22.778
Torsion angles, period  3. refined              268    13.754    15.000
Torsion angles, period  4. refined                9    12.108    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                   298     0.244     0.200
VDW repulsions.others                          1342     0.199     0.200
VDW; torsion: refined_atoms                     731     0.171     0.200
VDW; torsion.others                             744     0.086     0.200
HBOND: refined_atoms                            214     0.198     0.200
HBOND.others                                      1     0.089     0.200
VDW repulsions: symmetry: refined_atoms           8     0.221     0.200
VDW repulsions: symmetry: others                 24     0.169     0.200
HBOND: symmetry: refined_atoms                   18     0.202     0.200
HBOND: symmetry: others                           1     0.050     0.200
M. chain bond B values: refined atoms           746     1.690     1.511
M. chain bond B values: others                  746     1.687     1.511
M. chain angle B values: refined atoms          929     2.653     2.257
M. chain angle B values: others                 930     2.652     2.256
S. chain bond B values: refined atoms           811     3.113     1.916
S. chain bond B values: others                  810     3.107     1.916
S. chain angle B values: refined atoms         1177     4.808     2.705
S. chain angle B values: others                1178     4.806     2.705
Long range B values: refined atoms             1844     7.303    21.004
Long range B values: others                    1751     7.008    19.525
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0119
Partial structure    1: scale =     0.3853, B  =   42.8886
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3604 100.00   431.4   442.0  0.17  0.18     178   453.4   450.5  0.19  0.20
 0.147    6122  99.97   258.9   243.8  0.16  0.15     322   255.4   240.9  0.20  0.18
 0.244    7828 100.00   167.1   151.2  0.19  0.17     390   171.1   154.8  0.22  0.20
 0.342    9139 100.00    71.3    85.3  0.32  0.26     451    73.0    88.3  0.35  0.28
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2637   0.931    967   0.833   3604   0.905  0.951  0.9692  0.9737  0.8979  0.9375
  0.1468   5139   0.897    983   0.805   6122   0.882  1.026  0.9537  0.9655  0.9090  0.9422
  0.2444   6829   0.873    999   0.773   7828   0.860  1.053  0.9506  0.9579  0.9024  0.9354
  0.3419   8154   0.758    989   0.677   9143   0.749  0.741  0.8927  0.9029  0.8320  0.8652
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26696
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.7864
Overall R factor                     =     0.1919
Free R factor                        =     0.2208
Average Fourier shell correlation    =     0.9429
AverageFree Fourier shell correlation=     0.9343
Overall weighted R factor            =     0.1667
Free weighted R factor               =     0.1927
Overall weighted R2 factor           =     0.1977
Free weighted R2 factor              =     0.2303
Average correlation coefficient      =     0.9132
Overall correlation coefficient      =     0.9587
Free correlation coefficient         =     0.9398
Cruickshanks DPI for coordinate error=     0.0962
DPI based on free R factor           =     0.0942
Overall figure of merit              =     0.8333
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.8534
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    133134.47       8616.1426       723763.06       723772.13    

    ****                              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

 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_R03_1-60A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.012     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.777     1.644
Bond angles  : others                          3238     1.498     1.580
Torsion angles, period  1. refined              185     6.845     5.000
Torsion angles, period  2. refined               90    36.239    22.778
Torsion angles, period  3. refined              268    13.728    15.000
Torsion angles, period  4. refined                9    12.103    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                   298     0.244     0.200
VDW repulsions.others                          1343     0.199     0.200
VDW; torsion: refined_atoms                     730     0.172     0.200
VDW; torsion.others                             748     0.086     0.200
HBOND: refined_atoms                            214     0.198     0.200
HBOND.others                                      1     0.089     0.200
VDW repulsions: symmetry: refined_atoms           8     0.220     0.200
VDW repulsions: symmetry: others                 24     0.169     0.200
HBOND: symmetry: refined_atoms                   18     0.202     0.200
HBOND: symmetry: others                           1     0.050     0.200
M. chain bond B values: refined atoms           746     1.689     1.511
M. chain bond B values: others                  746     1.686     1.511
M. chain angle B values: refined atoms          929     2.651     2.256
M. chain angle B values: others                 930     2.650     2.256
S. chain bond B values: refined atoms           811     3.110     1.916
S. chain bond B values: others                  810     3.104     1.916
S. chain angle B values: refined atoms         1177     4.804     2.705
S. chain angle B values: others                1178     4.802     2.704
Long range B values: refined atoms             1843     7.303    20.994
Long range B values: others                    1750     7.007    19.513
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =   -0.0112
Partial structure    1: scale =     0.3853, B  =   42.8880
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3604 100.00   431.4   442.0  0.17  0.18     178   453.4   450.5  0.19  0.20
 0.147    6122  99.97   258.9   243.8  0.16  0.15     322   255.4   240.9  0.20  0.18
 0.244    7828 100.00   167.1   151.2  0.19  0.17     390   171.1   154.8  0.22  0.20
 0.342    9139 100.00    71.3    85.3  0.32  0.26     451    73.0    88.3  0.35  0.28
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2637   0.931    967   0.833   3604   0.905  0.951  0.9692  0.9737  0.8979  0.9374
  0.1468   5139   0.897    983   0.805   6122   0.882  1.026  0.9537  0.9655  0.9089  0.9422
  0.2444   6829   0.873    999   0.773   7828   0.860  1.053  0.9506  0.9579  0.9024  0.9353
  0.3419   8154   0.758    989   0.677   9143   0.749  0.741  0.8927  0.9029  0.8319  0.8653
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26696
Percentage observed                  =    99.9893
Percentage of free reflections       =     4.7864
Overall R factor                     =     0.1920
Free R factor                        =     0.2208
Average Fourier shell correlation    =     0.9429
AverageFree Fourier shell correlation=     0.9343
Overall weighted R factor            =     0.1667
Free weighted R factor               =     0.1928
Overall weighted R2 factor           =     0.1978
Free weighted R2 factor              =     0.2302
Average correlation coefficient      =     0.9132
Overall correlation coefficient      =     0.9587
Free correlation coefficient         =     0.9398
Cruickshanks DPI for coordinate error=     0.0962
DPI based on free R factor           =     0.0942
Overall figure of merit              =     0.8333
ML based su of positional parameters =     0.0622
ML based su of thermal parameters    =     1.8534
-----------------------------------------------------------------------------
  Time in seconds: CPU =        22.09
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1928   0.2221   0.798      134440.    6905.9   0.0124  0.922   1.774  1.032   0.087
       1   0.1921   0.2214   0.826      133391.    6878.5   0.0127  0.943   1.771  1.032   0.087
       2   0.1912   0.2207   0.832      133114.    6870.9   0.0136  1.008   1.816  1.059   0.090
       3   0.1910   0.2205   0.833      133028.    6868.1   0.0137  1.018   1.837  1.072   0.091
       4   0.1913   0.2207   0.834      133055.    6868.4   0.0131  0.977   1.818  1.061   0.089
       5   0.1919   0.2207   0.833      133121.    6869.6   0.0125  0.931   1.785  1.041   0.087
       6   0.1919   0.2207   0.833      133129.    6869.9   0.0125  0.930   1.782  1.040   0.087
       7   0.1919   0.2207   0.833      133133.    6870.2   0.0125  0.929   1.781  1.039   0.087
       8   0.1919   0.2208   0.833      133134.    6870.2   0.0124  0.929   1.780  1.038   0.087
       9   0.1919   0.2208   0.833      133134.    6870.2   0.0124  0.928   1.778  1.038   0.087
      10   0.1920   0.2208   0.833      133137.    6870.4   0.0124  0.927   1.777  1.037   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1928   0.1920
             R free    0.2221   0.2208
     Rms BondLength    0.0124   0.0124
      Rms BondAngle    1.7742   1.7770
     Rms ChirVolume    0.0866   0.0869
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      54.1s System:    0.1s Elapsed:     0:54