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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: 15:56:32 


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


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

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

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

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

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

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

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

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

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.80     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_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R16_1-80A.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_1-80A.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       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  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  1.8000

  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_1-90A.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=   2.007 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=   2.199 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=   1.827 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=   2.185 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=   2.343 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=   2.443 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=   2.051 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       1005
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 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.= 0.891 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        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.27224705    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                40.4
Norm of Geom. positional gradient                78.6
Norm of X_ray B-factor gradient                  134.
Norm of Geom. B-factor gradient                 0.228E+05
Product of X_ray and Geom posit. gradients     -0.106E+08
 Cosine of angle between them                      -0.345
Product of X_ray and Geom B-fact gradients     -0.425E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.7045E+06 GEOM=     0.2692E+05 TOTAL=     0.7315E+06
 function value    731464.00    

-------------------------------------------------------------------------------
             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     1.770     1.644
Bond angles  : others                          3242     2.341     1.582
Torsion angles, period  1. refined              184     6.983     5.000
Torsion angles, period  2. refined               90    36.719    22.778
Torsion angles, period  3. refined              268    14.129    15.000
Torsion angles, period  4. refined                9    11.226    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   312     0.265     0.200
VDW repulsions.others                          1346     0.231     0.200
VDW; torsion: refined_atoms                     713     0.172     0.200
VDW; torsion.others                             706     0.080     0.200
HBOND: refined_atoms                            237     0.197     0.200
HBOND.others                                      2     0.047     0.200
VDW repulsions: symmetry: refined_atoms           7     0.252     0.200
VDW repulsions: symmetry: others                 25     0.174     0.200
HBOND: symmetry: refined_atoms                   17     0.245     0.200
HBOND: symmetry: others                           1     0.039     0.200
M. chain bond B values: refined atoms           745     1.609     1.215
M. chain bond B values: others                  745     1.608     1.215
M. chain angle B values: refined atoms          926     2.544     1.802
M. chain angle B values: others                 927     2.543     1.802
S. chain bond B values: refined atoms           812     2.654     1.570
S. chain bond B values: others                  811     2.650     1.570
S. chain angle B values: refined atoms         1177     4.203     2.203
S. chain angle B values: others                1178     4.201     2.202
Long range B values: refined atoms             1869     7.046    17.173
Long range B values: others                    1772     6.681    15.769
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.9047
Partial structure    1: scale =     0.3852, B  =   50.6249
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2545 100.00   470.7   479.5  0.16  0.17     148   480.9   487.4  0.18  0.19
 0.116    4366 100.00   342.0   328.0  0.15  0.14     213   308.6   297.9  0.21  0.19
 0.193    5478  99.97   225.2   214.3  0.16  0.14     330   228.7   220.7  0.22  0.19
 0.270    6473 100.00   147.9   154.6  0.21  0.16     314   137.0   144.6  0.26  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1790   0.929    755   0.830   2545   0.900  0.950  0.9684  0.9734  0.9119  0.9407
  0.1161   3588   0.898    778   0.803   4366   0.881  0.998  0.9521  0.9677  0.9112  0.9483
  0.1931   4703   0.872    775   0.755   5478   0.856  1.008  0.9441  0.9580  0.8686  0.9389
  0.2701   5699   0.825    782   0.744   6481   0.815  0.897  0.9180  0.9414  0.8434  0.9079
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18870
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0566
Overall R factor                     =     0.1686
Free R factor                        =     0.2134
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9412
Overall weighted R factor            =     0.1516
Free weighted R factor               =     0.1931
Overall weighted R2 factor           =     0.1837
Free weighted R2 factor              =     0.2201
Average correlation coefficient      =     0.9307
Overall correlation coefficient      =     0.9561
Free correlation coefficient         =     0.9312
Cruickshanks DPI for coordinate error=     0.1232
DPI based on free R factor           =     0.1219
Overall figure of merit              =     0.8536
ML based su of positional parameters =     0.0777
ML based su of thermal parameters    =     2.5323
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100655.42       26920.201       731464.00      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30564833    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711438.63    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0666
Partial structure    1: scale =     0.3854, B  =   49.9788
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1675
Free R factor                        =     0.2103
Average Fourier shell correlation    =     0.9601
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9333
Overall figure of merit              =     0.8661
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100190.05       10152.219       711438.63       731464.00    


     CGMAT cycle number =      3

 Weight matrix   0.31209478    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709019.31    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0438
Partial structure    1: scale =     0.3854, B  =   47.3184
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1661
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9610
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9353
Overall figure of merit              =     0.8677
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    99946.477       9437.8320       709019.31       711438.63    


     CGMAT cycle number =      4

 Weight matrix   0.31432977    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    708245.00    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0485
Partial structure    1: scale =     0.3846, B  =   47.1493
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1656
Free R factor                        =     0.2080
Average Fourier shell correlation    =     0.9613
AverageFree Fourier shell correlation=     0.9468
Average correlation coefficient      =     0.9359
Overall figure of merit              =     0.8683
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    99865.195       9232.4590       708245.00       709019.31    


     CGMAT cycle number =      5

 Weight matrix   0.31510508    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707986.69    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0371
Partial structure    1: scale =     0.3842, B  =   47.1143
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1654
Free R factor                        =     0.2078
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9469
Average correlation coefficient      =     0.9362
Overall figure of merit              =     0.8685
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    99826.383       9245.8086       707986.69       708245.00    


     CGMAT cycle number =      6

 Weight matrix   0.31546709    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707873.63    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0363
Partial structure    1: scale =     0.3841, B  =   47.1742
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1653
Free R factor                        =     0.2081
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9469
Average correlation coefficient      =     0.9364
Overall figure of merit              =     0.8686
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    99805.875       9276.3379       707873.63       707986.69    


     CGMAT cycle number =      7

 Weight matrix   0.31501281    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707838.44    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0333
Partial structure    1: scale =     0.3839, B  =   47.1210
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1653
Free R factor                        =     0.2083
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9468
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8686
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    99799.297       9287.1406       707838.44       707873.63    


     CGMAT cycle number =      8

 Weight matrix   0.31449181    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707807.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0282
Partial structure    1: scale =     0.3838, B  =   46.9845
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1653
Free R factor                        =     0.2084
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9467
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8685
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    99794.172       9292.4531       707807.88       707838.44    


     CGMAT cycle number =      9

 Weight matrix   0.31409258    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    707785.50    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0251
Partial structure    1: scale =     0.3840, B  =   46.9538
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1653
Free R factor                        =     0.2086
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9467
Average correlation coefficient      =     0.9366
Overall figure of merit              =     0.8685
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    99792.328       9282.9902       707785.50       707807.88    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

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

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.31424081    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                38.9
Norm of Geom. positional gradient                38.9
Norm of X_ray B-factor gradient                  125.
Norm of Geom. B-factor gradient                  127.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.513E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.6985E+06 GEOM=      9281.     TOTAL=     0.7078E+06
 function value    707769.25    

-------------------------------------------------------------------------------
             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     1.816     1.644
Bond angles  : others                          3242     1.473     1.582
Torsion angles, period  1. refined              184     6.959     5.000
Torsion angles, period  2. refined               90    36.627    22.778
Torsion angles, period  3. refined              268    13.962    15.000
Torsion angles, period  4. refined                9    11.828    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.270     0.200
VDW repulsions.others                          1358     0.206     0.200
VDW; torsion: refined_atoms                     715     0.172     0.200
VDW; torsion.others                             778     0.084     0.200
HBOND: refined_atoms                            223     0.198     0.200
HBOND.others                                      1     0.125     0.200
VDW repulsions: symmetry: refined_atoms           8     0.217     0.200
VDW repulsions: symmetry: others                 22     0.169     0.200
HBOND: symmetry: refined_atoms                   20     0.226     0.200
HBOND: symmetry: others                           1     0.006     0.200
M. chain bond B values: refined atoms           745     1.693     1.295
M. chain bond B values: others                  745     1.692     1.295
M. chain angle B values: refined atoms          926     2.639     1.924
M. chain angle B values: others                 927     2.638     1.923
S. chain bond B values: refined atoms           811     2.918     1.686
S. chain bond B values: others                  810     2.914     1.686
S. chain angle B values: refined atoms         1177     4.600     2.363
S. chain angle B values: others                1178     4.598     2.362
Long range B values: refined atoms             1848     6.977    17.975
Long range B values: others                    1756     6.671    16.544
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0311
Partial structure    1: scale =     0.3843, B  =   47.1024
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2545 100.00   470.9   480.0  0.16  0.17     148   481.1   488.0  0.18  0.19
 0.116    4366 100.00   342.1   327.0  0.16  0.14     213   308.7   297.3  0.21  0.19
 0.193    5478  99.97   225.2   214.2  0.16  0.14     330   228.8   220.5  0.21  0.19
 0.270    6473 100.00   147.9   154.3  0.19  0.15     314   137.1   144.2  0.25  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1790   0.936    755   0.838   2545   0.907  0.950  0.9704  0.9750  0.9160  0.9411
  0.1161   3588   0.906    778   0.810   4366   0.889  0.999  0.9550  0.9691  0.9157  0.9483
  0.1931   4703   0.880    775   0.763   5478   0.863  1.008  0.9474  0.9599  0.8745  0.9383
  0.2701   5699   0.854    782   0.775   6481   0.844  0.909  0.9290  0.9525  0.8539  0.9255
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18870
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0566
Overall R factor                     =     0.1653
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9467
Overall weighted R factor            =     0.1506
Free weighted R factor               =     0.1896
Overall weighted R2 factor           =     0.1836
Free weighted R2 factor              =     0.2162
Average correlation coefficient      =     0.9366
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9346
Cruickshanks DPI for coordinate error=     0.1208
DPI based on free R factor           =     0.1193
Overall figure of merit              =     0.8685
ML based su of positional parameters =     0.0723
ML based su of thermal parameters    =     2.3304
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    99790.281       9281.0469       707769.25       707785.50    

    ****                              VDW outliers                              ****

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

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

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R16_1-80A.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     1.817     1.644
Bond angles  : others                          3242     1.473     1.582
Torsion angles, period  1. refined              184     6.955     5.000
Torsion angles, period  2. refined               90    36.619    22.778
Torsion angles, period  3. refined              268    13.967    15.000
Torsion angles, period  4. refined                9    11.833    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   302     0.269     0.200
VDW repulsions.others                          1359     0.206     0.200
VDW; torsion: refined_atoms                     715     0.172     0.200
VDW; torsion.others                             782     0.084     0.200
HBOND: refined_atoms                            225     0.198     0.200
HBOND.others                                      1     0.127     0.200
VDW repulsions: symmetry: refined_atoms           8     0.217     0.200
VDW repulsions: symmetry: others                 22     0.169     0.200
HBOND: symmetry: refined_atoms                   20     0.226     0.200
HBOND: symmetry: others                           1     0.002     0.200
M. chain bond B values: refined atoms           745     1.692     1.295
M. chain bond B values: others                  745     1.691     1.295
M. chain angle B values: refined atoms          926     2.638     1.923
M. chain angle B values: others                 927     2.636     1.923
S. chain bond B values: refined atoms           811     2.921     1.686
S. chain bond B values: others                  810     2.917     1.686
S. chain angle B values: refined atoms         1177     4.604     2.363
S. chain angle B values: others                1178     4.602     2.363
Long range B values: refined atoms             1852     6.980    18.036
Long range B values: others                    1758     6.673    16.571
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0288
Partial structure    1: scale =     0.3843, B  =   47.1124
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2545 100.00   470.9   480.0  0.16  0.17     148   481.1   487.9  0.18  0.19
 0.116    4366 100.00   342.1   327.0  0.16  0.14     213   308.7   297.3  0.21  0.19
 0.193    5478  99.97   225.2   214.1  0.16  0.14     330   228.8   220.5  0.21  0.18
 0.270    6473 100.00   148.0   154.2  0.19  0.15     314   137.1   144.2  0.25  0.21
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1790   0.936    755   0.838   2545   0.907  0.950  0.9704  0.9750  0.9158  0.9411
  0.1161   3588   0.906    778   0.810   4366   0.889  0.999  0.9550  0.9691  0.9157  0.9483
  0.1931   4703   0.880    775   0.763   5478   0.863  1.008  0.9475  0.9599  0.8746  0.9383
  0.2701   5699   0.854    782   0.775   6481   0.844  0.909  0.9290  0.9525  0.8539  0.9256
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18870
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0566
Overall R factor                     =     0.1653
Free R factor                        =     0.2088
Average Fourier shell correlation    =     0.9615
AverageFree Fourier shell correlation=     0.9467
Overall weighted R factor            =     0.1506
Free weighted R factor               =     0.1897
Overall weighted R2 factor           =     0.1835
Free weighted R2 factor              =     0.2162
Average correlation coefficient      =     0.9366
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9346
Cruickshanks DPI for coordinate error=     0.1208
DPI based on free R factor           =     0.1193
Overall figure of merit              =     0.8686
ML based su of positional parameters =     0.0723
ML based su of thermal parameters    =     2.3304
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.84
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1686   0.2134   0.854      100655.    5524.7   0.0121  0.898   1.770  1.023   0.086
       1   0.1675   0.2103   0.866      100190.    5507.5   0.0121  0.891   1.759  1.015   0.086
       2   0.1661   0.2086   0.868       99946.    5499.7   0.0128  0.946   1.789  1.033   0.088
       3   0.1656   0.2080   0.868       99865.    5496.5   0.0129  0.953   1.803  1.041   0.088
       4   0.1654   0.2078   0.869       99826.    5495.1   0.0129  0.957   1.810  1.045   0.088
       5   0.1653   0.2081   0.869       99806.    5494.8   0.0129  0.957   1.814  1.047   0.088
       6   0.1653   0.2083   0.869       99799.    5495.2   0.0129  0.958   1.816  1.048   0.088
       7   0.1653   0.2084   0.869       99794.    5495.5   0.0129  0.958   1.817  1.048   0.088
       8   0.1653   0.2086   0.868       99792.    5495.9   0.0129  0.959   1.817  1.047   0.088
       9   0.1653   0.2088   0.869       99790.    5495.9   0.0129  0.958   1.816  1.047   0.088
      10   0.1653   0.2088   0.869       99788.    5495.8   0.0129  0.959   1.817  1.047   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1686   0.1653
             R free    0.2134   0.2088
     Rms BondLength    0.0121   0.0129
      Rms BondAngle    1.7701   1.8166
     Rms ChirVolume    0.0856   0.0876
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.1s System:    0.1s Elapsed:     0:46