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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: 15:14:18 


 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 2
  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_R02_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R02_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_R02_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:     2
  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_R02_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=   2.026 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=   2.198 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=   1.854 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=   2.213 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=   2.386 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=   2.455 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=   2.095 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                            2
Number of "free" reflections        980
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

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A    171 THR C   . - A    172 GLY N   . mod.= 1.715 id.= 1.337 dev= -0.378 sig.= 0.011

    ****                              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.= 0.922 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.27942491    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                41.7
Norm of Geom. positional gradient                91.9
Norm of X_ray B-factor gradient                  138.
Norm of Geom. B-factor gradient                  116.
Product of X_ray and Geom posit. gradients     -0.104E+08
 Cosine of angle between them                      -0.280
Product of X_ray and Geom B-fact gradients     -0.407E+08
 Cosine of angle between them                      -0.784


Residuals: XRAY=     0.7055E+06 GEOM=     0.1414E+05 TOTAL=     0.7197E+06
 function value    719682.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.016     0.013
Bond distances: others                         1391     0.035     0.017
Bond angles  : refined atoms                   2106     1.833     1.644
Bond angles  : others                          3238     2.361     1.580
Torsion angles, period  1. refined              185     7.130     5.000
Torsion angles, period  2. refined               90    36.718    22.778
Torsion angles, period  3. refined              268    14.383    15.000
Torsion angles, period  4. refined                9    10.966    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1743     0.011     0.020
Planar groups: others                           332     0.016     0.020
VDW repulsions: refined_atoms                   295     0.251     0.200
VDW repulsions.others                          1336     0.222     0.200
VDW; torsion: refined_atoms                     724     0.172     0.200
VDW; torsion.others                             708     0.081     0.200
HBOND: refined_atoms                            220     0.205     0.200
HBOND.others                                      3     0.088     0.200
VDW repulsions: symmetry: refined_atoms          10     0.218     0.200
VDW repulsions: symmetry: others                 28     0.183     0.200
HBOND: symmetry: refined_atoms                   22     0.191     0.200
HBOND: symmetry: others                           1     0.041     0.200
M. chain bond B values: refined atoms           746     1.578     1.214
M. chain bond B values: others                  746     1.576     1.214
M. chain angle B values: refined atoms          929     2.521     1.807
M. chain angle B values: others                 930     2.520     1.806
S. chain bond B values: refined atoms           811     2.765     1.576
S. chain bond B values: others                  810     2.762     1.576
S. chain angle B values: refined atoms         1177     4.349     2.206
S. chain angle B values: others                1178     4.347     2.205
Long range B values: refined atoms             1840     7.097    16.736
Long range B values: others                    1750     6.806    15.483
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =    0.8902
Partial structure    1: scale =     0.3790, B  =   45.4981
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2549 100.00   473.0   481.4  0.15  0.16     144   457.2   469.6  0.19  0.20
 0.116    4352 100.00   341.7   327.8  0.16  0.15     227   328.9   318.6  0.23  0.20
 0.193    5512  99.97   226.0   214.6  0.16  0.14     296   220.7   216.4  0.22  0.18
 0.270    6474 100.00   147.5   154.1  0.21  0.16     313   150.9   160.1  0.25  0.20
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1795   0.932    754   0.838   2549   0.904  0.954  0.9692  0.9747  0.9113  0.9442
  0.1161   3581   0.884    771   0.788   4352   0.867  0.992  0.9492  0.9649  0.8906  0.9461
  0.1931   4742   0.873    770   0.763   5512   0.857  1.010  0.9434  0.9585  0.8797  0.9382
  0.2701   5701   0.839    781   0.755   6482   0.829  0.903  0.9359  0.9452  0.8598  0.9090
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18895
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9308
Overall R factor                     =     0.1689
Free R factor                        =     0.2183
Average Fourier shell correlation    =     0.9576
AverageFree Fourier shell correlation=     0.9461
Overall weighted R factor            =     0.1518
Free weighted R factor               =     0.1955
Overall weighted R2 factor           =     0.1820
Free weighted R2 factor              =     0.2305
Average correlation coefficient      =     0.9308
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9246
Cruickshanks DPI for coordinate error=     0.1233
DPI based on free R factor           =     0.1245
Overall figure of merit              =     0.8562
ML based su of positional parameters =     0.0767
ML based su of thermal parameters    =     2.4716
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100798.10       14139.770       719682.25      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.31156054    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710824.44    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0732
Partial structure    1: scale =     0.3792, B  =   45.8755
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1675
Free R factor                        =     0.2163
Average Fourier shell correlation    =     0.9608
AverageFree Fourier shell correlation=     0.9496
Average correlation coefficient      =     0.9338
Overall figure of merit              =     0.8668
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100331.21       8549.9941       710824.44       719682.25    


     CGMAT cycle number =      3

 Weight matrix   0.31799418    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709869.25    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0363
Partial structure    1: scale =     0.3782, B  =   45.6387
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2149
Average Fourier shell correlation    =     0.9616
AverageFree Fourier shell correlation=     0.9504
Average correlation coefficient      =     0.9356
Overall figure of merit              =     0.8686
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100127.55       9020.3779       709869.25       710824.44    


     CGMAT cycle number =      4

 Weight matrix   0.31997707    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709517.75    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0160
Partial structure    1: scale =     0.3779, B  =   45.4408
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1659
Free R factor                        =     0.2146
Average Fourier shell correlation    =     0.9619
AverageFree Fourier shell correlation=     0.9506
Average correlation coefficient      =     0.9362
Overall figure of merit              =     0.8691
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100051.64       9200.1758       709517.75       709869.25    


     CGMAT cycle number =      5

 Weight matrix   0.32138032    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709352.75    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0047
Partial structure    1: scale =     0.3779, B  =   45.3957
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1658
Free R factor                        =     0.2146
Average Fourier shell correlation    =     0.9621
AverageFree Fourier shell correlation=     0.9508
Average correlation coefficient      =     0.9365
Overall figure of merit              =     0.8695
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100017.42       9274.6777       709352.75       709517.75    


     CGMAT cycle number =      6

 Weight matrix   0.32263353    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709184.00    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0268
Partial structure    1: scale =     0.3781, B  =   45.4312
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1658
Free R factor                        =     0.2145
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9367
Overall figure of merit              =     0.8699
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    99990.438       9294.8164       709184.00       709352.75    


     CGMAT cycle number =      7

 Weight matrix   0.32283545    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709117.94    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0206
Partial structure    1: scale =     0.3781, B  =   45.4494
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1658
Free R factor                        =     0.2146
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9510
Average correlation coefficient      =     0.9368
Overall figure of merit              =     0.8700
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    99977.141       9321.8096       709117.94       709184.00    


     CGMAT cycle number =      8

 Weight matrix   0.32305044    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709107.81    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0203
Partial structure    1: scale =     0.3782, B  =   45.5518
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1658
Free R factor                        =     0.2150
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9510
Average correlation coefficient      =     0.9368
Overall figure of merit              =     0.8700
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    99974.352       9331.1885       709107.81       709117.94    


     CGMAT cycle number =      9

 Weight matrix   0.32283941    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709051.81    

-------------------------------------------------------------------------------
             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 =     0.0414, B  =   -0.0158
Partial structure    1: scale =     0.3783, B  =   45.4957
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1658
Free R factor                        =     0.2151
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9509
Average correlation coefficient      =     0.9369
Overall figure of merit              =     0.8699
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    99966.758       9328.3809       709051.81       709107.81    


     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.= 0.930 id.= 3.000 dev= -2.07 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   0.32276556    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                39.5
Norm of Geom. positional gradient                39.5
Norm of X_ray B-factor gradient                  127.
Norm of Geom. B-factor gradient                  128.
Product of X_ray and Geom posit. gradients     -0.151E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.522E+08
 Cosine of angle between them                      -0.999


Residuals: XRAY=     0.6997E+06 GEOM=      9330.     TOTAL=     0.7090E+06
 function value    709018.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.849     1.644
Bond angles  : others                          3238     1.496     1.580
Torsion angles, period  1. refined              185     6.964     5.000
Torsion angles, period  2. refined               90    36.309    22.778
Torsion angles, period  3. refined              268    14.218    15.000
Torsion angles, period  4. refined                9    11.789    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   301     0.249     0.200
VDW repulsions.others                          1360     0.195     0.200
VDW; torsion: refined_atoms                     727     0.173     0.200
VDW; torsion.others                             798     0.085     0.200
HBOND: refined_atoms                            213     0.197     0.200
HBOND.others                                      1     0.071     0.200
VDW repulsions: symmetry: refined_atoms           9     0.209     0.200
VDW repulsions: symmetry: others                 26     0.176     0.200
HBOND: symmetry: refined_atoms                   25     0.177     0.200
M. chain bond B values: refined atoms           746     1.638     1.293
M. chain bond B values: others                  746     1.636     1.293
M. chain angle B values: refined atoms          929     2.553     1.926
M. chain angle B values: others                 930     2.552     1.925
S. chain bond B values: refined atoms           811     3.022     1.687
S. chain bond B values: others                  810     3.020     1.687
S. chain angle B values: refined atoms         1177     4.734     2.360
S. chain angle B values: others                1178     4.732     2.360
Long range B values: refined atoms             1839     7.285    17.894
Long range B values: others                    1753     7.041    16.604
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0176
Partial structure    1: scale =     0.3782, B  =   45.3933
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2549 100.00   472.8   482.2  0.15  0.16     144   457.0   469.9  0.19  0.20
 0.116    4352 100.00   341.6   326.8  0.16  0.15     227   328.8   315.5  0.22  0.20
 0.193    5512  99.97   226.0   214.4  0.17  0.14     296   220.6   215.3  0.22  0.18
 0.270    6474 100.00   147.5   153.5  0.19  0.15     313   150.8   159.5  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1795   0.945    754   0.856   2549   0.918  0.956  0.9723  0.9770  0.9145  0.9446
  0.1161   3581   0.889    771   0.793   4352   0.872  0.992  0.9521  0.9659  0.8970  0.9456
  0.1931   4742   0.876    770   0.766   5512   0.860  1.010  0.9441  0.9587  0.8808  0.9361
  0.2701   5701   0.867    781   0.787   6482   0.857  0.914  0.9465  0.9569  0.8741  0.9287
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18895
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9308
Overall R factor                     =     0.1658
Free R factor                        =     0.2151
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9509
Overall weighted R factor            =     0.1512
Free weighted R factor               =     0.1937
Overall weighted R2 factor           =     0.1822
Free weighted R2 factor              =     0.2273
Average correlation coefficient      =     0.9369
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9277
Cruickshanks DPI for coordinate error=     0.1210
DPI based on free R factor           =     0.1228
Overall figure of merit              =     0.8699
ML based su of positional parameters =     0.0713
ML based su of thermal parameters    =     2.2705
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    99961.727       9329.7480       709018.00       709051.81    

    ****                              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.= 0.930 id.= 3.000 dev= -2.07 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_R02_1-80A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1558     0.013     0.013
Bond distances: others                         1391     0.001     0.017
Bond angles  : refined atoms                   2106     1.849     1.644
Bond angles  : others                          3238     1.496     1.580
Torsion angles, period  1. refined              185     6.956     5.000
Torsion angles, period  2. refined               90    36.275    22.778
Torsion angles, period  3. refined              268    14.218    15.000
Torsion angles, period  4. refined                9    11.800    15.000
Chiral centres: refined atoms                   196     0.089     0.200
Planar groups: refined atoms                   1743     0.010     0.020
Planar groups: others                           332     0.001     0.020
VDW repulsions: refined_atoms                   304     0.248     0.200
VDW repulsions.others                          1357     0.195     0.200
VDW; torsion: refined_atoms                     725     0.173     0.200
VDW; torsion.others                             800     0.085     0.200
HBOND: refined_atoms                            212     0.198     0.200
HBOND.others                                      1     0.074     0.200
VDW repulsions: symmetry: refined_atoms           9     0.208     0.200
VDW repulsions: symmetry: others                 27     0.174     0.200
HBOND: symmetry: refined_atoms                   25     0.178     0.200
M. chain bond B values: refined atoms           746     1.638     1.293
M. chain bond B values: others                  746     1.635     1.293
M. chain angle B values: refined atoms          929     2.551     1.926
M. chain angle B values: others                 930     2.550     1.925
S. chain bond B values: refined atoms           811     3.025     1.687
S. chain bond B values: others                  810     3.023     1.687
S. chain angle B values: refined atoms         1177     4.739     2.360
S. chain angle B values: others                1178     4.737     2.360
Long range B values: refined atoms             1841     7.249    17.902
Long range B values: others                    1755     7.002    16.614
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0414, B  =   -0.0136
Partial structure    1: scale =     0.3780, B  =   45.3268
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2549 100.00   472.8   482.2  0.15  0.16     144   457.0   469.8  0.19  0.20
 0.116    4352 100.00   341.6   326.8  0.16  0.15     227   328.8   315.4  0.22  0.20
 0.193    5512  99.97   226.0   214.4  0.17  0.14     296   220.6   215.2  0.22  0.18
 0.270    6474 100.00   147.5   153.5  0.19  0.15     313   150.8   159.5  0.23  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1795   0.944    754   0.856   2549   0.918  0.956  0.9721  0.9769  0.9140  0.9446
  0.1161   3581   0.889    771   0.793   4352   0.872  0.992  0.9521  0.9659  0.8968  0.9456
  0.1931   4742   0.876    770   0.767   5512   0.860  1.010  0.9441  0.9587  0.8808  0.9360
  0.2701   5701   0.867    781   0.788   6482   0.858  0.916  0.9465  0.9570  0.8739  0.9289
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18895
Percentage observed                  =    99.9849
Percentage of free reflections       =     4.9308
Overall R factor                     =     0.1658
Free R factor                        =     0.2153
Average Fourier shell correlation    =     0.9622
AverageFree Fourier shell correlation=     0.9508
Overall weighted R factor            =     0.1513
Free weighted R factor               =     0.1940
Overall weighted R2 factor           =     0.1822
Free weighted R2 factor              =     0.2280
Average correlation coefficient      =     0.9370
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9275
Cruickshanks DPI for coordinate error=     0.1210
DPI based on free R factor           =     0.1229
Overall figure of merit              =     0.8699
ML based su of positional parameters =     0.0713
ML based su of thermal parameters    =     2.2705
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.64
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1689   0.2183   0.856      100798.    5397.8   0.0160  1.276   1.833  1.058   0.087
       1   0.1675   0.2163   0.867      100331.    5379.4   0.0125  0.916   1.794  1.035   0.087
       2   0.1662   0.2149   0.869      100128.    5372.6   0.0132  0.966   1.821  1.051   0.089
       3   0.1659   0.2146   0.869      100052.    5370.0   0.0134  0.976   1.834  1.058   0.089
       4   0.1658   0.2146   0.870      100017.    5368.3   0.0134  0.978   1.840  1.062   0.089
       5   0.1658   0.2145   0.870       99990.    5367.6   0.0134  0.980   1.843  1.063   0.089
       6   0.1658   0.2146   0.870       99977.    5367.1   0.0134  0.981   1.846  1.065   0.089
       7   0.1658   0.2150   0.870       99974.    5367.1   0.0134  0.981   1.848  1.065   0.089
       8   0.1658   0.2151   0.870       99967.    5367.2   0.0134  0.982   1.849  1.066   0.089
       9   0.1658   0.2151   0.870       99962.    5367.0   0.0134  0.982   1.849  1.066   0.089
      10   0.1658   0.2153   0.870       99960.    5367.9   0.0134  0.982   1.849  1.066   0.089
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1689   0.1658
             R free    0.2183   0.2153
     Rms BondLength    0.0160   0.0134
      Rms BondAngle    1.8327   1.8490
     Rms ChirVolume    0.0867   0.0886
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      45.8s System:    0.1s Elapsed:     0:46