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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 19:53:37 


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


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

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

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

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

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

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

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

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

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.50     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 14
  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_R14_1-60A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R14_1-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R14_1-50A.mtz

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

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

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


  Residual                               : Rice Maximum Likelihood for Fs

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

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


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

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.1111
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.5000
  Estimated number of reflections :      43652
  Free R exclusion - flag equals:    14
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.5000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R14_1-60A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.047 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=   2.189 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=   1.813 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=   2.218 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=   2.423 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=   2.382 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  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                           14
Number of "free" reflections       1629
Number of   all  reflections      33910
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          33910

   Current auto weighting coefficient =    6.2496691    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.878 id.= 3.000 dev= -2.12 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.30349559    
 Actual weight    6.2496691      is applied to the X-ray term
Norm of X_ray positional gradient                41.1
Norm of Geom. positional gradient                80.1
Norm of X_ray B-factor gradient                  117.
Norm of Geom. B-factor gradient                 0.223E+05
Product of X_ray and Geom posit. gradients     -0.145E+08
 Cosine of angle between them                      -0.456
Product of X_ray and Geom B-fact gradients     -0.363E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.9773E+06 GEOM=     0.2642E+05 TOTAL=     0.1004E+07
 function value    1003672.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.794     1.644
Bond angles  : others                          3242     2.346     1.582
Torsion angles, period  1. refined              184     6.852     5.000
Torsion angles, period  2. refined               90    35.920    22.778
Torsion angles, period  3. refined              268    13.774    15.000
Torsion angles, period  4. refined                9    12.089    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   312     0.264     0.200
VDW repulsions.others                          1358     0.229     0.200
VDW; torsion: refined_atoms                     720     0.174     0.200
VDW; torsion.others                             733     0.080     0.200
HBOND: refined_atoms                            220     0.202     0.200
HBOND.others                                      2     0.058     0.200
VDW repulsions: symmetry: refined_atoms           9     0.204     0.200
VDW repulsions: symmetry: others                 24     0.187     0.200
HBOND: symmetry: refined_atoms                   22     0.181     0.200
M. chain bond B values: refined atoms           745     1.705     1.509
M. chain bond B values: others                  745     1.702     1.509
M. chain angle B values: refined atoms          926     2.694     2.249
M. chain angle B values: others                 927     2.693     2.249
S. chain bond B values: refined atoms           811     3.073     1.914
S. chain bond B values: others                  810     3.068     1.914
S. chain angle B values: refined atoms         1177     4.723     2.703
S. chain angle B values: others                1178     4.721     2.703
Long range B values: refined atoms             1856     7.145    21.077
Long range B values: others                    1762     6.808    19.582
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =    1.1756
Partial structure    1: scale =     0.3901, B  =   45.6078
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.37 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4329 100.00   404.7   414.8  0.17  0.18     218   427.5   433.9  0.18  0.20
 0.167    7418  99.97   227.5   207.9  0.18  0.16     380   238.0   215.5  0.20  0.17
 0.278    9444 100.00   123.9   114.2  0.21  0.19     466   123.5   115.3  0.24  0.21
 0.389   11076 100.00    50.0    62.5  0.42  0.37     565    52.7    64.3  0.41  0.36
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3219   0.913   1110   0.811   4329   0.887  0.947  0.9704  0.9697  0.9366  0.9332
  0.1670   6302   0.884   1116   0.783   7418   0.869  1.064  0.9581  0.9615  0.9198  0.9368
  0.2780   8317   0.839   1127   0.758   9444   0.829  1.019  0.9381  0.9469  0.9039  0.9290
  0.3890   9956   0.568   1132   0.491  11088   0.560  0.570  0.7852  0.7696  0.7573  0.7651
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32279
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8042
Overall R factor                     =     0.2086
Free R factor                        =     0.2232
Average Fourier shell correlation    =     0.8924
AverageFree Fourier shell correlation=     0.8940
Overall weighted R factor            =     0.1767
Free weighted R factor               =     0.1938
Overall weighted R2 factor           =     0.2071
Free weighted R2 factor              =     0.2240
Average correlation coefficient      =     0.8751
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9555
Cruickshanks DPI for coordinate error=     0.0863
DPI based on free R factor           =     0.0812
Overall figure of merit              =     0.7536
ML based su of positional parameters =     0.0696
ML based su of thermal parameters    =     2.0459
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    156368.42       26421.588       1003672.4      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36120301    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    981610.81    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0800
Partial structure    1: scale =     0.3909, B  =   45.0958
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2083
Free R factor                        =     0.2227
Average Fourier shell correlation    =     0.9017
AverageFree Fourier shell correlation=     0.9027
Average correlation coefficient      =     0.8762
Overall figure of merit              =     0.7702
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    155477.66       9926.9082       981610.81       1003672.4    


     CGMAT cycle number =      3

 Weight matrix   0.36701208    
 Actual weight    6.2496691      is applied to the X-ray term


 function value    979703.06    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0143
Partial structure    1: scale =     0.3907, B  =   41.0715
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2073
Free R factor                        =     0.2225
Average Fourier shell correlation    =     0.9030
AverageFree Fourier shell correlation=     0.9037
Average correlation coefficient      =     0.8777
Overall figure of merit              =     0.7711
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    155269.45       9320.3623       979703.06       981610.81    


     CGMAT cycle number =      4

 Weight matrix   0.33439890    
 Actual weight    5.6815171      is applied to the X-ray term


 function value    891080.56    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0136
Partial structure    1: scale =     0.3907, B  =   39.4760
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2070
Free R factor                        =     0.2223
Average Fourier shell correlation    =     0.9031
AverageFree Fourier shell correlation=     0.9038
Average correlation coefficient      =     0.8783
Overall figure of merit              =     0.7709
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    155233.50       9118.7393       891080.56       979703.06    


     CGMAT cycle number =      5

 Weight matrix   0.30432409    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    810829.81    

-------------------------------------------------------------------------------
             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 =     0.0456, B  =   -0.0133
Partial structure    1: scale =     0.3910, B  =   39.3225
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2073
Free R factor                        =     0.2224
Average Fourier shell correlation    =     0.9032
AverageFree Fourier shell correlation=     0.9039
Average correlation coefficient      =     0.8781
Overall figure of merit              =     0.7711
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    155274.53       8834.4814       810829.81       891080.56    


     CGMAT cycle number =      6

 Weight matrix   0.30448452    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    810820.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0291
Partial structure    1: scale =     0.3912, B  =   39.1582
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2076
Free R factor                        =     0.2224
Average Fourier shell correlation    =     0.9033
AverageFree Fourier shell correlation=     0.9041
Average correlation coefficient      =     0.8777
Overall figure of merit              =     0.7714
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    155334.06       8517.2275       810820.06       810829.81    


     CGMAT cycle number =      7

 Weight matrix   0.30454016    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    810843.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0182
Partial structure    1: scale =     0.3913, B  =   39.0924
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2077
Free R factor                        =     0.2223
Average Fourier shell correlation    =     0.9032
AverageFree Fourier shell correlation=     0.9041
Average correlation coefficient      =     0.8777
Overall figure of merit              =     0.7715
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    155354.58       8449.2051       810878.75       810820.06    

 fvalues    155354.58       8449.2051       810886.31       810857.94    
 fvalues    155354.58       8449.2051       810886.31       810857.94    


     CGMAT cycle number =      8

 Weight matrix   0.30482221    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    810849.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0249
Partial structure    1: scale =     0.3914, B  =   39.0635
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2077
Free R factor                        =     0.2223
Average Fourier shell correlation    =     0.9033
AverageFree Fourier shell correlation=     0.9042
Average correlation coefficient      =     0.8776
Overall figure of merit              =     0.7716
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    155355.05       8438.1719       810849.38       810857.94    


     CGMAT cycle number =      9

 Weight matrix   0.30431259    
 Actual weight    5.1650152      is applied to the X-ray term


 function value    810883.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0187
Partial structure    1: scale =     0.3915, B  =   39.0629
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2078
Free R factor                        =     0.2223
Average Fourier shell correlation    =     0.9032
AverageFree Fourier shell correlation=     0.9041
Average correlation coefficient      =     0.8776
Overall figure of merit              =     0.7714
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    155366.08       8428.3672       810877.06       810849.38    
 fvalues    155366.08       8428.3672       810877.06       810896.56    


     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.= 0.898 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  280
 Maximuum H,K,L                 :    39   39   82
 Minimum acceptable grid spacing:    87   87  184
 Weight matrix   0.30490902    
 Actual weight    5.1650152      is applied to the X-ray term
Norm of X_ray positional gradient                38.6
Norm of Geom. positional gradient                38.6
Norm of X_ray B-factor gradient                  98.6
Norm of Geom. B-factor gradient                  100.
Product of X_ray and Geom posit. gradients     -0.144E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.317E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.8025E+06 GEOM=      8420.     TOTAL=     0.8109E+06
 function value    810879.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.784     1.644
Bond angles  : others                          3242     1.490     1.582
Torsion angles, period  1. refined              184     6.878     5.000
Torsion angles, period  2. refined               90    35.725    22.778
Torsion angles, period  3. refined              268    13.603    15.000
Torsion angles, period  4. refined                9    12.245    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   307     0.265     0.200
VDW repulsions.others                          1367     0.204     0.200
VDW; torsion: refined_atoms                     720     0.173     0.200
VDW; torsion.others                             767     0.084     0.200
HBOND: refined_atoms                            215     0.202     0.200
HBOND.others                                      1     0.100     0.200
VDW repulsions: symmetry: refined_atoms           9     0.201     0.200
VDW repulsions: symmetry: others                 25     0.171     0.200
HBOND: symmetry: refined_atoms                   20     0.190     0.200
M. chain bond B values: refined atoms           745     1.746     1.624
M. chain bond B values: others                  745     1.742     1.624
M. chain angle B values: refined atoms          926     2.732     2.422
M. chain angle B values: others                 927     2.730     2.421
S. chain bond B values: refined atoms           811     3.149     2.037
S. chain bond B values: others                  810     3.144     2.036
S. chain angle B values: refined atoms         1177     4.821     2.886
S. chain angle B values: others                1178     4.819     2.885
Long range B values: refined atoms             1846     7.129    22.320
Long range B values: others                    1757     6.847    20.895
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0281
Partial structure    1: scale =     0.3915, B  =   39.0960
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4329 100.00   405.3   415.1  0.17  0.18     218   428.2   434.7  0.18  0.19
 0.167    7418  99.97   227.8   208.2  0.18  0.16     380   238.4   216.1  0.20  0.17
 0.278    9444 100.00   124.1   114.5  0.21  0.18     466   123.7   115.6  0.24  0.21
 0.389   11076 100.00    50.1    62.5  0.41  0.36     565    52.8    64.4  0.41  0.36
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3219   0.925   1110   0.828   4329   0.900  0.948  0.9730  0.9724  0.9378  0.9330
  0.1670   6302   0.900   1116   0.803   7418   0.886  1.067  0.9617  0.9654  0.9204  0.9379
  0.2780   8317   0.853   1127   0.774   9444   0.843  1.020  0.9441  0.9526  0.9050  0.9294
  0.3890   9956   0.591   1132   0.520  11088   0.584  0.576  0.8060  0.7927  0.7612  0.7714
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32279
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8042
Overall R factor                     =     0.2078
Free R factor                        =     0.2223
Average Fourier shell correlation    =     0.9033
AverageFree Fourier shell correlation=     0.9042
Overall weighted R factor            =     0.1763
Free weighted R factor               =     0.1924
Overall weighted R2 factor           =     0.2065
Free weighted R2 factor              =     0.2215
Average correlation coefficient      =     0.8776
Overall correlation coefficient      =     0.9587
Free correlation coefficient         =     0.9561
Cruickshanks DPI for coordinate error=     0.0860
DPI based on free R factor           =     0.0809
Overall figure of merit              =     0.7716
ML based su of positional parameters =     0.0630
ML based su of thermal parameters    =     1.8555
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    155364.52       8419.6553       810879.69       810896.56    

    ****                              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.= 0.898 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R14_1-50A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.783     1.644
Bond angles  : others                          3242     1.490     1.582
Torsion angles, period  1. refined              184     6.879     5.000
Torsion angles, period  2. refined               90    35.711    22.778
Torsion angles, period  3. refined              268    13.592    15.000
Torsion angles, period  4. refined                9    12.237    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   307     0.265     0.200
VDW repulsions.others                          1367     0.203     0.200
VDW; torsion: refined_atoms                     720     0.173     0.200
VDW; torsion.others                             769     0.084     0.200
HBOND: refined_atoms                            216     0.201     0.200
HBOND.others                                      1     0.101     0.200
VDW repulsions: symmetry: refined_atoms           9     0.201     0.200
VDW repulsions: symmetry: others                 25     0.171     0.200
HBOND: symmetry: refined_atoms                   20     0.190     0.200
M. chain bond B values: refined atoms           745     1.745     1.624
M. chain bond B values: others                  745     1.741     1.624
M. chain angle B values: refined atoms          926     2.730     2.421
M. chain angle B values: others                 927     2.729     2.421
S. chain bond B values: refined atoms           811     3.147     2.036
S. chain bond B values: others                  810     3.142     2.036
S. chain angle B values: refined atoms         1177     4.817     2.885
S. chain angle B values: others                1178     4.815     2.885
Long range B values: refined atoms             1847     7.151    22.337
Long range B values: others                    1758     6.871    20.915
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0456, B  =   -0.0257
Partial structure    1: scale =     0.3915, B  =   39.0682
Overall anisotropic scale factors
   B11 =  -0.18 B22 =  -0.18 B33 =   0.36 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.056    4329 100.00   405.3   415.1  0.17  0.18     218   428.2   434.6  0.18  0.19
 0.167    7418  99.97   227.9   208.2  0.18  0.16     380   238.4   216.1  0.20  0.17
 0.278    9444 100.00   124.1   114.5  0.21  0.18     466   123.7   115.6  0.24  0.21
 0.389   11076 100.00    50.1    62.5  0.41  0.36     565    52.8    64.4  0.41  0.36
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0561   3219   0.925   1110   0.828   4329   0.900  0.948  0.9730  0.9723  0.9378  0.9330
  0.1670   6302   0.900   1116   0.803   7418   0.886  1.067  0.9617  0.9654  0.9204  0.9379
  0.2780   8317   0.853   1127   0.774   9444   0.843  1.020  0.9441  0.9526  0.9050  0.9294
  0.3890   9956   0.591   1132   0.520  11088   0.584  0.576  0.8059  0.7927  0.7612  0.7715
 $$
Resolution limits                    =     41.964     1.500
Number of used reflections           =      32279
Percentage observed                  =    99.9912
Percentage of free reflections       =     4.8042
Overall R factor                     =     0.2078
Free R factor                        =     0.2223
Average Fourier shell correlation    =     0.9032
AverageFree Fourier shell correlation=     0.9041
Overall weighted R factor            =     0.1763
Free weighted R factor               =     0.1923
Overall weighted R2 factor           =     0.2063
Free weighted R2 factor              =     0.2215
Average correlation coefficient      =     0.8776
Overall correlation coefficient      =     0.9587
Free correlation coefficient         =     0.9561
Cruickshanks DPI for coordinate error=     0.0860
DPI based on free R factor           =     0.0808
Overall figure of merit              =     0.7715
ML based su of positional parameters =     0.0630
ML based su of thermal parameters    =     1.8555
-----------------------------------------------------------------------------
  Time in seconds: CPU =        25.08
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2086   0.2232   0.754      156368.    8051.7   0.0122  0.923   1.794  1.041   0.088
       1   0.2083   0.2227   0.770      155478.    8027.1   0.0123  0.927   1.780  1.034   0.089
       2   0.2073   0.2225   0.771      155269.    8022.0   0.0132  1.001   1.828  1.062   0.091
       3   0.2070   0.2223   0.771      155234.    8021.2   0.0133  1.008   1.849  1.074   0.092
       4   0.2073   0.2224   0.771      155275.    8021.0   0.0127  0.965   1.830  1.061   0.090
       5   0.2076   0.2224   0.771      155334.    8021.8   0.0121  0.920   1.796  1.042   0.088
       6   0.2077   0.2223   0.771      155352.    8022.1   0.0121  0.916   1.787  1.036   0.087
       7   0.2077   0.2223   0.772      155355.    8022.3   0.0121  0.916   1.786  1.036   0.087
       8   0.2078   0.2223   0.771      155363.    8022.5   0.0121  0.915   1.785  1.035   0.087
       9   0.2078   0.2223   0.772      155365.    8022.5   0.0121  0.915   1.784  1.035   0.087
      10   0.2078   0.2223   0.772      155370.    8022.7   0.0121  0.915   1.783  1.035   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2086   0.2078
             R free    0.2232   0.2223
     Rms BondLength    0.0122   0.0121
      Rms BondAngle    1.7943   1.7828
     Rms ChirVolume    0.0877   0.0875
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      57.2s System:    0.2s Elapsed:     0:57