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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: 15:44:28 


 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 12
  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_R12_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R12_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_R12_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:    12
  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_R12_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=   2.001 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=   2.218 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=   1.803 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=   2.172 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=   2.333 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=   2.440 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=   2.075 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                           12
Number of "free" reflections        994
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.870 id.= 3.000 dev= -2.13 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   0.26837885    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                39.7
Norm of Geom. positional gradient                79.2
Norm of X_ray B-factor gradient                  129.
Norm of Geom. B-factor gradient                 0.216E+05
Product of X_ray and Geom posit. gradients     -0.111E+08
 Cosine of angle between them                      -0.364
Product of X_ray and Geom B-fact gradients     -0.420E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7065E+06 GEOM=     0.2633E+05 TOTAL=     0.7328E+06
 function value    732838.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.801     1.644
Bond angles  : others                          3242     2.340     1.582
Torsion angles, period  1. refined              184     6.916     5.000
Torsion angles, period  2. refined               90    37.023    22.778
Torsion angles, period  3. refined              268    14.359    15.000
Torsion angles, period  4. refined                9    10.363    15.000
Chiral centres: refined atoms                   196     0.084     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   293     0.268     0.200
VDW repulsions.others                          1344     0.231     0.200
VDW; torsion: refined_atoms                     712     0.172     0.200
VDW; torsion.others                             706     0.081     0.200
HBOND: refined_atoms                            240     0.208     0.200
HBOND.others                                      1     0.015     0.200
VDW repulsions: symmetry: refined_atoms          11     0.225     0.200
VDW repulsions: symmetry: others                 30     0.164     0.200
HBOND: symmetry: refined_atoms                   25     0.184     0.200
M. chain bond B values: refined atoms           745     1.644     1.211
M. chain bond B values: others                  745     1.643     1.211
M. chain angle B values: refined atoms          926     2.579     1.798
M. chain angle B values: others                 927     2.578     1.797
S. chain bond B values: refined atoms           811     2.686     1.571
S. chain bond B values: others                  810     2.684     1.571
S. chain angle B values: refined atoms         1177     4.235     2.201
S. chain angle B values: others                1178     4.233     2.200
Long range B values: refined atoms             1852     7.169    16.944
Long range B values: others                    1752     6.708    15.495
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0412, B  =    0.8425
Partial structure    1: scale =     0.3780, B  =   50.2870
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2565 100.00   474.2   482.2  0.16  0.17     128   466.5   480.0  0.18  0.19
 0.116    4352 100.00   341.9   326.8  0.16  0.15     227   350.9   333.3  0.21  0.19
 0.193    5518  99.97   226.7   215.6  0.16  0.14     290   224.7   216.4  0.23  0.20
 0.270    6438 100.00   148.1   155.1  0.21  0.16     349   149.2   157.5  0.25  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1806   0.925    759   0.842   2565   0.900  0.952  0.9637  0.9715  0.9118  0.9413
  0.1161   3586   0.894    766   0.795   4352   0.877  1.002  0.9527  0.9652  0.9017  0.9468
  0.1931   4747   0.872    771   0.757   5518   0.856  1.009  0.9423  0.9587  0.8656  0.9396
  0.2701   5663   0.822    783   0.738   6446   0.812  0.893  0.9334  0.9399  0.8812  0.9072
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18881
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0013
Overall R factor                     =     0.1691
Free R factor                        =     0.2178
Average Fourier shell correlation    =     0.9555
AverageFree Fourier shell correlation=     0.9443
Overall weighted R factor            =     0.1521
Free weighted R factor               =     0.1918
Overall weighted R2 factor           =     0.1828
Free weighted R2 factor              =     0.2202
Average correlation coefficient      =     0.9304
Overall correlation coefficient      =     0.9560
Free correlation coefficient         =     0.9262
Cruickshanks DPI for coordinate error=     0.1235
DPI based on free R factor           =     0.1243
Overall figure of merit              =     0.8517
ML based su of positional parameters =     0.0783
ML based su of thermal parameters    =     2.5511
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100936.40       26327.715       732838.19      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30385223    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    713659.00    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0674
Partial structure    1: scale =     0.3779, B  =   50.0538
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1680
Free R factor                        =     0.2155
Average Fourier shell correlation    =     0.9594
AverageFree Fourier shell correlation=     0.9481
Average correlation coefficient      =     0.9328
Overall figure of merit              =     0.8664
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100505.63       10163.713       713659.00       732838.19    


     CGMAT cycle number =      3

 Weight matrix   0.31014398    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    711162.75    

-------------------------------------------------------------------------------
             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 =     0.0412, B  =   -0.0221
Partial structure    1: scale =     0.3790, B  =   47.3954
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1668
Free R factor                        =     0.2141
Average Fourier shell correlation    =     0.9603
AverageFree Fourier shell correlation=     0.9490
Average correlation coefficient      =     0.9347
Overall figure of merit              =     0.8680
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100245.66       9487.0928       711162.75       713659.00    


     CGMAT cycle number =      4

 Weight matrix   0.31362444    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710288.75    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0089
Partial structure    1: scale =     0.3788, B  =   47.2359
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1665
Free R factor                        =     0.2135
Average Fourier shell correlation    =     0.9606
AverageFree Fourier shell correlation=     0.9494
Average correlation coefficient      =     0.9354
Overall figure of merit              =     0.8688
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100147.56       9299.7754       710288.75       711162.75    


     CGMAT cycle number =      5

 Weight matrix   0.31514284    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709860.00    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0246
Partial structure    1: scale =     0.3787, B  =   47.1689
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2132
Average Fourier shell correlation    =     0.9608
AverageFree Fourier shell correlation=     0.9495
Average correlation coefficient      =     0.9358
Overall figure of merit              =     0.8691
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100086.20       9300.5781       709860.00       710288.75    


     CGMAT cycle number =      6

 Weight matrix   0.31529784    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709767.75    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0277
Partial structure    1: scale =     0.3788, B  =   47.0995
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2133
Average Fourier shell correlation    =     0.9609
AverageFree Fourier shell correlation=     0.9495
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8691
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100067.12       9341.8193       709767.75       709860.00    


     CGMAT cycle number =      7

 Weight matrix   0.31543559    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709697.06    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0236
Partial structure    1: scale =     0.3789, B  =   47.0235
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1661
Free R factor                        =     0.2135
Average Fourier shell correlation    =     0.9609
AverageFree Fourier shell correlation=     0.9495
Average correlation coefficient      =     0.9361
Overall figure of merit              =     0.8691
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100055.40       9353.2012       709697.06       709767.75    


     CGMAT cycle number =      8

 Weight matrix   0.31567726    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709662.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0176
Partial structure    1: scale =     0.3790, B  =   47.1942
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2133
Average Fourier shell correlation    =     0.9609
AverageFree Fourier shell correlation=     0.9496
Average correlation coefficient      =     0.9362
Overall figure of merit              =     0.8691
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    100049.61       9358.9189       709662.31       709697.06    


     CGMAT cycle number =      9

 Weight matrix   0.31570080    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709617.75    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0173
Partial structure    1: scale =     0.3789, B  =   47.2039
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1662
Free R factor                        =     0.2134
Average Fourier shell correlation    =     0.9609
AverageFree Fourier shell correlation=     0.9495
Average correlation coefficient      =     0.9362
Overall figure of merit              =     0.8691
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    100043.39       9357.8633       709617.75       709662.31    


     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.= 0.889 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.31604442    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                39.8
Norm of Geom. positional gradient                39.7
Norm of X_ray B-factor gradient                  127.
Norm of Geom. B-factor gradient                  129.
Product of X_ray and Geom posit. gradients     -0.153E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.525E+08
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.7003E+06 GEOM=      9366.     TOTAL=     0.7097E+06
 function value    709684.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.851     1.644
Bond angles  : others                          3242     1.498     1.582
Torsion angles, period  1. refined              184     6.946     5.000
Torsion angles, period  2. refined               90    37.008    22.778
Torsion angles, period  3. refined              268    14.196    15.000
Torsion angles, period  4. refined                9    11.048    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   296     0.269     0.200
VDW repulsions.others                          1358     0.205     0.200
VDW; torsion: refined_atoms                     711     0.173     0.200
VDW; torsion.others                             784     0.085     0.200
HBOND: refined_atoms                            240     0.200     0.200
VDW repulsions: symmetry: refined_atoms          11     0.216     0.200
VDW repulsions: symmetry: others                 29     0.154     0.200
HBOND: symmetry: refined_atoms                   25     0.188     0.200
M. chain bond B values: refined atoms           745     1.675     1.286
M. chain bond B values: others                  745     1.674     1.286
M. chain angle B values: refined atoms          926     2.598     1.911
M. chain angle B values: others                 927     2.596     1.911
S. chain bond B values: refined atoms           811     2.931     1.670
S. chain bond B values: others                  810     2.928     1.670
S. chain angle B values: refined atoms         1177     4.570     2.342
S. chain angle B values: others                1178     4.568     2.342
Long range B values: refined atoms             1855     7.945    18.264
Long range B values: others                    1752     7.329    16.611
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0215
Partial structure    1: scale =     0.3788, B  =   47.2487
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2565 100.00   473.3   482.3  0.16  0.17     128   465.6   481.7  0.18  0.19
 0.116    4352 100.00   341.2   325.5  0.16  0.15     227   350.2   329.4  0.21  0.19
 0.193    5518  99.97   226.3   214.8  0.16  0.14     290   224.3   214.4  0.23  0.19
 0.270    6438 100.00   147.9   154.4  0.19  0.15     349   148.9   156.4  0.24  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1806   0.932    759   0.856   2565   0.909  0.953  0.9652  0.9727  0.9135  0.9413
  0.1161   3586   0.896    766   0.801   4352   0.880  1.003  0.9537  0.9660  0.9041  0.9472
  0.1931   4747   0.877    771   0.760   5518   0.860  1.009  0.9444  0.9594  0.8717  0.9377
  0.2701   5663   0.863    783   0.783   6446   0.853  0.911  0.9451  0.9539  0.8914  0.9255
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18881
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0013
Overall R factor                     =     0.1662
Free R factor                        =     0.2135
Average Fourier shell correlation    =     0.9609
AverageFree Fourier shell correlation=     0.9494
Overall weighted R factor            =     0.1515
Free weighted R factor               =     0.1892
Overall weighted R2 factor           =     0.1827
Free weighted R2 factor              =     0.2187
Average correlation coefficient      =     0.9362
Overall correlation coefficient      =     0.9571
Free correlation coefficient         =     0.9282
Cruickshanks DPI for coordinate error=     0.1214
DPI based on free R factor           =     0.1219
Overall figure of merit              =     0.8691
ML based su of positional parameters =     0.0721
ML based su of thermal parameters    =     2.3059
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    100051.81       9366.2861       709676.69       709617.75    
 fvalues    100051.81       9366.2861       709676.69       709685.13    

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.889 id.= 3.000 dev= -2.11 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_R12_1-80A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.852     1.644
Bond angles  : others                          3242     1.498     1.582
Torsion angles, period  1. refined              184     6.941     5.000
Torsion angles, period  2. refined               90    37.025    22.778
Torsion angles, period  3. refined              268    14.213    15.000
Torsion angles, period  4. refined                9    11.037    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   299     0.268     0.200
VDW repulsions.others                          1361     0.205     0.200
VDW; torsion: refined_atoms                     713     0.173     0.200
VDW; torsion.others                             785     0.085     0.200
HBOND: refined_atoms                            238     0.202     0.200
VDW repulsions: symmetry: refined_atoms          11     0.214     0.200
VDW repulsions: symmetry: others                 28     0.156     0.200
HBOND: symmetry: refined_atoms                   25     0.189     0.200
M. chain bond B values: refined atoms           745     1.674     1.287
M. chain bond B values: others                  745     1.672     1.287
M. chain angle B values: refined atoms          926     2.595     1.913
M. chain angle B values: others                 927     2.594     1.912
S. chain bond B values: refined atoms           811     2.929     1.671
S. chain bond B values: others                  810     2.926     1.671
S. chain angle B values: refined atoms         1177     4.567     2.344
S. chain angle B values: others                1178     4.565     2.343
Long range B values: refined atoms             1856     8.136    18.276
Long range B values: others                    1755     7.525    16.664
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0410
Partial structure    1: scale =     0.3787, B  =   47.2520
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2565 100.00   473.4   482.3  0.16  0.17     128   465.7   481.7  0.18  0.19
 0.116    4352 100.00   341.2   325.5  0.16  0.15     227   350.3   329.5  0.21  0.19
 0.193    5518  99.97   226.3   214.9  0.16  0.14     290   224.3   214.4  0.23  0.19
 0.270    6438 100.00   147.9   154.4  0.19  0.15     349   148.9   156.4  0.24  0.18
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1806   0.932    759   0.855   2565   0.909  0.953  0.9652  0.9727  0.9135  0.9414
  0.1161   3586   0.896    766   0.801   4352   0.879  1.003  0.9535  0.9659  0.9035  0.9471
  0.1931   4747   0.876    771   0.761   5518   0.860  1.009  0.9443  0.9593  0.8715  0.9376
  0.2701   5663   0.863    783   0.783   6446   0.854  0.911  0.9452  0.9540  0.8917  0.9258
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18881
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.0013
Overall R factor                     =     0.1662
Free R factor                        =     0.2138
Average Fourier shell correlation    =     0.9608
AverageFree Fourier shell correlation=     0.9494
Overall weighted R factor            =     0.1515
Free weighted R factor               =     0.1896
Overall weighted R2 factor           =     0.1827
Free weighted R2 factor              =     0.2191
Average correlation coefficient      =     0.9363
Overall correlation coefficient      =     0.9571
Free correlation coefficient         =     0.9281
Cruickshanks DPI for coordinate error=     0.1214
DPI based on free R factor           =     0.1221
Overall figure of merit              =     0.8690
ML based su of positional parameters =     0.0721
ML based su of thermal parameters    =     2.3059
-----------------------------------------------------------------------------
  Time in seconds: CPU =        15.25
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1691   0.2178   0.852      100936.    5471.3   0.0128  0.931   1.801  1.038   0.084
       1   0.1680   0.2155   0.866      100506.    5456.3   0.0124  0.902   1.772  1.022   0.084
       2   0.1668   0.2141   0.868      100246.    5447.6   0.0132  0.962   1.808  1.042   0.085
       3   0.1665   0.2135   0.869      100148.    5442.9   0.0133  0.971   1.825  1.051   0.085
       4   0.1662   0.2132   0.869      100086.    5439.9   0.0133  0.975   1.835  1.056   0.085
       5   0.1662   0.2133   0.869      100067.    5439.3   0.0133  0.976   1.841  1.059   0.085
       6   0.1661   0.2135   0.869      100055.    5438.8   0.0133  0.976   1.844  1.061   0.085
       7   0.1662   0.2133   0.869      100050.    5437.5   0.0133  0.975   1.846  1.061   0.085
       8   0.1662   0.2134   0.869      100043.    5436.6   0.0133  0.977   1.848  1.063   0.085
       9   0.1662   0.2135   0.869      100052.    5437.0   0.0133  0.978   1.851  1.064   0.085
      10   0.1662   0.2138   0.869      100053.    5437.6   0.0134  0.979   1.852  1.065   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1691   0.1662
             R free    0.2178   0.2138
     Rms BondLength    0.0128   0.0134
      Rms BondAngle    1.8008   1.8522
     Rms ChirVolume    0.0841   0.0849
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      47.5s System:    0.1s Elapsed:     0:48