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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: 17:37:35 


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


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

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

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

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

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

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

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

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

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.60     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 4
  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_R04_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R04_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R04_1-60A.mtz

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

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

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


  Residual                               : Rice Maximum Likelihood for Fs

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

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


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

No map sharpening will be performed

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

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

  Scaling and SigmaA resln:    41.9635  1.6000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R04_1-70A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.053 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.198 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.838 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=   2.225 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=   2.387 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=   2.391 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=   2.090 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                            4
Number of "free" reflections       1462
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.904 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.31802976    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                41.7
Norm of Geom. positional gradient                79.2
Norm of X_ray B-factor gradient                  124.
Norm of Geom. B-factor gradient                 0.207E+05
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.432
Product of X_ray and Geom B-fact gradients     -0.393E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8700E+06 GEOM=     0.2546E+05 TOTAL=     0.8955E+06
 function value    895482.69    

-------------------------------------------------------------------------------
             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     1.767     1.644
Bond angles  : others                          3242     2.339     1.582
Torsion angles, period  1. refined              184     6.852     5.000
Torsion angles, period  2. refined               90    36.404    22.778
Torsion angles, period  3. refined              268    13.883    15.000
Torsion angles, period  4. refined                9    11.230    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   304     0.269     0.200
VDW repulsions.others                          1356     0.229     0.200
VDW; torsion: refined_atoms                     727     0.170     0.200
VDW; torsion.others                             714     0.081     0.200
HBOND: refined_atoms                            215     0.203     0.200
HBOND.others                                      3     0.080     0.200
VDW repulsions: symmetry: refined_atoms           9     0.215     0.200
VDW repulsions: symmetry: others                 22     0.206     0.200
HBOND: symmetry: refined_atoms                   23     0.209     0.200
HBOND: symmetry: others                           1     0.006     0.200
M. chain bond B values: refined atoms           745     1.632     1.393
M. chain bond B values: others                  745     1.630     1.393
M. chain angle B values: refined atoms          926     2.584     2.075
M. chain angle B values: others                 927     2.583     2.075
S. chain bond B values: refined atoms           811     2.917     1.787
S. chain bond B values: others                  810     2.910     1.786
S. chain angle B values: refined atoms         1177     4.580     2.515
S. chain angle B values: others                1178     4.578     2.514
Long range B values: refined atoms             1846     7.079    19.468
Long range B values: others                    1757     6.799    18.076
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    1.2523
Partial structure    1: scale =     0.3877, B  =   48.0499
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3580 100.00   433.6   442.8  0.16  0.17     202   417.2   431.5  0.20  0.20
 0.147    6130  99.97   258.7   243.3  0.17  0.15     314   262.0   248.7  0.22  0.19
 0.244    7804 100.00   167.6   151.7  0.19  0.17     414   164.5   148.7  0.22  0.18
 0.342    9058 100.00    71.5    85.7  0.33  0.26     532    69.3    84.0  0.35  0.29
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2614   0.922    966   0.826   3580   0.896  0.953  0.9682  0.9713  0.9302  0.9366
  0.1468   5157   0.882    973   0.784   6130   0.866  1.023  0.9540  0.9611  0.9111  0.9387
  0.2444   6814   0.869    990   0.767   7804   0.856  1.053  0.9466  0.9557  0.9125  0.9372
  0.3419   8092   0.690    971   0.613   9063   0.682  0.717  0.8585  0.8759  0.8158  0.8540
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26576
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.2144
Overall R factor                     =     0.1931
Free R factor                        =     0.2288
Average Fourier shell correlation    =     0.9318
AverageFree Fourier shell correlation=     0.9191
Overall weighted R factor            =     0.1669
Free weighted R factor               =     0.1987
Overall weighted R2 factor           =     0.1961
Free weighted R2 factor              =     0.2392
Average correlation coefficient      =     0.9091
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9466
Cruickshanks DPI for coordinate error=     0.0972
DPI based on free R factor           =     0.0979
Overall figure of merit              =     0.8043
ML based su of positional parameters =     0.0693
ML based su of thermal parameters    =     2.0820
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    133857.23       25457.199       895482.69      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.39506400    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872871.25    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =   -0.0421
Partial structure    1: scale =     0.3878, B  =   47.7311
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1926
Free R factor                        =     0.2280
Average Fourier shell correlation    =     0.9433
AverageFree Fourier shell correlation=     0.9325
Average correlation coefficient      =     0.9107
Overall figure of merit              =     0.8377
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    132787.56       9798.2422       872871.25       895482.69    


     CGMAT cycle number =      3

 Weight matrix   0.41081530    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    870373.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0078
Partial structure    1: scale =     0.3881, B  =   44.0957
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1913
Free R factor                        =     0.2272
Average Fourier shell correlation    =     0.9458
AverageFree Fourier shell correlation=     0.9351
Average correlation coefficient      =     0.9132
Overall figure of merit              =     0.8447
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132465.44       9393.7480       870373.06       872871.25    


     CGMAT cycle number =      4

 Weight matrix   0.37709585    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    791389.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0069
Partial structure    1: scale =     0.3883, B  =   43.6133
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1910
Free R factor                        =     0.2267
Average Fourier shell correlation    =     0.9465
AverageFree Fourier shell correlation=     0.9358
Average correlation coefficient      =     0.9142
Overall figure of merit              =     0.8462
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132352.41       9348.5723       791389.13       870373.06    


     CGMAT cycle number =      5

 Weight matrix   0.34306258    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    720161.56    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0122
Partial structure    1: scale =     0.3874, B  =   43.3724
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1913
Free R factor                        =     0.2266
Average Fourier shell correlation    =     0.9466
AverageFree Fourier shell correlation=     0.9359
Average correlation coefficient      =     0.9143
Overall figure of merit              =     0.8464
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132367.05       9136.9219       720161.56       791389.13    


     CGMAT cycle number =      6

 Weight matrix   0.34265706    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    720165.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0142
Partial structure    1: scale =     0.3873, B  =   43.3368
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1917
Free R factor                        =     0.2266
Average Fourier shell correlation    =     0.9465
AverageFree Fourier shell correlation=     0.9359
Average correlation coefficient      =     0.9140
Overall figure of merit              =     0.8464
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03


 fvalues    132425.78       8836.8887       720171.44       720161.56    
 fvalues    132425.78       8836.8887       720171.44       720177.00    


     CGMAT cycle number =      7

 Weight matrix   0.34228316    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    720167.75    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0197
Partial structure    1: scale =     0.3871, B  =   43.3556
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1918
Free R factor                        =     0.2267
Average Fourier shell correlation    =     0.9464
AverageFree Fourier shell correlation=     0.9358
Average correlation coefficient      =     0.9140
Overall figure of merit              =     0.8463
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    132437.69       8763.6582       720167.75       720177.00    


     CGMAT cycle number =      8

 Weight matrix   0.34196958    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    720198.06    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0225
Partial structure    1: scale =     0.3871, B  =   43.2388
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1919
Free R factor                        =     0.2269
Average Fourier shell correlation    =     0.9464
AverageFree Fourier shell correlation=     0.9358
Average correlation coefficient      =     0.9139
Overall figure of merit              =     0.8462
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    132448.09       8728.3857       720188.31       720167.75    
 fvalues    132448.09       8728.3857       720188.31       720188.38    


     CGMAT cycle number =      9

 Weight matrix   0.34166881    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    720197.69    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0233
Partial structure    1: scale =     0.3871, B  =   43.2912
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1920
Free R factor                        =     0.2268
Average Fourier shell correlation    =     0.9464
AverageFree Fourier shell correlation=     0.9358
Average correlation coefficient      =     0.9140
Overall figure of merit              =     0.8461
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    132454.67       8702.7725       720197.38       720188.38    
 fvalues    132454.67       8702.7725       720197.38       720198.06    


     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.= 0.906 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.34154490    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                39.6
Norm of Geom. positional gradient                39.6
Norm of X_ray B-factor gradient                  111.
Norm of Geom. B-factor gradient                  109.
Product of X_ray and Geom posit. gradients     -0.152E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.389E+08
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.7115E+06 GEOM=      8692.     TOTAL=     0.7202E+06
 function value    720213.75    

-------------------------------------------------------------------------------
             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     1.797     1.644
Bond angles  : others                          3242     1.501     1.582
Torsion angles, period  1. refined              184     6.844     5.000
Torsion angles, period  2. refined               90    35.971    22.778
Torsion angles, period  3. refined              268    13.484    15.000
Torsion angles, period  4. refined                9    11.271    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   314     0.266     0.200
VDW repulsions.others                          1370     0.204     0.200
VDW; torsion: refined_atoms                     729     0.171     0.200
VDW; torsion.others                             785     0.084     0.200
HBOND: refined_atoms                            213     0.208     0.200
HBOND.others                                      2     0.130     0.200
VDW repulsions: symmetry: refined_atoms           8     0.232     0.200
VDW repulsions: symmetry: others                 24     0.199     0.200
HBOND: symmetry: refined_atoms                   22     0.206     0.200
HBOND: symmetry: others                           1     0.020     0.200
M. chain bond B values: refined atoms           745     1.686     1.509
M. chain bond B values: others                  745     1.682     1.509
M. chain angle B values: refined atoms          926     2.652     2.251
M. chain angle B values: others                 927     2.650     2.251
S. chain bond B values: refined atoms           811     3.049     1.908
S. chain bond B values: others                  810     3.043     1.907
S. chain angle B values: refined atoms         1177     4.724     2.695
S. chain angle B values: others                1178     4.722     2.695
Long range B values: refined atoms             1857     7.340    21.079
Long range B values: others                    1770     7.077    19.716
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0227
Partial structure    1: scale =     0.3872, B  =   43.3015
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3580 100.00   433.8   443.2  0.16  0.17     202   417.4   431.1  0.19  0.20
 0.147    6130  99.97   258.9   243.2  0.17  0.15     314   262.1   249.9  0.22  0.19
 0.244    7804 100.00   167.7   151.7  0.19  0.17     414   164.6   148.5  0.22  0.18
 0.342    9058 100.00    71.6    85.4  0.32  0.25     532    69.4    83.8  0.35  0.28
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2614   0.934    966   0.846   3580   0.911  0.954  0.9711  0.9741  0.9301  0.9366
  0.1468   5157   0.887    973   0.791   6130   0.872  1.023  0.9560  0.9627  0.9124  0.9394
  0.2444   6814   0.882    990   0.783   7804   0.870  1.053  0.9513  0.9596  0.9143  0.9355
  0.3419   8092   0.791    971   0.713   9063   0.782  0.758  0.8982  0.9131  0.8200  0.8693
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26576
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.2144
Overall R factor                     =     0.1920
Free R factor                        =     0.2269
Average Fourier shell correlation    =     0.9464
AverageFree Fourier shell correlation=     0.9357
Overall weighted R factor            =     0.1668
Free weighted R factor               =     0.1969
Overall weighted R2 factor           =     0.1963
Free weighted R2 factor              =     0.2383
Average correlation coefficient      =     0.9140
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9472
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0972
Overall figure of merit              =     0.8461
ML based su of positional parameters =     0.0607
ML based su of thermal parameters    =     1.7824
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    132458.14       8692.0752       720221.31       720198.06    

 fvalues    132458.14       8692.0752       720208.94       720206.00    
 fvalues    132458.14       8692.0752       720208.94       720206.00    

    ****                              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.= 0.906 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R04_1-60A.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     1.797     1.644
Bond angles  : others                          3242     1.501     1.582
Torsion angles, period  1. refined              184     6.843     5.000
Torsion angles, period  2. refined               90    35.962    22.778
Torsion angles, period  3. refined              268    13.479    15.000
Torsion angles, period  4. refined                9    11.270    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   314     0.266     0.200
VDW repulsions.others                          1372     0.204     0.200
VDW; torsion: refined_atoms                     729     0.171     0.200
VDW; torsion.others                             784     0.084     0.200
HBOND: refined_atoms                            213     0.208     0.200
HBOND.others                                      2     0.130     0.200
VDW repulsions: symmetry: refined_atoms           8     0.232     0.200
VDW repulsions: symmetry: others                 24     0.199     0.200
HBOND: symmetry: refined_atoms                   23     0.202     0.200
HBOND: symmetry: others                           1     0.020     0.200
M. chain bond B values: refined atoms           745     1.686     1.509
M. chain bond B values: others                  745     1.682     1.509
M. chain angle B values: refined atoms          926     2.651     2.251
M. chain angle B values: others                 927     2.650     2.251
S. chain bond B values: refined atoms           811     3.048     1.908
S. chain bond B values: others                  810     3.043     1.907
S. chain angle B values: refined atoms         1177     4.723     2.695
S. chain angle B values: others                1178     4.721     2.694
Long range B values: refined atoms             1857     7.340    21.078
Long range B values: others                    1770     7.077    19.716
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0170
Partial structure    1: scale =     0.3871, B  =   43.2861
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3580 100.00   433.7   443.2  0.16  0.17     202   417.3   431.1  0.19  0.20
 0.147    6130  99.97   258.8   243.3  0.17  0.15     314   262.1   250.0  0.22  0.19
 0.244    7804 100.00   167.6   151.8  0.19  0.17     414   164.6   148.6  0.22  0.18
 0.342    9058 100.00    71.6    85.5  0.32  0.25     532    69.3    83.8  0.35  0.28
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2614   0.934    966   0.846   3580   0.911  0.954  0.9711  0.9741  0.9300  0.9367
  0.1468   5157   0.887    973   0.791   6130   0.872  1.023  0.9560  0.9627  0.9124  0.9394
  0.2444   6814   0.883    990   0.783   7804   0.870  1.053  0.9514  0.9597  0.9143  0.9355
  0.3419   8092   0.791    971   0.713   9063   0.783  0.758  0.8983  0.9131  0.8199  0.8693
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26576
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.2144
Overall R factor                     =     0.1920
Free R factor                        =     0.2269
Average Fourier shell correlation    =     0.9464
AverageFree Fourier shell correlation=     0.9358
Overall weighted R factor            =     0.1668
Free weighted R factor               =     0.1969
Overall weighted R2 factor           =     0.1963
Free weighted R2 factor              =     0.2384
Average correlation coefficient      =     0.9140
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9472
Cruickshanks DPI for coordinate error=     0.0966
DPI based on free R factor           =     0.0972
Overall figure of merit              =     0.8462
ML based su of positional parameters =     0.0607
ML based su of thermal parameters    =     1.7824
-----------------------------------------------------------------------------
  Time in seconds: CPU =        21.61
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1931   0.2288   0.804      133857.    7486.5   0.0122  0.909   1.767  1.027   0.087
       1   0.1926   0.2280   0.838      132788.    7444.0   0.0125  0.927   1.768  1.030   0.088
       2   0.1913   0.2272   0.845      132465.    7432.1   0.0135  1.005   1.825  1.064   0.091
       3   0.1910   0.2267   0.846      132352.    7426.8   0.0137  1.022   1.854  1.082   0.092
       4   0.1913   0.2266   0.846      132367.    7426.2   0.0132  0.983   1.841  1.073   0.090
       5   0.1917   0.2266   0.846      132424.    7426.7   0.0126  0.939   1.811  1.055   0.088
       6   0.1918   0.2267   0.846      132438.    7427.1   0.0125  0.935   1.803  1.050   0.088
       7   0.1919   0.2269   0.846      132450.    7428.1   0.0125  0.932   1.799  1.048   0.088
       8   0.1920   0.2268   0.846      132455.    7428.6   0.0125  0.931   1.798  1.047   0.088
       9   0.1920   0.2269   0.846      132460.    7428.8   0.0125  0.930   1.797  1.046   0.088
      10   0.1920   0.2269   0.846      132456.    7428.8   0.0125  0.930   1.797  1.046   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1931   0.1920
             R free    0.2288   0.2269
     Rms BondLength    0.0122   0.0125
      Rms BondAngle    1.7669   1.7967
     Rms ChirVolume    0.0871   0.0875
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      53.9s System:    0.2s Elapsed:     0:54