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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: 16:12:07 


 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 1.70     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 1
  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_R01_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R01_1-70A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R01_1-70A.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       0.0865
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.7000
  Estimated number of reflections :      29131
  Free R exclusion - flag equals:     1
  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  1.7000

  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_R01_1-80A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.047 ideal_dist=   2.090
            ch:AAA  res:  86  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.217 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=   1.844 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=   2.176 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=   2.422 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=   2.417 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=   2.104 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                            1
Number of "free" reflections       1171
Number of   all  reflections      23491
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          23491

   Current auto weighting coefficient =    6.7496872    

 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.= 0.907 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.30440235    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                41.8
Norm of Geom. positional gradient                79.6
Norm of X_ray B-factor gradient                  137.
Norm of Geom. B-factor gradient                 0.219E+05
Product of X_ray and Geom posit. gradients     -0.125E+08
 Cosine of angle between them                      -0.387
Product of X_ray and Geom B-fact gradients     -0.432E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.7825E+06 GEOM=     0.2649E+05 TOTAL=     0.8090E+06
 function value    809013.94    

-------------------------------------------------------------------------------
             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     1.806     1.644
Bond angles  : others                          3242     2.347     1.582
Torsion angles, period  1. refined              184     6.931     5.000
Torsion angles, period  2. refined               90    36.468    22.778
Torsion angles, period  3. refined              268    13.775    15.000
Torsion angles, period  4. refined                9    11.478    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   298     0.272     0.200
VDW repulsions.others                          1316     0.232     0.200
VDW; torsion: refined_atoms                     719     0.171     0.200
VDW; torsion.others                             711     0.081     0.200
HBOND: refined_atoms                            221     0.203     0.200
HBOND.others                                      1     0.067     0.200
VDW repulsions: symmetry: refined_atoms           7     0.239     0.200
VDW repulsions: symmetry: others                 22     0.203     0.200
HBOND: symmetry: refined_atoms                   24     0.193     0.200
HBOND: symmetry: others                           1     0.036     0.200
M. chain bond B values: refined atoms           745     1.660     1.292
M. chain bond B values: others                  745     1.659     1.292
M. chain angle B values: refined atoms          926     2.582     1.919
M. chain angle B values: others                 927     2.581     1.919
S. chain bond B values: refined atoms           811     2.844     1.669
S. chain bond B values: others                  810     2.841     1.668
S. chain angle B values: refined atoms         1177     4.473     2.342
S. chain angle B values: others                1178     4.471     2.342
Long range B values: refined atoms             1841     6.868    17.974
Long range B values: others                    1746     6.607    16.541
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =    1.1426
Partial structure    1: scale =     0.3867, B  =   48.7705
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3006 100.00   454.2   463.5  0.16  0.17     165   442.0   449.4  0.20  0.20
 0.130    5121 100.00   298.3   285.0  0.16  0.14     279   309.8   302.9  0.20  0.18
 0.216    6543  99.97   202.0   185.7  0.17  0.15     329   208.2   195.7  0.22  0.19
 0.303    7645 100.00   103.9   116.7  0.27  0.20     398   108.3   120.2  0.28  0.21
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2164   0.909    842   0.801   3006   0.878  0.947  0.9573  0.9688  0.8900  0.9395
  0.1301   4273   0.889    848   0.783   5121   0.871  1.004  0.9578  0.9655  0.9079  0.9480
  0.2165   5647   0.875    896   0.759   6543   0.859  1.041  0.9468  0.9575  0.8935  0.9385
  0.3028   6778   0.783    870   0.709   7648   0.775  0.821  0.9213  0.9219  0.8918  0.8889
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22318
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9853
Overall R factor                     =     0.1794
Free R factor                        =     0.2185
Average Fourier shell correlation    =     0.9487
AverageFree Fourier shell correlation=     0.9422
Overall weighted R factor            =     0.1584
Free weighted R factor               =     0.1914
Overall weighted R2 factor           =     0.1906
Free weighted R2 factor              =     0.2195
Average correlation coefficient      =     0.9238
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9304
Cruickshanks DPI for coordinate error=     0.1086
DPI based on free R factor           =     0.1084
Overall figure of merit              =     0.8357
ML based su of positional parameters =     0.0722
ML based su of thermal parameters    =     2.2369
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    115934.97       26489.207       809013.94      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.33707127    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788433.06    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0500
Partial structure    1: scale =     0.3880, B  =   48.4307
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1790
Free R factor                        =     0.2177
Average Fourier shell correlation    =     0.9530
AverageFree Fourier shell correlation=     0.9459
Average correlation coefficient      =     0.9260
Overall figure of merit              =     0.8501
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115334.02       9964.5762       788433.06       809013.94    


     CGMAT cycle number =      3

 Weight matrix   0.34322491    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786378.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0376
Partial structure    1: scale =     0.3887, B  =   44.9872
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1779
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9540
AverageFree Fourier shell correlation=     0.9467
Average correlation coefficient      =     0.9277
Overall figure of merit              =     0.8523
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    115131.44       9277.5947       786378.81       788433.06    


     CGMAT cycle number =      4

 Weight matrix   0.34463066    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785696.56    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0068
Partial structure    1: scale =     0.3889, B  =   44.9088
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1775
Free R factor                        =     0.2153
Average Fourier shell correlation    =     0.9543
AverageFree Fourier shell correlation=     0.9470
Average correlation coefficient      =     0.9284
Overall figure of merit              =     0.8527
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    115054.74       9113.0469       785696.56       786378.81    


     CGMAT cycle number =      5

 Weight matrix   0.34566328    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785433.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0036
Partial structure    1: scale =     0.3894, B  =   45.0554
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1773
Free R factor                        =     0.2150
Average Fourier shell correlation    =     0.9545
AverageFree Fourier shell correlation=     0.9472
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8530
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    115015.12       9117.1729       785433.25       785696.56    


     CGMAT cycle number =      6

 Weight matrix   0.34633294    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785329.81    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0001
Partial structure    1: scale =     0.3894, B  =   45.0566
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1773
Free R factor                        =     0.2149
Average Fourier shell correlation    =     0.9546
AverageFree Fourier shell correlation=     0.9473
Average correlation coefficient      =     0.9289
Overall figure of merit              =     0.8532
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114995.13       9148.6045       785329.81       785433.25    


     CGMAT cycle number =      7

 Weight matrix   0.34716234    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785194.94    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =    0.0051
Partial structure    1: scale =     0.3900, B  =   45.0652
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1772
Free R factor                        =     0.2146
Average Fourier shell correlation    =     0.9547
AverageFree Fourier shell correlation=     0.9475
Average correlation coefficient      =     0.9290
Overall figure of merit              =     0.8535
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    114972.38       9167.3223       785194.94       785329.81    


     CGMAT cycle number =      8

 Weight matrix   0.34770676    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785109.50    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =    0.0067
Partial structure    1: scale =     0.3905, B  =   45.0459
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1772
Free R factor                        =     0.2145
Average Fourier shell correlation    =     0.9548
AverageFree Fourier shell correlation=     0.9476
Average correlation coefficient      =     0.9291
Overall figure of merit              =     0.8536
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    114957.48       9182.4785       785109.50       785194.94    


     CGMAT cycle number =      9

 Weight matrix   0.34739518    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785055.31    

-------------------------------------------------------------------------------
             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 =     0.0427, B  =    0.0116
Partial structure    1: scale =     0.3913, B  =   44.9007
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1771
Free R factor                        =     0.2147
Average Fourier shell correlation    =     0.9548
AverageFree Fourier shell correlation=     0.9476
Average correlation coefficient      =     0.9291
Overall figure of merit              =     0.8536
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    114949.22       9184.0771       785055.31       785109.50    


     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.= 0.920 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.34761974    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                41.5
Norm of Geom. positional gradient                41.4
Norm of X_ray B-factor gradient                  123.
Norm of Geom. B-factor gradient                  122.
Product of X_ray and Geom posit. gradients     -0.166E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.485E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.7759E+06 GEOM=      9187.     TOTAL=     0.7850E+06
 function value    785041.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.817     1.644
Bond angles  : others                          3242     1.495     1.582
Torsion angles, period  1. refined              184     6.878     5.000
Torsion angles, period  2. refined               90    36.231    22.778
Torsion angles, period  3. refined              268    13.418    15.000
Torsion angles, period  4. refined                9    11.856    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.271     0.200
VDW repulsions.others                          1350     0.204     0.200
VDW; torsion: refined_atoms                     723     0.172     0.200
VDW; torsion.others                             790     0.084     0.200
HBOND: refined_atoms                            219     0.195     0.200
HBOND.others                                      1     0.103     0.200
VDW repulsions: symmetry: refined_atoms           8     0.203     0.200
VDW repulsions: symmetry: others                 23     0.171     0.200
HBOND: symmetry: refined_atoms                   23     0.186     0.200
HBOND: symmetry: others                           1     0.003     0.200
M. chain bond B values: refined atoms           745     1.717     1.391
M. chain bond B values: others                  745     1.714     1.391
M. chain angle B values: refined atoms          926     2.674     2.071
M. chain angle B values: others                 927     2.673     2.071
S. chain bond B values: refined atoms           811     3.076     1.795
S. chain bond B values: others                  810     3.068     1.794
S. chain angle B values: refined atoms         1177     4.764     2.522
S. chain angle B values: others                1178     4.762     2.521
Long range B values: refined atoms             1842     7.070    19.302
Long range B values: others                    1751     6.833    17.881
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =    0.0027
Partial structure    1: scale =     0.3914, B  =   44.9360
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3006 100.00   454.0   463.5  0.16  0.17     165   441.7   450.1  0.20  0.20
 0.130    5121 100.00   298.1   284.4  0.16  0.14     279   309.6   300.6  0.19  0.17
 0.216    6543  99.97   201.9   185.7  0.17  0.15     329   208.1   195.7  0.22  0.18
 0.303    7645 100.00   103.9   116.0  0.25  0.19     398   108.2   120.0  0.28  0.21
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2164   0.927    842   0.829   3006   0.900  0.949  0.9614  0.9731  0.8886  0.9388
  0.1301   4273   0.896    848   0.791   5121   0.878  1.004  0.9611  0.9675  0.9149  0.9483
  0.2165   5647   0.882    896   0.767   6543   0.866  1.041  0.9505  0.9597  0.8993  0.9383
  0.3028   6778   0.817    870   0.739   7648   0.808  0.834  0.9300  0.9349  0.8928  0.9045
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22318
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9853
Overall R factor                     =     0.1772
Free R factor                        =     0.2147
Average Fourier shell correlation    =     0.9548
AverageFree Fourier shell correlation=     0.9476
Overall weighted R factor            =     0.1580
Free weighted R factor               =     0.1873
Overall weighted R2 factor           =     0.1903
Free weighted R2 factor              =     0.2158
Average correlation coefficient      =     0.9291
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9321
Cruickshanks DPI for coordinate error=     0.1073
DPI based on free R factor           =     0.1065
Overall figure of merit              =     0.8536
ML based su of positional parameters =     0.0675
ML based su of thermal parameters    =     2.0795
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    114946.73       9186.6973       785041.13       785055.31    

    ****                              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.= 0.920 id.= 3.000 dev= -2.08 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_R01_1-70A.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     1.818     1.644
Bond angles  : others                          3242     1.495     1.582
Torsion angles, period  1. refined              184     6.876     5.000
Torsion angles, period  2. refined               90    36.208    22.778
Torsion angles, period  3. refined              268    13.402    15.000
Torsion angles, period  4. refined                9    11.866    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   300     0.271     0.200
VDW repulsions.others                          1346     0.204     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             791     0.084     0.200
HBOND: refined_atoms                            219     0.196     0.200
HBOND.others                                      1     0.104     0.200
VDW repulsions: symmetry: refined_atoms           8     0.202     0.200
VDW repulsions: symmetry: others                 23     0.170     0.200
HBOND: symmetry: refined_atoms                   23     0.185     0.200
HBOND: symmetry: others                           1     0.001     0.200
M. chain bond B values: refined atoms           745     1.717     1.391
M. chain bond B values: others                  745     1.714     1.391
M. chain angle B values: refined atoms          926     2.674     2.071
M. chain angle B values: others                 927     2.673     2.071
S. chain bond B values: refined atoms           811     3.080     1.795
S. chain bond B values: others                  810     3.072     1.794
S. chain angle B values: refined atoms         1177     4.769     2.522
S. chain angle B values: others                1178     4.767     2.521
Long range B values: refined atoms             1841     7.074    19.294
Long range B values: others                    1750     6.839    17.877
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =    0.0034
Partial structure    1: scale =     0.3905, B  =   44.6973
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.45 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3006 100.00   454.1   463.6  0.16  0.17     165   441.9   449.6  0.20  0.20
 0.130    5121 100.00   298.2   284.4  0.16  0.14     279   309.7   300.6  0.19  0.17
 0.216    6543  99.97   201.9   185.7  0.17  0.15     329   208.2   195.8  0.22  0.18
 0.303    7645 100.00   103.9   116.0  0.25  0.19     398   108.3   120.0  0.28  0.21
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2164   0.927    842   0.829   3006   0.899  0.949  0.9611  0.9730  0.8892  0.9389
  0.1301   4273   0.896    848   0.791   5121   0.878  1.004  0.9612  0.9675  0.9149  0.9484
  0.2165   5647   0.882    896   0.767   6543   0.866  1.041  0.9505  0.9597  0.8993  0.9382
  0.3028   6778   0.817    870   0.739   7648   0.808  0.834  0.9300  0.9350  0.8929  0.9046
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22318
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.9853
Overall R factor                     =     0.1771
Free R factor                        =     0.2149
Average Fourier shell correlation    =     0.9548
AverageFree Fourier shell correlation=     0.9476
Overall weighted R factor            =     0.1580
Free weighted R factor               =     0.1875
Overall weighted R2 factor           =     0.1903
Free weighted R2 factor              =     0.2160
Average correlation coefficient      =     0.9291
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9323
Cruickshanks DPI for coordinate error=     0.1073
DPI based on free R factor           =     0.1066
Overall figure of merit              =     0.8535
ML based su of positional parameters =     0.0675
ML based su of thermal parameters    =     2.0795
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.32
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1794   0.2185   0.836      115935.    6292.6   0.0127  0.934   1.806  1.041   0.086
       1   0.1790   0.2177   0.850      115334.    6278.1   0.0124  0.919   1.776  1.026   0.086
       2   0.1779   0.2161   0.852      115131.    6271.4   0.0129  0.962   1.793  1.038   0.088
       3   0.1775   0.2153   0.853      115055.    6267.7   0.0130  0.970   1.801  1.045   0.089
       4   0.1773   0.2150   0.853      115015.    6265.4   0.0130  0.972   1.806  1.047   0.089
       5   0.1773   0.2149   0.853      114995.    6264.0   0.0130  0.974   1.809  1.049   0.089
       6   0.1772   0.2146   0.853      114972.    6262.5   0.0131  0.975   1.811  1.051   0.090
       7   0.1772   0.2145   0.854      114957.    6261.3   0.0131  0.976   1.814  1.052   0.090
       8   0.1771   0.2147   0.854      114949.    6261.2   0.0131  0.977   1.816  1.053   0.090
       9   0.1772   0.2147   0.854      114947.    6261.1   0.0131  0.977   1.817  1.053   0.090
      10   0.1771   0.2149   0.853      114958.    6262.1   0.0131  0.977   1.818  1.053   0.090
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1794   0.1771
             R free    0.2185   0.2149
     Rms BondLength    0.0127   0.0131
      Rms BondAngle    1.8060   1.8178
     Rms ChirVolume    0.0862   0.0898
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.4s System:    0.1s Elapsed:     0:47