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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: 16:22:57 


 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 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_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R04_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_R04_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:     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  1.7000

  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_R04_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=   2.053 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=   2.196 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=   1.837 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=   2.194 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=   2.404 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=   2.403 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=   2.110 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       1209
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.= 0.898 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   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   0.30802071    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                41.4
Norm of Geom. positional gradient                81.2
Norm of X_ray B-factor gradient                  132.
Norm of Geom. B-factor gradient                 0.195E+05
Product of X_ray and Geom posit. gradients     -0.135E+08
 Cosine of angle between them                      -0.415
Product of X_ray and Geom B-fact gradients     -0.443E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7808E+06 GEOM=     0.2552E+05 TOTAL=     0.8063E+06
 function value    806308.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.013     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.856     1.644
Bond angles  : others                          3242     2.355     1.582
Torsion angles, period  1. refined              184     7.003     5.000
Torsion angles, period  2. refined               90    36.876    22.778
Torsion angles, period  3. refined              268    14.194    15.000
Torsion angles, period  4. refined                9    11.905    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   314     0.267     0.200
VDW repulsions.others                          1344     0.233     0.200
VDW; torsion: refined_atoms                     712     0.172     0.200
VDW; torsion.others                             726     0.082     0.200
HBOND: refined_atoms                            225     0.205     0.200
HBOND.others                                      3     0.094     0.200
VDW repulsions: symmetry: refined_atoms           8     0.239     0.200
VDW repulsions: symmetry: others                 24     0.195     0.200
HBOND: symmetry: refined_atoms                   25     0.206     0.200
HBOND: symmetry: others                           1     0.037     0.200
M. chain bond B values: refined atoms           745     1.672     1.294
M. chain bond B values: others                  745     1.670     1.294
M. chain angle B values: refined atoms          926     2.607     1.922
M. chain angle B values: others                 927     2.606     1.922
S. chain bond B values: refined atoms           811     2.980     1.689
S. chain bond B values: others                  810     2.976     1.689
S. chain angle B values: refined atoms         1177     4.687     2.366
S. chain angle B values: others                1178     4.685     2.365
Long range B values: refined atoms             1857     7.192    18.267
Long range B values: others                    1762     6.866    16.828
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0427, B  =    1.1106
Partial structure    1: scale =     0.3866, B  =   48.5588
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3005 100.00   454.0   462.8  0.16  0.17     166   441.9   457.4  0.18  0.20
 0.130    5135 100.00   299.0   285.9  0.16  0.14     265   292.7   281.0  0.21  0.19
 0.216    6535  99.97   201.8   185.5  0.17  0.15     337   208.8   192.4  0.22  0.19
 0.303    7602 100.00   104.4   116.8  0.26  0.19     441   100.0   112.4  0.29  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2156   0.925    849   0.837   3005   0.900  0.955  0.9698  0.9727  0.9349  0.9406
  0.1301   4275   0.886    860   0.780   5135   0.868  1.002  0.9558  0.9639  0.9248  0.9456
  0.2165   5657   0.876    878   0.769   6535   0.862  1.043  0.9470  0.9577  0.8946  0.9360
  0.3028   6750   0.782    855   0.716   7605   0.775  0.823  0.9120  0.9249  0.8633  0.8960
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22280
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1471
Overall R factor                     =     0.1787
Free R factor                        =     0.2180
Average Fourier shell correlation    =     0.9499
AverageFree Fourier shell correlation=     0.9393
Overall weighted R factor            =     0.1572
Free weighted R factor               =     0.1931
Overall weighted R2 factor           =     0.1857
Free weighted R2 factor              =     0.2331
Average correlation coefficient      =     0.9252
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9436
Cruickshanks DPI for coordinate error=     0.1084
DPI based on free R factor           =     0.1083
Overall figure of merit              =     0.8388
ML based su of positional parameters =     0.0718
ML based su of thermal parameters    =     2.2220
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    115677.24       25522.977       806308.19      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36076784    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786569.69    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0582
Partial structure    1: scale =     0.3869, B  =   48.0254
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                     =     0.1783
Free R factor                        =     0.2179
Average Fourier shell correlation    =     0.9552
AverageFree Fourier shell correlation=     0.9453
Average correlation coefficient      =     0.9268
Overall figure of merit              =     0.8587
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115037.31       10103.840       786569.69       806308.19    


     CGMAT cycle number =      3

 Weight matrix   0.36980665    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784345.69    

-------------------------------------------------------------------------------
             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  =   -0.0189
Partial structure    1: scale =     0.3869, B  =   44.5628
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                        =     0.2169
Average Fourier shell correlation    =     0.9563
AverageFree Fourier shell correlation=     0.9464
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8611
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    114784.32       9587.4668       784345.69       786569.69    


     CGMAT cycle number =      4

 Weight matrix   0.37234277    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    783668.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0057
Partial structure    1: scale =     0.3877, B  =   44.6367
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1769
Free R factor                        =     0.2164
Average Fourier shell correlation    =     0.9566
AverageFree Fourier shell correlation=     0.9467
Average correlation coefficient      =     0.9293
Overall figure of merit              =     0.8616
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    114699.77       9480.5313       783668.13       784345.69    


     CGMAT cycle number =      5

 Weight matrix   0.33999091    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    713067.44    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0072
Partial structure    1: scale =     0.3878, B  =   44.7272
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1768
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9568
AverageFree Fourier shell correlation=     0.9469
Average correlation coefficient      =     0.9295
Overall figure of merit              =     0.8619
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114659.16       9509.6777       713067.44       783668.13    


     CGMAT cycle number =      6

 Weight matrix   0.30899748    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649112.38    

-------------------------------------------------------------------------------
             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  =   -0.0016
Partial structure    1: scale =     0.3874, B  =   44.6331
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                        =     0.2159
Average Fourier shell correlation    =     0.9567
AverageFree Fourier shell correlation=     0.9469
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8619
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114708.09       9241.5654       649112.38       713067.44    


     CGMAT cycle number =      7

 Weight matrix   0.30972809    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649105.25    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0017
Partial structure    1: scale =     0.3874, B  =   44.5312
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                        =     0.2159
Average Fourier shell correlation    =     0.9565
AverageFree Fourier shell correlation=     0.9469
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8621
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    114769.20       8893.5908       649105.25       649112.38    


     CGMAT cycle number =      8

 Weight matrix   0.30997089    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649116.13    

-------------------------------------------------------------------------------
             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  =   -0.0185
Partial structure    1: scale =     0.3874, B  =   44.5595
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1780
Free R factor                        =     0.2159
Average Fourier shell correlation    =     0.9565
AverageFree Fourier shell correlation=     0.9469
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8623
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    114791.73       8795.9209       649131.38       649105.25    
 fvalues    114791.73       8795.9209       649131.38       649133.31    


     CGMAT cycle number =      9

 Weight matrix   0.30964065    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649142.25    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0054
Partial structure    1: scale =     0.3875, B  =   44.6431
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 B33 =   0.45 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1781
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9565
AverageFree Fourier shell correlation=     0.9469
Average correlation coefficient      =     0.9286
Overall figure of merit              =     0.8622
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    114799.94       8764.7402       649167.38       649133.31    

 fvalues    114799.94       8764.7402       649156.31       649147.94    
 fvalues    114799.94       8764.7402       649156.31       649147.94    


     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   0.30943736    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                37.4
Norm of Geom. positional gradient                37.5
Norm of X_ray B-factor gradient                  115.
Norm of Geom. B-factor gradient                  115.
Product of X_ray and Geom posit. gradients     -0.136E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.426E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.6404E+06 GEOM=      8759.     TOTAL=     0.6491E+06
 function value    649148.31    

-------------------------------------------------------------------------------
             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     1.768     1.644
Bond angles  : others                          3242     1.486     1.582
Torsion angles, period  1. refined              184     6.854     5.000
Torsion angles, period  2. refined               90    36.424    22.778
Torsion angles, period  3. refined              268    13.895    15.000
Torsion angles, period  4. refined                9    11.206    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.269     0.200
VDW repulsions.others                          1376     0.203     0.200
VDW; torsion: refined_atoms                     727     0.170     0.200
VDW; torsion.others                             774     0.084     0.200
HBOND: refined_atoms                            215     0.203     0.200
HBOND.others                                      2     0.115     0.200
VDW repulsions: symmetry: refined_atoms           9     0.215     0.200
VDW repulsions: symmetry: others                 21     0.209     0.200
HBOND: symmetry: refined_atoms                   23     0.209     0.200
HBOND: symmetry: others                           1     0.016     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     2.585     2.075
M. chain angle B values: others                 927     2.584     2.075
S. chain bond B values: refined atoms           811     2.919     1.787
S. chain bond B values: others                  810     2.912     1.786
S. chain angle B values: refined atoms         1177     4.582     2.515
S. chain angle B values: others                1178     4.580     2.514
Long range B values: refined atoms             1846     7.080    19.469
Long range B values: others                    1757     6.799    18.074
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0024
Partial structure    1: scale =     0.3875, B  =   44.6552
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3005 100.00   455.0   464.1  0.16  0.17     166   443.0   457.0  0.18  0.20
 0.130    5135 100.00   299.7   285.8  0.16  0.15     265   293.4   281.8  0.21  0.18
 0.216    6535  99.97   202.3   185.9  0.17  0.15     337   209.3   193.0  0.21  0.18
 0.303    7602 100.00   104.6   116.4  0.25  0.19     441   100.2   112.5  0.29  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2156   0.936    849   0.854   3005   0.913  0.955  0.9719  0.9745  0.9328  0.9389
  0.1301   4275   0.891    860   0.785   5135   0.873  1.002  0.9580  0.9647  0.9270  0.9439
  0.2165   5657   0.887    878   0.781   6535   0.872  1.043  0.9517  0.9607  0.9007  0.9368
  0.3028   6750   0.834    855   0.762   7605   0.826  0.844  0.9270  0.9402  0.8668  0.9071
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22280
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1471
Overall R factor                     =     0.1781
Free R factor                        =     0.2161
Average Fourier shell correlation    =     0.9565
AverageFree Fourier shell correlation=     0.9469
Overall weighted R factor            =     0.1585
Free weighted R factor               =     0.1921
Overall weighted R2 factor           =     0.1885
Free weighted R2 factor              =     0.2379
Average correlation coefficient      =     0.9286
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9441
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.1073
Overall figure of merit              =     0.8622
ML based su of positional parameters =     0.0650
ML based su of thermal parameters    =     1.9792
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    114800.98       8759.2148       649150.44       649147.94    

 fvalues    114800.98       8759.2148       649146.19       649148.19    
 fvalues    114800.98       8759.2148       649146.19       649148.19    

    ****                              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_R04_1-70A.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     1.767     1.644
Bond angles  : others                          3242     1.486     1.582
Torsion angles, period  1. refined              184     6.854     5.000
Torsion angles, period  2. refined               90    36.409    22.778
Torsion angles, period  3. refined              268    13.884    15.000
Torsion angles, period  4. refined                9    11.203    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   304     0.269     0.200
VDW repulsions.others                          1373     0.203     0.200
VDW; torsion: refined_atoms                     727     0.170     0.200
VDW; torsion.others                             775     0.084     0.200
HBOND: refined_atoms                            214     0.203     0.200
HBOND.others                                      2     0.115     0.200
VDW repulsions: symmetry: refined_atoms           9     0.215     0.200
VDW repulsions: symmetry: others                 21     0.209     0.200
HBOND: symmetry: refined_atoms                   23     0.209     0.200
HBOND: symmetry: others                           1     0.016     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             1845     7.079    19.459
Long range B values: others                    1757     6.798    18.074
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0044
Partial structure    1: scale =     0.3874, B  =   44.5997
Overall anisotropic scale factors
   B11 =  -0.22 B22 =  -0.22 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3005 100.00   455.0   464.1  0.16  0.17     166   443.0   457.1  0.18  0.20
 0.130    5135 100.00   299.7   285.9  0.16  0.15     265   293.4   281.8  0.21  0.18
 0.216    6535  99.97   202.3   186.0  0.17  0.15     337   209.3   193.0  0.21  0.18
 0.303    7602 100.00   104.6   116.4  0.25  0.19     441   100.2   112.5  0.29  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2156   0.936    849   0.854   3005   0.913  0.955  0.9720  0.9745  0.9328  0.9390
  0.1301   4275   0.891    860   0.785   5135   0.873  1.002  0.9580  0.9647  0.9270  0.9438
  0.2165   5657   0.887    878   0.781   6535   0.872  1.043  0.9517  0.9607  0.9006  0.9368
  0.3028   6750   0.834    855   0.763   7605   0.826  0.844  0.9270  0.9402  0.8667  0.9071
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22280
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.1471
Overall R factor                     =     0.1781
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9565
AverageFree Fourier shell correlation=     0.9469
Overall weighted R factor            =     0.1585
Free weighted R factor               =     0.1920
Overall weighted R2 factor           =     0.1885
Free weighted R2 factor              =     0.2377
Average correlation coefficient      =     0.9286
Overall correlation coefficient      =     0.9577
Free correlation coefficient         =     0.9442
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.1073
Overall figure of merit              =     0.8622
ML based su of positional parameters =     0.0650
ML based su of thermal parameters    =     1.9792
-----------------------------------------------------------------------------
  Time in seconds: CPU =        18.12
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1787   0.2180   0.839      115677.    6416.5   0.0135  0.982   1.856  1.073   0.090
       1   0.1783   0.2179   0.859      115037.    6391.7   0.0126  0.930   1.802  1.043   0.088
       2   0.1772   0.2169   0.861      114784.    6383.1   0.0134  0.991   1.828  1.061   0.091
       3   0.1769   0.2164   0.862      114700.    6379.8   0.0135  1.001   1.840  1.069   0.092
       4   0.1768   0.2161   0.862      114659.    6377.8   0.0135  1.004   1.845  1.072   0.092
       5   0.1773   0.2159   0.862      114708.    6378.8   0.0129  0.961   1.820  1.057   0.090
       6   0.1779   0.2159   0.862      114769.    6379.7   0.0123  0.915   1.783  1.036   0.088
       7   0.1780   0.2159   0.862      114789.    6380.0   0.0122  0.910   1.772  1.030   0.087
       8   0.1781   0.2161   0.862      114799.    6380.9   0.0122  0.909   1.768  1.028   0.087
       9   0.1781   0.2161   0.862      114801.    6381.1   0.0122  0.908   1.768  1.027   0.087
      10   0.1781   0.2160   0.862      114800.    6381.0   0.0122  0.908   1.767  1.027   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1787   0.1781
             R free    0.2180   0.2160
     Rms BondLength    0.0135   0.0122
      Rms BondAngle    1.8557   1.7670
     Rms ChirVolume    0.0896   0.0873
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      50.2s System:    0.2s Elapsed:     0:50