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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: 17:46:02 


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


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

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

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

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

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

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

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

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

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.60     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 6
  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_R06_1-70A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R06_1-60A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R06_1-60A.mtz

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

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

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


  Residual                               : Rice Maximum Likelihood for Fs

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

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


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

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0977
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.6000
  Estimated number of reflections :      36894
  Free R exclusion - flag equals:     6
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.6000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R06_1-70A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.037 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=   2.197 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=   1.816 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=   2.196 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=   2.376 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=   2.398 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=   2.113 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                            6
Number of "free" reflections       1428
Number of   all  reflections      28041
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          28041

   Current auto weighting coefficient =    6.4996524    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                              VDW outliers                              ****

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

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.882 id.= 3.000 dev= -2.12 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.29887748    
 Actual weight    6.4996524      is applied to the X-ray term
Norm of X_ray positional gradient                38.2
Norm of Geom. positional gradient                81.5
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                 0.214E+05
Product of X_ray and Geom posit. gradients     -0.140E+08
 Cosine of angle between them                      -0.464
Product of X_ray and Geom B-fact gradients     -0.396E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.8726E+06 GEOM=     0.2636E+05 TOTAL=     0.8990E+06
 function value    898958.56    

-------------------------------------------------------------------------------
             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     1.813     1.644
Bond angles  : others                          3242     2.353     1.582
Torsion angles, period  1. refined              184     6.885     5.000
Torsion angles, period  2. refined               90    35.642    22.778
Torsion angles, period  3. refined              268    13.055    15.000
Torsion angles, period  4. refined                9    11.230    15.000
Chiral centres: refined atoms                   196     0.090     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   309     0.262     0.200
VDW repulsions.others                          1333     0.232     0.200
VDW; torsion: refined_atoms                     721     0.173     0.200
VDW; torsion.others                             707     0.082     0.200
HBOND: refined_atoms                            234     0.186     0.200
HBOND.others                                      1     0.016     0.200
VDW repulsions: symmetry: refined_atoms           8     0.200     0.200
VDW repulsions: symmetry: others                 28     0.166     0.200
HBOND: symmetry: refined_atoms                   20     0.194     0.200
M. chain bond B values: refined atoms           745     1.692     1.377
M. chain bond B values: others                  745     1.689     1.377
M. chain angle B values: refined atoms          926     2.600     2.050
M. chain angle B values: others                 927     2.598     2.050
S. chain bond B values: refined atoms           811     2.999     1.772
S. chain bond B values: others                  810     2.992     1.772
S. chain angle B values: refined atoms         1177     4.575     2.495
S. chain angle B values: others                1178     4.573     2.494
Long range B values: refined atoms             1865     7.211    19.481
Long range B values: others                    1766     6.893    17.966
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0442, B  =    1.2603
Partial structure    1: scale =     0.3861, B  =   48.3225
Overall anisotropic scale factors
   B11 =  -0.21 B22 =  -0.21 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3581 100.00   432.0   441.0  0.17  0.18     201   440.2   466.3  0.22  0.23
 0.147    6137  99.97   258.4   243.5  0.16  0.14     307   265.2   247.0  0.20  0.18
 0.244    7770 100.00   167.2   151.6  0.19  0.16     448   169.7   153.8  0.22  0.19
 0.342    9118 100.00    71.7    86.2  0.33  0.26     472    65.2    79.3  0.37  0.31
$$

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

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2614   0.883    967   0.781   3581   0.855  0.936  0.9547  0.9614  0.8987  0.9321
  0.1468   5157   0.881    980   0.784   6137   0.866  1.022  0.9541  0.9619  0.9118  0.9435
  0.2444   6794   0.862    976   0.752   7770   0.848  1.050  0.9473  0.9552  0.9018  0.9387
  0.3419   8132   0.692    991   0.605   9123   0.683  0.713  0.8371  0.8759  0.7716  0.8564
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26610
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0931
Overall R factor                     =     0.1932
Free R factor                        =     0.2305
Average Fourier shell correlation    =     0.9304
AverageFree Fourier shell correlation=     0.9134
Overall weighted R factor            =     0.1682
Free weighted R factor               =     0.2114
Overall weighted R2 factor           =     0.2010
Free weighted R2 factor              =     0.2580
Average correlation coefficient      =     0.9107
Overall correlation coefficient      =     0.9574
Free correlation coefficient         =     0.9387
Cruickshanks DPI for coordinate error=     0.0971
DPI based on free R factor           =     0.0986
Overall figure of merit              =     0.7964
ML based su of positional parameters =     0.0715
ML based su of thermal parameters    =     2.1339
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    134252.38       26364.787       898958.56      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.38688418    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    875043.81    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =   -0.0621
Partial structure    1: scale =     0.3860, B  =   47.9994
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1937
Free R factor                        =     0.2300
Average Fourier shell correlation    =     0.9431
AverageFree Fourier shell correlation=     0.9286
Average correlation coefficient      =     0.9114
Overall figure of merit              =     0.8356
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    133140.78       9674.9775       875043.81       898958.56    


     CGMAT cycle number =      3

 Weight matrix   0.40226069    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    872610.81    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0199
Partial structure    1: scale =     0.3861, B  =   44.1271
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1928
Free R factor                        =     0.2296
Average Fourier shell correlation    =     0.9453
AverageFree Fourier shell correlation=     0.9310
Average correlation coefficient      =     0.9139
Overall figure of merit              =     0.8416
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    132841.34       9188.2695       872610.81       875043.81    


     CGMAT cycle number =      4

 Weight matrix   0.40667918    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    871801.63    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0127
Partial structure    1: scale =     0.3864, B  =   43.7602
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1927
Free R factor                        =     0.2294
Average Fourier shell correlation    =     0.9459
AverageFree Fourier shell correlation=     0.9317
Average correlation coefficient      =     0.9148
Overall figure of merit              =     0.8431
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    132734.33       9074.6484       871801.63       872610.81    


     CGMAT cycle number =      5

 Weight matrix   0.40891054    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    871500.69    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0223
Partial structure    1: scale =     0.3863, B  =   43.6627
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1926
Free R factor                        =     0.2291
Average Fourier shell correlation    =     0.9462
AverageFree Fourier shell correlation=     0.9320
Average correlation coefficient      =     0.9153
Overall figure of merit              =     0.8436
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    132679.03       9133.1523       871500.69       871801.63    


     CGMAT cycle number =      6

 Weight matrix   0.40926799    
 Actual weight    6.4996524      is applied to the X-ray term


 function value    871366.44    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0337
Partial structure    1: scale =     0.3865, B  =   43.6551
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1926
Free R factor                        =     0.2290
Average Fourier shell correlation    =     0.9463
AverageFree Fourier shell correlation=     0.9321
Average correlation coefficient      =     0.9156
Overall figure of merit              =     0.8438
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    132651.38       9178.5957       871366.44       871500.69    


     CGMAT cycle number =      7

 Weight matrix   0.37230948    
 Actual weight    5.9087749      is applied to the X-ray term


 function value    792955.56    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0375
Partial structure    1: scale =     0.3866, B  =   43.6333
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1927
Free R factor                        =     0.2291
Average Fourier shell correlation    =     0.9463
AverageFree Fourier shell correlation=     0.9321
Average correlation coefficient      =     0.9157
Overall figure of merit              =     0.8439
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    132642.84       9198.8994       792955.56       871366.44    


     CGMAT cycle number =      8

 Weight matrix   0.33830327    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    721712.50    

-------------------------------------------------------------------------------
             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 =     0.0441, B  =    0.0354
Partial structure    1: scale =     0.3864, B  =   43.4718
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1931
Free R factor                        =     0.2290
Average Fourier shell correlation    =     0.9462
AverageFree Fourier shell correlation=     0.9321
Average correlation coefficient      =     0.9154
Overall figure of merit              =     0.8439
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    132696.34       8919.0137       721712.50       792955.56    


     CGMAT cycle number =      9

 Weight matrix   0.33809733    
 Actual weight    5.3716135      is applied to the X-ray term


 function value    721734.13    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0342
Partial structure    1: scale =     0.3863, B  =   43.2795
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1936
Free R factor                        =     0.2291
Average Fourier shell correlation    =     0.9461
AverageFree Fourier shell correlation=     0.9321
Average correlation coefficient      =     0.9148
Overall figure of merit              =     0.8441
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    132763.80       8586.9590       721751.38       721712.50    

 fvalues    132763.80       8586.9590       721764.56       721742.75    
 fvalues    132763.80       8586.9590       721764.56       721742.75    


     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.= 0.902 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   128  128  264
 Maximuum H,K,L                 :    37   37   77
 Minimum acceptable grid spacing:    83   83  175
 Weight matrix   0.33804867    
 Actual weight    5.3716135      is applied to the X-ray term
Norm of X_ray positional gradient                38.6
Norm of Geom. positional gradient                39.0
Norm of X_ray B-factor gradient                  112.
Norm of Geom. B-factor gradient                  112.
Product of X_ray and Geom posit. gradients     -0.146E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.404E+08
 Cosine of angle between them                      -0.993


Residuals: XRAY=     0.7132E+06 GEOM=      8563.     TOTAL=     0.7218E+06
 function value    721761.19    

-------------------------------------------------------------------------------
             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     1.793     1.644
Bond angles  : others                          3242     1.515     1.582
Torsion angles, period  1. refined              184     6.870     5.000
Torsion angles, period  2. refined               90    35.195    22.778
Torsion angles, period  3. refined              268    12.725    15.000
Torsion angles, period  4. refined                9    11.413    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     0.264     0.200
VDW repulsions.others                          1366     0.205     0.200
VDW; torsion: refined_atoms                     719     0.174     0.200
VDW; torsion.others                             786     0.084     0.200
HBOND: refined_atoms                            229     0.186     0.200
HBOND.others                                      1     0.071     0.200
VDW repulsions: symmetry: refined_atoms           9     0.182     0.200
VDW repulsions: symmetry: others                 25     0.170     0.200
HBOND: symmetry: refined_atoms                   20     0.171     0.200
M. chain bond B values: refined atoms           745     1.678     1.496
M. chain bond B values: others                  745     1.675     1.496
M. chain angle B values: refined atoms          926     2.600     2.231
M. chain angle B values: others                 927     2.599     2.231
S. chain bond B values: refined atoms           811     2.914     1.878
S. chain bond B values: others                  810     2.909     1.878
S. chain angle B values: refined atoms         1177     4.451     2.661
S. chain angle B values: others                1178     4.449     2.660
Long range B values: refined atoms             1855     7.037    20.862
Long range B values: others                    1761     6.716    19.333
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0337
Partial structure    1: scale =     0.3864, B  =   43.2174
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3581 100.00   432.7   441.6  0.17  0.18     201   440.9   465.9  0.22  0.23
 0.147    6137  99.97   258.8   243.6  0.17  0.15     307   265.6   247.1  0.20  0.18
 0.244    7770 100.00   167.5   151.7  0.19  0.17     448   169.9   153.5  0.22  0.19
 0.342    9118 100.00    71.8    85.9  0.32  0.25     472    65.3    79.2  0.36  0.31
$$

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

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2614   0.901    967   0.808   3581   0.876  0.940  0.9593  0.9660  0.8988  0.9310
  0.1468   5157   0.891    980   0.793   6137   0.875  1.024  0.9562  0.9635  0.9128  0.9420
  0.2444   6794   0.877    976   0.771   7770   0.863  1.050  0.9525  0.9594  0.9042  0.9368
  0.3419   8132   0.804    991   0.721   9123   0.795  0.761  0.8856  0.9152  0.7795  0.8715
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26610
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0931
Overall R factor                     =     0.1936
Free R factor                        =     0.2291
Average Fourier shell correlation    =     0.9461
AverageFree Fourier shell correlation=     0.9321
Overall weighted R factor            =     0.1699
Free weighted R factor               =     0.2106
Overall weighted R2 factor           =     0.2033
Free weighted R2 factor              =     0.2575
Average correlation coefficient      =     0.9148
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9394
Cruickshanks DPI for coordinate error=     0.0973
DPI based on free R factor           =     0.0980
Overall figure of merit              =     0.8443
ML based su of positional parameters =     0.0610
ML based su of thermal parameters    =     1.7690
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    132772.08       8563.4609       721773.63       721742.75    

 fvalues    132772.08       8563.4609       721751.69       721763.75    
 fvalues    132772.08       8563.4609       721751.69       721763.75    

    ****                              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.= 0.903 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R06_1-60A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.791     1.644
Bond angles  : others                          3242     1.515     1.582
Torsion angles, period  1. refined              184     6.870     5.000
Torsion angles, period  2. refined               90    35.190    22.778
Torsion angles, period  3. refined              268    12.721    15.000
Torsion angles, period  4. refined                9    11.405    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     0.264     0.200
VDW repulsions.others                          1366     0.205     0.200
VDW; torsion: refined_atoms                     719     0.174     0.200
VDW; torsion.others                             786     0.084     0.200
HBOND: refined_atoms                            229     0.186     0.200
HBOND.others                                      1     0.070     0.200
VDW repulsions: symmetry: refined_atoms           9     0.182     0.200
VDW repulsions: symmetry: others                 25     0.170     0.200
HBOND: symmetry: refined_atoms                   20     0.171     0.200
M. chain bond B values: refined atoms           745     1.676     1.496
M. chain bond B values: others                  745     1.673     1.496
M. chain angle B values: refined atoms          926     2.598     2.232
M. chain angle B values: others                 927     2.596     2.231
S. chain bond B values: refined atoms           811     2.909     1.878
S. chain bond B values: others                  810     2.904     1.877
S. chain angle B values: refined atoms         1177     4.444     2.660
S. chain angle B values: others                1178     4.442     2.660
Long range B values: refined atoms             1855     7.032    20.861
Long range B values: others                    1761     6.711    19.333
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0441, B  =    0.0277
Partial structure    1: scale =     0.3864, B  =   43.1798
Overall anisotropic scale factors
   B11 =  -0.20 B22 =  -0.20 B33 =   0.41 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.049    3581 100.00   432.7   441.6  0.17  0.18     201   440.8   465.9  0.22  0.23
 0.147    6137  99.97   258.8   243.6  0.17  0.15     307   265.5   247.2  0.20  0.18
 0.244    7770 100.00   167.4   151.8  0.19  0.17     448   169.9   153.6  0.22  0.19
 0.342    9118 100.00    71.8    85.9  0.32  0.25     472    65.3    79.2  0.36  0.31
$$

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

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0493   2614   0.901    967   0.808   3581   0.876  0.940  0.9593  0.9659  0.8987  0.9310
  0.1468   5157   0.891    980   0.793   6137   0.875  1.024  0.9562  0.9635  0.9128  0.9420
  0.2444   6794   0.877    976   0.771   7770   0.863  1.050  0.9525  0.9594  0.9041  0.9367
  0.3419   8132   0.804    991   0.721   9123   0.795  0.761  0.8856  0.9153  0.7795  0.8715
 $$
Resolution limits                    =     41.964     1.600
Number of used reflections           =      26610
Percentage observed                  =    99.9893
Percentage of free reflections       =     5.0931
Overall R factor                     =     0.1937
Free R factor                        =     0.2291
Average Fourier shell correlation    =     0.9461
AverageFree Fourier shell correlation=     0.9321
Overall weighted R factor            =     0.1699
Free weighted R factor               =     0.2105
Overall weighted R2 factor           =     0.2033
Free weighted R2 factor              =     0.2576
Average correlation coefficient      =     0.9148
Overall correlation coefficient      =     0.9570
Free correlation coefficient         =     0.9394
Cruickshanks DPI for coordinate error=     0.0973
DPI based on free R factor           =     0.0980
Overall figure of merit              =     0.8443
ML based su of positional parameters =     0.0610
ML based su of thermal parameters    =     1.7690
-----------------------------------------------------------------------------
  Time in seconds: CPU =        20.58
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1932   0.2305   0.796      134252.    7367.2   0.0128  0.965   1.813  1.053   0.090
       1   0.1937   0.2300   0.836      133141.    7323.0   0.0119  0.898   1.763  1.026   0.088
       2   0.1928   0.2296   0.842      132841.    7310.6   0.0129  0.976   1.804  1.052   0.090
       3   0.1927   0.2294   0.843      132734.    7306.1   0.0131  0.992   1.828  1.066   0.091
       4   0.1926   0.2291   0.844      132679.    7303.4   0.0132  0.998   1.843  1.075   0.091
       5   0.1926   0.2290   0.844      132651.    7301.4   0.0132  1.002   1.852  1.079   0.091
       6   0.1927   0.2291   0.844      132643.    7300.7   0.0133  1.004   1.858  1.082   0.091
       7   0.1931   0.2290   0.844      132696.    7301.1   0.0127  0.961   1.830  1.065   0.089
       8   0.1936   0.2291   0.844      132762.    7302.3   0.0121  0.918   1.796  1.045   0.087
       9   0.1936   0.2291   0.844      132772.    7302.5   0.0121  0.917   1.793  1.044   0.087
      10   0.1937   0.2291   0.844      132771.    7302.6   0.0121  0.916   1.791  1.042   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1932   0.1937
             R free    0.2305   0.2291
     Rms BondLength    0.0128   0.0121
      Rms BondAngle    1.8128   1.7906
     Rms ChirVolume    0.0902   0.0871
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      52.6s System:    0.1s Elapsed:     0:53