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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 16:59:08 


 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 14
  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_R14_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R14_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_R14_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:    14
  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_R14_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=   2.037 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=   1.829 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=   2.190 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=   2.449 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=   2.393 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=   2.116 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                           14
Number of "free" reflections       1124
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.= 0.891 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  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   0.32346827    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                42.1
Norm of Geom. positional gradient                82.0
Norm of X_ray B-factor gradient                  135.
Norm of Geom. B-factor gradient                 0.207E+05
Product of X_ray and Geom posit. gradients     -0.148E+08
 Cosine of angle between them                      -0.444
Product of X_ray and Geom B-fact gradients     -0.484E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7821E+06 GEOM=     0.2659E+05 TOTAL=     0.8087E+06
 function value    808691.63    

-------------------------------------------------------------------------------
             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     1.889     1.644
Bond angles  : others                          3242     2.366     1.582
Torsion angles, period  1. refined              184     6.978     5.000
Torsion angles, period  2. refined               90    36.473    22.778
Torsion angles, period  3. refined              268    14.120    15.000
Torsion angles, period  4. refined                9    12.428    15.000
Chiral centres: refined atoms                   196     0.091     0.200
Planar groups: refined atoms                   1736     0.011     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   309     0.266     0.200
VDW repulsions.others                          1338     0.232     0.200
VDW; torsion: refined_atoms                     722     0.173     0.200
VDW; torsion.others                             730     0.082     0.200
HBOND: refined_atoms                            227     0.204     0.200
HBOND.others                                      2     0.032     0.200
VDW repulsions: symmetry: refined_atoms          11     0.200     0.200
VDW repulsions: symmetry: others                 24     0.188     0.200
HBOND: symmetry: refined_atoms                   21     0.204     0.200
M. chain bond B values: refined atoms           745     1.705     1.286
M. chain bond B values: others                  745     1.703     1.286
M. chain angle B values: refined atoms          926     2.657     1.909
M. chain angle B values: others                 927     2.656     1.909
S. chain bond B values: refined atoms           811     3.029     1.684
S. chain bond B values: others                  810     3.026     1.683
S. chain angle B values: refined atoms         1177     4.688     2.358
S. chain angle B values: others                1178     4.686     2.358
Long range B values: refined atoms             1860     7.275    18.263
Long range B values: others                    1763     6.974    16.754
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.0656
Partial structure    1: scale =     0.3832, B  =   47.7239
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3015 100.00   452.5   461.9  0.16  0.17     156   484.7   483.1  0.17  0.19
 0.130    5150 100.00   298.7   285.8  0.16  0.15     250   309.5   293.6  0.19  0.17
 0.216    6530  99.97   202.3   186.2  0.17  0.14     342   206.6   191.6  0.19  0.17
 0.303    7667 100.00   104.2   117.2  0.26  0.20     376   106.2   119.9  0.29  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2165   0.926    850   0.839   3015   0.902  0.951  0.9735  0.9733  0.9396  0.9388
  0.1301   4287   0.894    863   0.781   5150   0.875  1.005  0.9590  0.9640  0.9239  0.9444
  0.2165   5646   0.888    884   0.783   6530   0.874  1.048  0.9580  0.9633  0.9234  0.9429
  0.3028   6805   0.764    865   0.696   7670   0.756  0.812  0.9091  0.9190  0.8708  0.8914
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22365
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.7852
Overall R factor                     =     0.1792
Free R factor                        =     0.1998
Average Fourier shell correlation    =     0.9496
AverageFree Fourier shell correlation=     0.9440
Overall weighted R factor            =     0.1584
Free weighted R factor               =     0.1803
Overall weighted R2 factor           =     0.1899
Free weighted R2 factor              =     0.2109
Average correlation coefficient      =     0.9250
Overall correlation coefficient      =     0.9575
Free correlation coefficient         =     0.9510
Cruickshanks DPI for coordinate error=     0.1083
DPI based on free R factor           =     0.0989
Overall figure of merit              =     0.8376
ML based su of positional parameters =     0.0700
ML based su of thermal parameters    =     2.1947
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    115872.98       26585.250       808691.63      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.36663312    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    789050.13    

-------------------------------------------------------------------------------
             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  =   -0.0741
Partial structure    1: scale =     0.3830, B  =   46.9773
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1788
Free R factor                        =     0.1996
Average Fourier shell correlation    =     0.9542
AverageFree Fourier shell correlation=     0.9486
Average correlation coefficient      =     0.9263
Overall figure of merit              =     0.8534
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115346.58       10496.793       789050.13       808691.63    


     CGMAT cycle number =      3

 Weight matrix   0.37463006    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    786913.44    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0443
Partial structure    1: scale =     0.3829, B  =   43.5021
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1778
Free R factor                        =     0.1991
Average Fourier shell correlation    =     0.9554
AverageFree Fourier shell correlation=     0.9495
Average correlation coefficient      =     0.9280
Overall figure of merit              =     0.8567
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    115128.80       9830.0840       786913.44       789050.13    


     CGMAT cycle number =      4

 Weight matrix   0.34235874    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    715663.69    

-------------------------------------------------------------------------------
             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  =   -0.0408
Partial structure    1: scale =     0.3839, B  =   43.8055
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1777
Free R factor                        =     0.1988
Average Fourier shell correlation    =     0.9557
AverageFree Fourier shell correlation=     0.9498
Average correlation coefficient      =     0.9285
Overall figure of merit              =     0.8577
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    115060.22       9645.0918       715663.69       786913.44    


     CGMAT cycle number =      5

 Weight matrix   0.31126890    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651327.38    

-------------------------------------------------------------------------------
             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  =   -0.0341
Partial structure    1: scale =     0.3841, B  =   43.7330
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1781
Free R factor                        =     0.1985
Average Fourier shell correlation    =     0.9557
AverageFree Fourier shell correlation=     0.9497
Average correlation coefficient      =     0.9283
Overall figure of merit              =     0.8578
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    115085.45       9351.5273       651327.38       715663.69    


     CGMAT cycle number =      6

 Weight matrix   0.31105116    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651328.19    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0339
Partial structure    1: scale =     0.3840, B  =   43.6085
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1786
Free R factor                        =     0.1984
Average Fourier shell correlation    =     0.9555
AverageFree Fourier shell correlation=     0.9497
Average correlation coefficient      =     0.9279
Overall figure of merit              =     0.8578
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03

 fvalues    115144.16       9008.1699       651311.56       651327.38    


     CGMAT cycle number =      7

 Weight matrix   0.31096846    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651319.13    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0424
Partial structure    1: scale =     0.3838, B  =   43.4971
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1788
Free R factor                        =     0.1983
Average Fourier shell correlation    =     0.9555
AverageFree Fourier shell correlation=     0.9497
Average correlation coefficient      =     0.9278
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    115164.87       8909.7129       651332.25       651311.56    

 fvalues    115164.87       8909.7129       651325.06       651328.56    
 fvalues    115164.87       8909.7129       651325.06       651328.56    


     CGMAT cycle number =      8

 Weight matrix   0.31096679    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651322.56    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0437
Partial structure    1: scale =     0.3837, B  =   43.4926
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1788
Free R factor                        =     0.1985
Average Fourier shell correlation    =     0.9555
AverageFree Fourier shell correlation=     0.9497
Average correlation coefficient      =     0.9278
Overall figure of merit              =     0.8579
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    115167.88       8886.8594       651322.56       651328.56    


     CGMAT cycle number =      9

 Weight matrix   0.31046331    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    651355.50    

-------------------------------------------------------------------------------
             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 =     0.0425, B  =   -0.0381
Partial structure    1: scale =     0.3837, B  =   43.5099
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.46 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1789
Free R factor                        =     0.1986
Average Fourier shell correlation    =     0.9555
AverageFree Fourier shell correlation=     0.9496
Average correlation coefficient      =     0.9278
Overall figure of merit              =     0.8578
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    115175.80       8870.6611       651360.94       651322.56    

 fvalues    115175.80       8870.6611       651361.44       651350.56    
 fvalues    115175.80       8870.6611       651361.44       651350.56    


     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.= 0.905 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.31068495    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                37.7
Norm of Geom. positional gradient                37.8
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                  117.
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.430E+08
 Cosine of angle between them                      -0.995


Residuals: XRAY=     0.6425E+06 GEOM=      8867.     TOTAL=     0.6513E+06
 function value    651333.06    

-------------------------------------------------------------------------------
             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     1.788     1.644
Bond angles  : others                          3242     1.491     1.582
Torsion angles, period  1. refined              184     6.865     5.000
Torsion angles, period  2. refined               90    36.238    22.778
Torsion angles, period  3. refined              268    13.864    15.000
Torsion angles, period  4. refined                9    11.861    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.266     0.200
VDW repulsions.others                          1368     0.203     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             785     0.083     0.200
HBOND: refined_atoms                            227     0.197     0.200
HBOND.others                                      1     0.079     0.200
VDW repulsions: symmetry: refined_atoms          10     0.195     0.200
VDW repulsions: symmetry: others                 26     0.167     0.200
HBOND: symmetry: refined_atoms                   20     0.209     0.200
M. chain bond B values: refined atoms           745     1.652     1.390
M. chain bond B values: others                  745     1.650     1.390
M. chain angle B values: refined atoms          926     2.629     2.068
M. chain angle B values: others                 927     2.627     2.068
S. chain bond B values: refined atoms           811     2.954     1.787
S. chain bond B values: others                  810     2.947     1.786
S. chain angle B values: refined atoms         1177     4.582     2.515
S. chain angle B values: others                1178     4.580     2.515
Long range B values: refined atoms             1854     7.145    19.612
Long range B values: others                    1757     6.845    18.048
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0403
Partial structure    1: scale =     0.3837, B  =   43.4956
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3015 100.00   453.3   462.9  0.16  0.17     156   485.4   483.0  0.17  0.19
 0.130    5150 100.00   299.2   285.7  0.16  0.15     250   310.0   294.3  0.19  0.17
 0.216    6530  99.97   202.6   186.5  0.17  0.15     342   206.9   191.6  0.19  0.16
 0.303    7667 100.00   104.4   116.6  0.25  0.19     376   106.3   120.1  0.28  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2165   0.932    850   0.849   3015   0.909  0.951  0.9748  0.9741  0.9406  0.9374
  0.1301   4287   0.897    863   0.787   5150   0.878  1.005  0.9602  0.9646  0.9255  0.9439
  0.2165   5646   0.897    884   0.795   6530   0.883  1.048  0.9603  0.9650  0.9245  0.9407
  0.3028   6805   0.811    865   0.738   7670   0.802  0.832  0.9225  0.9339  0.8706  0.9022
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22365
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.7852
Overall R factor                     =     0.1789
Free R factor                        =     0.1986
Average Fourier shell correlation    =     0.9555
AverageFree Fourier shell correlation=     0.9496
Overall weighted R factor            =     0.1594
Free weighted R factor               =     0.1799
Overall weighted R2 factor           =     0.1915
Free weighted R2 factor              =     0.2112
Average correlation coefficient      =     0.9278
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9517
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.0983
Overall figure of merit              =     0.8578
ML based su of positional parameters =     0.0649
ML based su of thermal parameters    =     2.0033
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    115173.36       8866.8262       651333.06       651350.56    

    ****                              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.= 0.905 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R14_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     1.787     1.644
Bond angles  : others                          3242     1.491     1.582
Torsion angles, period  1. refined              184     6.864     5.000
Torsion angles, period  2. refined               90    36.234    22.778
Torsion angles, period  3. refined              268    13.861    15.000
Torsion angles, period  4. refined                9    11.853    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   303     0.266     0.200
VDW repulsions.others                          1368     0.203     0.200
VDW; torsion: refined_atoms                     722     0.172     0.200
VDW; torsion.others                             785     0.083     0.200
HBOND: refined_atoms                            228     0.196     0.200
HBOND.others                                      1     0.079     0.200
VDW repulsions: symmetry: refined_atoms          10     0.195     0.200
VDW repulsions: symmetry: others                 26     0.167     0.200
HBOND: symmetry: refined_atoms                   20     0.209     0.200
M. chain bond B values: refined atoms           745     1.651     1.390
M. chain bond B values: others                  745     1.650     1.390
M. chain angle B values: refined atoms          926     2.628     2.068
M. chain angle B values: others                 927     2.627     2.068
S. chain bond B values: refined atoms           811     2.952     1.787
S. chain bond B values: others                  810     2.945     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             1855     7.143    19.608
Long range B values: others                    1758     6.843    18.044
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0425, B  =   -0.0349
Partial structure    1: scale =     0.3837, B  =   43.4381
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   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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3015 100.00   453.3   462.8  0.16  0.17     156   485.5   483.0  0.17  0.19
 0.130    5150 100.00   299.2   285.6  0.16  0.15     250   310.0   294.3  0.19  0.17
 0.216    6530  99.97   202.6   186.5  0.17  0.15     342   206.9   191.5  0.19  0.16
 0.303    7667 100.00   104.4   116.6  0.25  0.19     376   106.4   120.0  0.28  0.22
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2165   0.932    850   0.849   3015   0.909  0.951  0.9748  0.9741  0.9406  0.9374
  0.1301   4287   0.897    863   0.787   5150   0.878  1.005  0.9602  0.9646  0.9254  0.9439
  0.2165   5646   0.897    884   0.795   6530   0.883  1.048  0.9602  0.9650  0.9245  0.9407
  0.3028   6805   0.810    865   0.738   7670   0.802  0.832  0.9224  0.9339  0.8706  0.9022
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22365
Percentage observed                  =    99.9872
Percentage of free reflections       =     4.7852
Overall R factor                     =     0.1789
Free R factor                        =     0.1986
Average Fourier shell correlation    =     0.9555
AverageFree Fourier shell correlation=     0.9496
Overall weighted R factor            =     0.1594
Free weighted R factor               =     0.1800
Overall weighted R2 factor           =     0.1916
Free weighted R2 factor              =     0.2113
Average correlation coefficient      =     0.9278
Overall correlation coefficient      =     0.9573
Free correlation coefficient         =     0.9517
Cruickshanks DPI for coordinate error=     0.1081
DPI based on free R factor           =     0.0983
Overall figure of merit              =     0.8577
ML based su of positional parameters =     0.0649
ML based su of thermal parameters    =     2.0033
-----------------------------------------------------------------------------
  Time in seconds: CPU =        19.02
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1792   0.1998   0.838      115873.    5980.4   0.0134  0.995   1.889  1.085   0.091
       1   0.1788   0.1996   0.853      115347.    5966.7   0.0128  0.956   1.847  1.062   0.090
       2   0.1778   0.1991   0.857      115129.    5961.0   0.0134  1.004   1.866  1.075   0.092
       3   0.1777   0.1988   0.858      115060.    5959.5   0.0135  1.010   1.873  1.081   0.093
       4   0.1781   0.1985   0.858      115085.    5959.2   0.0128  0.966   1.847  1.067   0.091
       5   0.1786   0.1984   0.858      115147.    5960.5   0.0122  0.920   1.809  1.045   0.088
       6   0.1788   0.1983   0.858      115163.    5961.1   0.0122  0.915   1.795  1.038   0.088
       7   0.1788   0.1985   0.858      115168.    5961.6   0.0121  0.913   1.791  1.036   0.088
       8   0.1789   0.1986   0.858      115177.    5962.4   0.0121  0.912   1.788  1.035   0.088
       9   0.1789   0.1986   0.858      115173.    5962.4   0.0121  0.912   1.788  1.034   0.088
      10   0.1789   0.1986   0.858      115179.    5962.6   0.0121  0.912   1.787  1.034   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1792   0.1789
             R free    0.1998   0.1986
     Rms BondLength    0.0134   0.0121
      Rms BondAngle    1.8891   1.7866
     Rms ChirVolume    0.0906   0.0878
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      50.7s System:    2.3s Elapsed:     0:53