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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
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 User: maly  Run date: 26/ 5/2020 Run time: 17:17:05 


 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 19
  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_R19_1-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R19_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_R19_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:    19
  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_R19_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=   2.048 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=   2.206 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=   1.863 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=   2.406 ideal_dist=   1.945
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:N   .
  INFO:     link is found (not be used) dist=   2.403 ideal_dist=   2.235
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:SG  .
  INFO:     link is found (not be used) dist=   2.113 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                           19
Number of "free" reflections       1184
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.= 0.923 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.29111198    
 Actual weight    6.7496872      is applied to the X-ray term
Norm of X_ray positional gradient                39.0
Norm of Geom. positional gradient                79.9
Norm of X_ray B-factor gradient                  128.
Norm of Geom. B-factor gradient                 0.206E+05
Product of X_ray and Geom posit. gradients     -0.124E+08
 Cosine of angle between them                      -0.411
Product of X_ray and Geom B-fact gradients     -0.424E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7836E+06 GEOM=     0.2573E+05 TOTAL=     0.8093E+06
 function value    809315.44    

-------------------------------------------------------------------------------
             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     1.818     1.644
Bond angles  : others                          3242     2.342     1.582
Torsion angles, period  1. refined              184     6.987     5.000
Torsion angles, period  2. refined               90    36.777    22.778
Torsion angles, period  3. refined              268    13.940    15.000
Torsion angles, period  4. refined                9    11.553    15.000
Chiral centres: refined atoms                   196     0.088     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   313     0.262     0.200
VDW repulsions.others                          1347     0.230     0.200
VDW; torsion: refined_atoms                     712     0.173     0.200
VDW; torsion.others                             723     0.081     0.200
HBOND: refined_atoms                            225     0.196     0.200
VDW repulsions: symmetry: refined_atoms           9     0.224     0.200
VDW repulsions: symmetry: others                 28     0.166     0.200
HBOND: symmetry: refined_atoms                   22     0.232     0.200
HBOND: symmetry: others                           1     0.032     0.200
M. chain bond B values: refined atoms           745     1.637     1.286
M. chain bond B values: others                  745     1.636     1.286
M. chain angle B values: refined atoms          926     2.547     1.909
M. chain angle B values: others                 927     2.546     1.908
S. chain bond B values: refined atoms           811     2.811     1.662
S. chain bond B values: others                  810     2.809     1.662
S. chain angle B values: refined atoms         1177     4.381     2.335
S. chain angle B values: others                1178     4.379     2.334
Long range B values: refined atoms             1855     7.061    18.128
Long range B values: others                    1767     6.796    16.765
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    1.0844
Partial structure    1: scale =     0.3894, B  =   49.1994
Overall anisotropic scale factors
   B11 =  -0.23 B22 =  -0.23 B33 =   0.47 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3010 100.00   453.3   461.4  0.16  0.17     161   475.3   479.1  0.20  0.21
 0.130    5132 100.00   298.7   285.4  0.16  0.15     268   313.3   302.4  0.21  0.19
 0.216    6537  99.97   202.8   186.8  0.16  0.14     335   198.7   185.3  0.21  0.18
 0.303    7623 100.00   104.4   117.1  0.27  0.20     420   103.7   119.1  0.31  0.24
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2170   0.911    840   0.819   3010   0.886  0.947  0.9673  0.9694  0.9252  0.9368
  0.1301   4265   0.882    867   0.766   5132   0.863  1.001  0.9492  0.9602  0.8929  0.9431
  0.2165   5665   0.881    872   0.770   6537   0.866  1.044  0.9479  0.9623  0.8844  0.9450
  0.3028   6765   0.758    861   0.684   7626   0.750  0.808  0.9041  0.9150  0.8527  0.8892
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22305
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0407
Overall R factor                     =     0.1799
Free R factor                        =     0.2245
Average Fourier shell correlation    =     0.9466
AverageFree Fourier shell correlation=     0.9353
Overall weighted R factor            =     0.1593
Free weighted R factor               =     0.1967
Overall weighted R2 factor           =     0.1905
Free weighted R2 factor              =     0.2199
Average correlation coefficient      =     0.9244
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9381
Cruickshanks DPI for coordinate error=     0.1090
DPI based on free R factor           =     0.1114
Overall figure of merit              =     0.8283
ML based su of positional parameters =     0.0738
ML based su of thermal parameters    =     2.3018
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    116092.57       25726.891       809315.44      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.35543364    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    788370.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0431
Partial structure    1: scale =     0.3891, B  =   48.1943
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                     =     0.1795
Free R factor                        =     0.2231
Average Fourier shell correlation    =     0.9536
AverageFree Fourier shell correlation=     0.9431
Average correlation coefficient      =     0.9260
Overall figure of merit              =     0.8554
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    115332.45       9912.0723       788370.06       809315.44    


     CGMAT cycle number =      3

 Weight matrix   0.37055346    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    785582.75    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0075
Partial structure    1: scale =     0.3885, B  =   44.6257
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                     =     0.1783
Free R factor                        =     0.2215
Average Fourier shell correlation    =     0.9552
AverageFree Fourier shell correlation=     0.9446
Average correlation coefficient      =     0.9283
Overall figure of merit              =     0.8595
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    114988.41       9447.0293       785582.75       788370.06    


     CGMAT cycle number =      4

 Weight matrix   0.37528980    
 Actual weight    6.7496872      is applied to the X-ray term


 function value    784629.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0062
Partial structure    1: scale =     0.3885, B  =   44.5949
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                        =     0.2204
Average Fourier shell correlation    =     0.9557
AverageFree Fourier shell correlation=     0.9453
Average correlation coefficient      =     0.9291
Overall figure of merit              =     0.8607
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    114856.05       9386.8066       784629.25       785582.75    


     CGMAT cycle number =      5

 Weight matrix   0.34324348    
 Actual weight    6.1360793      is applied to the X-ray term


 function value    713853.06    

-------------------------------------------------------------------------------
             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  =    0.0254
Partial structure    1: scale =     0.3888, B  =   44.6498
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                     =     0.1780
Free R factor                        =     0.2202
Average Fourier shell correlation    =     0.9559
AverageFree Fourier shell correlation=     0.9455
Average correlation coefficient      =     0.9294
Overall figure of merit              =     0.8612
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    114794.68       9463.8057       713853.06       784629.25    


     CGMAT cycle number =      6

 Weight matrix   0.31208256    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649707.63    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =    0.0042
Partial structure    1: scale =     0.3887, B  =   44.6122
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                     =     0.1783
Free R factor                        =     0.2201
Average Fourier shell correlation    =     0.9559
AverageFree Fourier shell correlation=     0.9456
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8613
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    114821.88       9202.0938       649707.63       713853.06    


     CGMAT cycle number =      7

 Weight matrix   0.31154850    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649683.25    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0001
Partial structure    1: scale =     0.3887, B  =   44.6105
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                        =     0.2203
Average Fourier shell correlation    =     0.9557
AverageFree Fourier shell correlation=     0.9455
Average correlation coefficient      =     0.9288
Overall figure of merit              =     0.8613
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    114877.14       8869.4453       649683.25       649707.63    


     CGMAT cycle number =      8

 Weight matrix   0.31142429    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649744.88    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =    0.0014
Partial structure    1: scale =     0.3883, B  =   44.4737
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                     =     0.1790
Free R factor                        =     0.2203
Average Fourier shell correlation    =     0.9557
AverageFree Fourier shell correlation=     0.9455
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8613
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    114901.29       8779.6445       649732.25       649683.25    

 fvalues    114901.29       8779.6445       649726.13       649728.19    
 fvalues    114901.29       8779.6445       649726.13       649728.19    


     CGMAT cycle number =      9

 Weight matrix   0.31157044    
 Actual weight    5.5782537      is applied to the X-ray term


 function value    649736.13    

-------------------------------------------------------------------------------
             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 =     0.0426, B  =   -0.0012
Partial structure    1: scale =     0.3883, B  =   44.4790
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                     =     0.1790
Free R factor                        =     0.2204
Average Fourier shell correlation    =     0.9558
AverageFree Fourier shell correlation=     0.9455
Average correlation coefficient      =     0.9287
Overall figure of merit              =     0.8614
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02


 fvalues    114907.53       8753.7383       649740.25       649728.19    

 fvalues    114907.53       8753.7383       649735.38       649737.13    
 fvalues    114907.53       8753.7383       649735.38       649737.13    


     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.= 0.923 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  256
 Maximuum H,K,L                 :    34   34   73
 Minimum acceptable grid spacing:    79   79  167
 Weight matrix   0.31148839    
 Actual weight    5.5782537      is applied to the X-ray term
Norm of X_ray positional gradient                37.6
Norm of Geom. positional gradient                37.6
Norm of X_ray B-factor gradient                  118.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.137E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.449E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.6410E+06 GEOM=      8745.     TOTAL=     0.6497E+06
 function value    649736.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.767     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.907     5.000
Torsion angles, period  2. refined               90    36.474    22.778
Torsion angles, period  3. refined              268    13.625    15.000
Torsion angles, period  4. refined                9    11.296    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                   305     0.266     0.200
VDW repulsions.others                          1376     0.201     0.200
VDW; torsion: refined_atoms                     721     0.172     0.200
VDW; torsion.others                             794     0.083     0.200
HBOND: refined_atoms                            225     0.186     0.200
HBOND.others                                      1     0.036     0.200
VDW repulsions: symmetry: refined_atoms           9     0.201     0.200
VDW repulsions: symmetry: others                 26     0.162     0.200
HBOND: symmetry: refined_atoms                   23     0.221     0.200
HBOND: symmetry: others                           1     0.040     0.200
M. chain bond B values: refined atoms           745     1.627     1.387
M. chain bond B values: others                  745     1.625     1.387
M. chain angle B values: refined atoms          926     2.570     2.064
M. chain angle B values: others                 927     2.569     2.064
S. chain bond B values: refined atoms           811     2.865     1.772
S. chain bond B values: others                  810     2.858     1.771
S. chain angle B values: refined atoms         1177     4.432     2.497
S. chain angle B values: others                1178     4.430     2.497
Long range B values: refined atoms             1852     7.145    19.724
Long range B values: others                    1760     6.887    18.269
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0005
Partial structure    1: scale =     0.3883, B  =   44.4787
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3010 100.00   453.2   462.5  0.17  0.18     161   475.2   480.7  0.20  0.20
 0.130    5132 100.00   298.6   284.6  0.16  0.15     268   313.3   300.6  0.21  0.18
 0.216    6537  99.97   202.8   186.5  0.17  0.15     335   198.6   184.9  0.21  0.18
 0.303    7623 100.00   104.4   116.3  0.25  0.19     420   103.7   118.3  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2170   0.923    840   0.840   3010   0.900  0.947  0.9698  0.9715  0.9254  0.9352
  0.1301   4265   0.889    867   0.777   5132   0.870  1.001  0.9530  0.9620  0.9007  0.9432
  0.2165   5665   0.891    872   0.781   6537   0.876  1.044  0.9518  0.9641  0.8892  0.9418
  0.3028   6765   0.836    861   0.757   7626   0.827  0.842  0.9266  0.9382  0.8613  0.9050
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22305
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0407
Overall R factor                     =     0.1790
Free R factor                        =     0.2204
Average Fourier shell correlation    =     0.9558
AverageFree Fourier shell correlation=     0.9455
Overall weighted R factor            =     0.1605
Free weighted R factor               =     0.1935
Overall weighted R2 factor           =     0.1930
Free weighted R2 factor              =     0.2173
Average correlation coefficient      =     0.9287
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9406
Cruickshanks DPI for coordinate error=     0.1085
DPI based on free R factor           =     0.1094
Overall figure of merit              =     0.8614
ML based su of positional parameters =     0.0648
ML based su of thermal parameters    =     1.9672
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    114909.03       8744.5020       649736.25       649737.13    

    ****                              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.= 0.923 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R19_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     1.766     1.644
Bond angles  : others                          3242     1.499     1.582
Torsion angles, period  1. refined              184     6.907     5.000
Torsion angles, period  2. refined               90    36.472    22.778
Torsion angles, period  3. refined              268    13.610    15.000
Torsion angles, period  4. refined                9    11.293    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                   305     0.266     0.200
VDW repulsions.others                          1372     0.201     0.200
VDW; torsion: refined_atoms                     720     0.172     0.200
VDW; torsion.others                             793     0.083     0.200
HBOND: refined_atoms                            224     0.187     0.200
HBOND.others                                      1     0.036     0.200
VDW repulsions: symmetry: refined_atoms           9     0.201     0.200
VDW repulsions: symmetry: others                 26     0.163     0.200
HBOND: symmetry: refined_atoms                   23     0.221     0.200
HBOND: symmetry: others                           1     0.040     0.200
M. chain bond B values: refined atoms           745     1.626     1.387
M. chain bond B values: others                  745     1.623     1.387
M. chain angle B values: refined atoms          926     2.569     2.064
M. chain angle B values: others                 927     2.567     2.064
S. chain bond B values: refined atoms           811     2.863     1.771
S. chain bond B values: others                  810     2.856     1.771
S. chain angle B values: refined atoms         1177     4.428     2.497
S. chain angle B values: others                1178     4.426     2.496
Long range B values: refined atoms             1850     7.125    19.699
Long range B values: others                    1758     6.863    18.241
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0426, B  =   -0.0029
Partial structure    1: scale =     0.3883, B  =   44.4072
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.044    3010 100.00   453.2   462.5  0.17  0.18     161   475.2   480.7  0.20  0.20
 0.130    5132 100.00   298.6   284.6  0.16  0.15     268   313.3   300.6  0.21  0.18
 0.216    6537  99.97   202.8   186.5  0.17  0.15     335   198.7   184.9  0.21  0.18
 0.303    7623 100.00   104.4   116.3  0.25  0.19     420   103.7   118.4  0.30  0.23
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0437   2170   0.923    840   0.840   3010   0.900  0.947  0.9698  0.9715  0.9254  0.9352
  0.1301   4265   0.889    867   0.777   5132   0.870  1.001  0.9530  0.9620  0.9007  0.9432
  0.2165   5665   0.891    872   0.781   6537   0.876  1.044  0.9518  0.9641  0.8891  0.9417
  0.3028   6765   0.836    861   0.757   7626   0.827  0.842  0.9266  0.9382  0.8613  0.9051
 $$
Resolution limits                    =     41.964     1.700
Number of used reflections           =      22305
Percentage observed                  =    99.9872
Percentage of free reflections       =     5.0407
Overall R factor                     =     0.1790
Free R factor                        =     0.2204
Average Fourier shell correlation    =     0.9558
AverageFree Fourier shell correlation=     0.9456
Overall weighted R factor            =     0.1604
Free weighted R factor               =     0.1935
Overall weighted R2 factor           =     0.1930
Free weighted R2 factor              =     0.2173
Average correlation coefficient      =     0.9287
Overall correlation coefficient      =     0.9567
Free correlation coefficient         =     0.9406
Cruickshanks DPI for coordinate error=     0.1085
DPI based on free R factor           =     0.1094
Overall figure of merit              =     0.8615
ML based su of positional parameters =     0.0648
ML based su of thermal parameters    =     1.9672
-----------------------------------------------------------------------------
  Time in seconds: CPU =        17.94
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1799   0.2245   0.828      116093.    6345.5   0.0128  0.948   1.818  1.043   0.088
       1   0.1795   0.2231   0.855      115332.    6307.5   0.0123  0.914   1.781  1.024   0.088
       2   0.1783   0.2215   0.859      114988.    6293.3   0.0132  0.988   1.812  1.046   0.091
       3   0.1781   0.2204   0.861      114856.    6286.8   0.0134  1.003   1.829  1.059   0.092
       4   0.1780   0.2202   0.861      114795.    6284.2   0.0134  1.009   1.840  1.066   0.092
       5   0.1783   0.2201   0.861      114822.    6283.8   0.0128  0.966   1.817  1.053   0.091
       6   0.1788   0.2203   0.861      114877.    6284.8   0.0122  0.920   1.783  1.033   0.089
       7   0.1790   0.2203   0.861      114904.    6285.2   0.0121  0.915   1.771  1.027   0.088
       8   0.1790   0.2204   0.861      114907.    6285.5   0.0121  0.913   1.768  1.025   0.088
       9   0.1790   0.2204   0.861      114909.    6285.5   0.0121  0.913   1.767  1.025   0.088
      10   0.1790   0.2204   0.861      114913.    6285.7   0.0121  0.912   1.766  1.024   0.088
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1799   0.1790
             R free    0.2245   0.2204
     Rms BondLength    0.0128   0.0121
      Rms BondAngle    1.8180   1.7658
     Rms ChirVolume    0.0881   0.0883
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      49.9s System:    0.1s Elapsed:     0:50