###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 14:21:53 


 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 1.90     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 1
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: CDO_R.mtz 

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R01_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R01_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R01_1-90A.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       0.0693
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9000
  Estimated number of reflections :      21862
  Free R exclusion - flag equals:     1
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.9000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R01_2-00A.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=   2.025 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=   2.248 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=   1.842 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.196 ideal_dist=   2.090
            ch:AAA  res: 140  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   2.364 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=   2.447 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=   2.082 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:26-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  THR               171  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO               190  AAA  is missing in the structure
  Number of chains                  :       4
  Total number of monomers          :     502
  Number of atoms                   :    3948
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    1482
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0490
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.2805


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:      2950         0      2950
               Angles:      5345         0      5345
              Chirals:       196         0       196
               Planes:       451         0       451
             Torsions:      1553         0      1553
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            1
Number of "free" reflections        855
Number of   all  reflections      16986
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16986

   Current auto weighting coefficient =    7.2495699    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A    125 LEU C   . - A    126 ARG N   . mod.= 1.536 id.= 1.337 dev= -0.199 sig.= 0.011
A    164 CYS C   . - A    165 HIS N   . mod.= 1.457 id.= 1.337 dev= -0.120 sig.= 0.011

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     10 ARG C     deviation=   0.20 sigma.=   0.02

    ****                              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        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.23164102    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                40.6
Norm of Geom. positional gradient                87.8
Norm of X_ray B-factor gradient                  133.
Norm of Geom. B-factor gradient                 0.216E+05
Product of X_ray and Geom posit. gradients     -0.664E+07
 Cosine of angle between them                      -0.192
Product of X_ray and Geom B-fact gradients     -0.362E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.6381E+06 GEOM=     0.2625E+05 TOTAL=     0.6643E+06
 function value    664337.44    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.831     1.644
Bond angles  : others                          3242     2.356     1.582
Torsion angles, period  1. refined              184     7.326     5.000
Torsion angles, period  2. refined               90    36.870    22.778
Torsion angles, period  3. refined              268    14.458    15.000
Torsion angles, period  4. refined                9    10.592    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.012     0.020
Planar groups: others                           331     0.016     0.020
VDW repulsions: refined_atoms                   319     0.257     0.200
VDW repulsions.others                          1326     0.232     0.200
VDW; torsion: refined_atoms                     703     0.169     0.200
VDW; torsion.others                             690     0.080     0.200
HBOND: refined_atoms                            225     0.217     0.200
HBOND.others                                      4     0.032     0.200
VDW repulsions: symmetry: refined_atoms           7     0.271     0.200
VDW repulsions: symmetry: others                 26     0.187     0.200
HBOND: symmetry: refined_atoms                   14     0.267     0.200
HBOND: symmetry: others                           1     0.103     0.200
M. chain bond B values: refined atoms           745     1.543     1.182
M. chain bond B values: others                  745     1.542     1.182
M. chain angle B values: refined atoms          926     2.476     1.754
M. chain angle B values: others                 927     2.475     1.754
S. chain bond B values: refined atoms           812     2.396     1.503
S. chain bond B values: others                  811     2.392     1.503
S. chain angle B values: refined atoms         1177     3.826     2.115
S. chain angle B values: others                1178     3.824     2.115
Long range B values: refined atoms             1856     6.569    16.572
Long range B values: others                    1761     6.271    15.284
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =    0.3493
Partial structure    1: scale =     0.3758, B  =   48.6160
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2196 100.00   479.6   484.1  0.16  0.17     115   494.8   486.5  0.19  0.19
 0.104    3716 100.00   386.5   369.6  0.15  0.14     208   372.6   374.2  0.21  0.19
 0.173    4687  99.96   247.1   241.8  0.16  0.14     255   263.6   257.5  0.22  0.18
 0.242    5527 100.00   188.3   188.6  0.18  0.14     277   189.8   197.4  0.21  0.17
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1515   0.908    681   0.789   2196   0.871  0.958  0.9560  0.9676  0.8917  0.9415
  0.1042   3032   0.901    684   0.800   3716   0.882  1.002  0.9556  0.9688  0.8908  0.9495
  0.1733   3995   0.863    692   0.764   4687   0.848  0.977  0.9481  0.9562  0.8959  0.9380
  0.2425   4821   0.869    709   0.755   5530   0.855  0.952  0.9473  0.9514  0.8999  0.9178
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16129
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0341
Overall R factor                     =     0.1635
Free R factor                        =     0.2083
Average Fourier shell correlation    =     0.9590
AverageFree Fourier shell correlation=     0.9508
Overall weighted R factor            =     0.1509
Free weighted R factor               =     0.1876
Overall weighted R2 factor           =     0.1833
Free weighted R2 factor              =     0.2167
Average correlation coefficient      =     0.9342
Overall correlation coefficient      =     0.9546
Free correlation coefficient         =     0.9175
Cruickshanks DPI for coordinate error=     0.1445
DPI based on free R factor           =     0.1359
Overall figure of merit              =     0.8614
ML based su of positional parameters =     0.0858
ML based su of thermal parameters    =     2.8748
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88017.781       26246.379       664337.44      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.25390813    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644840.63    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0799
Partial structure    1: scale =     0.3764, B  =   48.5735
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1612
Free R factor                        =     0.2063
Average Fourier shell correlation    =     0.9619
AverageFree Fourier shell correlation=     0.9531
Average correlation coefficient      =     0.9381
Overall figure of merit              =     0.8692
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    87508.703       10440.193       644840.63       664337.44    


     CGMAT cycle number =      3

 Weight matrix   0.25721595    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    642316.38    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0895
Partial structure    1: scale =     0.3762, B  =   46.6425
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1597
Free R factor                        =     0.2052
Average Fourier shell correlation    =     0.9626
AverageFree Fourier shell correlation=     0.9537
Average correlation coefficient      =     0.9398
Overall figure of merit              =     0.8703
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87332.398       9194.0879       642316.38       644840.63    


     CGMAT cycle number =      4

 Weight matrix   0.25906381    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    641385.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0808
Partial structure    1: scale =     0.3770, B  =   46.5733
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1591
Free R factor                        =     0.2048
Average Fourier shell correlation    =     0.9629
AverageFree Fourier shell correlation=     0.9539
Average correlation coefficient      =     0.9404
Overall figure of merit              =     0.8708
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87257.586       8805.3652       641385.31       642316.38    


     CGMAT cycle number =      5

 Weight matrix   0.25996435    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640984.88    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0724
Partial structure    1: scale =     0.3809, B  =   47.2862
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1587
Free R factor                        =     0.2049
Average Fourier shell correlation    =     0.9630
AverageFree Fourier shell correlation=     0.9540
Average correlation coefficient      =     0.9407
Overall figure of merit              =     0.8709
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87210.906       8743.3369       640984.88       641385.31    


     CGMAT cycle number =      6

 Weight matrix   0.26056993    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640796.75    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0868
Partial structure    1: scale =     0.3815, B  =   47.4018
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1585
Free R factor                        =     0.2049
Average Fourier shell correlation    =     0.9632
AverageFree Fourier shell correlation=     0.9540
Average correlation coefficient      =     0.9409
Overall figure of merit              =     0.8712
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87183.328       8755.1094       640796.75       640984.88    


     CGMAT cycle number =      7

 Weight matrix   0.26072368    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640728.88    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0862
Partial structure    1: scale =     0.3811, B  =   47.3517
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1584
Free R factor                        =     0.2049
Average Fourier shell correlation    =     0.9632
AverageFree Fourier shell correlation=     0.9540
Average correlation coefficient      =     0.9410
Overall figure of merit              =     0.8713
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87171.188       8775.2412       640728.88       640796.75    


     CGMAT cycle number =      8

 Weight matrix   0.26079413    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640689.19    

-------------------------------------------------------------------------------
             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 =     0.0403, B  =   -0.0872
Partial structure    1: scale =     0.3808, B  =   47.2493
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1583
Free R factor                        =     0.2050
Average Fourier shell correlation    =     0.9632
AverageFree Fourier shell correlation=     0.9541
Average correlation coefficient      =     0.9411
Overall figure of merit              =     0.8713
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87164.398       8784.8164       640689.19       640728.88    


     CGMAT cycle number =      9

 Weight matrix   0.26071328    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    640680.31    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0824
Partial structure    1: scale =     0.3808, B  =   47.1729
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1582
Free R factor                        =     0.2050
Average Fourier shell correlation    =     0.9632
AverageFree Fourier shell correlation=     0.9540
Average correlation coefficient      =     0.9412
Overall figure of merit              =     0.8713
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87162.883       8786.8652       640680.31       640689.19    


     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.= 0.925 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        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.26034227    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                35.1
Norm of Geom. positional gradient                35.1
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                  118.
Product of X_ray and Geom posit. gradients     -0.119E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.431E+08
 Cosine of angle between them                      -0.991


Residuals: XRAY=     0.6319E+06 GEOM=      8791.     TOTAL=     0.6407E+06
 function value    640711.56    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.781     1.644
Bond angles  : others                          3242     1.432     1.582
Torsion angles, period  1. refined              184     6.959     5.000
Torsion angles, period  2. refined               90    36.773    22.778
Torsion angles, period  3. refined              268    13.868    15.000
Torsion angles, period  4. refined                9    10.831    15.000
Chiral centres: refined atoms                   196     0.086     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   299     0.271     0.200
VDW repulsions.others                          1356     0.205     0.200
VDW; torsion: refined_atoms                     713     0.170     0.200
VDW; torsion.others                             775     0.083     0.200
HBOND: refined_atoms                            231     0.206     0.200
HBOND.others                                      1     0.069     0.200
VDW repulsions: symmetry: refined_atoms           7     0.268     0.200
VDW repulsions: symmetry: others                 23     0.202     0.200
HBOND: symmetry: refined_atoms                   20     0.208     0.200
HBOND: symmetry: others                           1     0.093     0.200
M. chain bond B values: refined atoms           745     1.599     1.214
M. chain bond B values: others                  745     1.598     1.214
M. chain angle B values: refined atoms          926     2.522     1.802
M. chain angle B values: others                 927     2.521     1.802
S. chain bond B values: refined atoms           812     2.655     1.564
S. chain bond B values: others                  811     2.652     1.564
S. chain angle B values: refined atoms         1177     4.180     2.197
S. chain angle B values: others                1178     4.179     2.196
Long range B values: refined atoms             1849     6.808    17.050
Long range B values: others                    1751     6.514    15.639
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0827
Partial structure    1: scale =     0.3805, B  =   46.9925
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2196 100.00   479.1   484.0  0.16  0.17     115   494.3   490.0  0.19  0.19
 0.104    3716 100.00   386.0   368.3  0.15  0.14     208   372.2   372.1  0.20  0.19
 0.173    4687  99.96   246.8   241.6  0.16  0.14     255   263.3   256.5  0.22  0.18
 0.242    5527 100.00   188.1   188.8  0.16  0.13     277   189.5   198.3  0.21  0.16
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1515   0.924    681   0.812   2196   0.889  0.958  0.9597  0.9713  0.8888  0.9415
  0.1042   3032   0.905    684   0.803   3716   0.886  1.002  0.9577  0.9696  0.8948  0.9490
  0.1733   3995   0.869    692   0.769   4687   0.854  0.977  0.9503  0.9578  0.8988  0.9377
  0.2425   4821   0.883    709   0.769   5530   0.868  0.957  0.9522  0.9602  0.9058  0.9388
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16129
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0341
Overall R factor                     =     0.1582
Free R factor                        =     0.2051
Average Fourier shell correlation    =     0.9632
AverageFree Fourier shell correlation=     0.9540
Overall weighted R factor            =     0.1485
Free weighted R factor               =     0.1840
Overall weighted R2 factor           =     0.1825
Free weighted R2 factor              =     0.2120
Average correlation coefficient      =     0.9412
Overall correlation coefficient      =     0.9562
Free correlation coefficient         =     0.9189
Cruickshanks DPI for coordinate error=     0.1398
DPI based on free R factor           =     0.1338
Overall figure of merit              =     0.8712
ML based su of positional parameters =     0.0808
ML based su of thermal parameters    =     2.6932
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    87167.781       8790.9297       640715.06       640680.31    
 fvalues    87167.781       8790.9297       640715.06       640719.88    

    ****                              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.= 0.925 id.= 3.000 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R01_1-90A.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     1.780     1.644
Bond angles  : others                          3242     1.432     1.582
Torsion angles, period  1. refined              184     6.954     5.000
Torsion angles, period  2. refined               90    36.763    22.778
Torsion angles, period  3. refined              268    13.857    15.000
Torsion angles, period  4. refined                9    10.857    15.000
Chiral centres: refined atoms                   196     0.085     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   299     0.271     0.200
VDW repulsions.others                          1356     0.205     0.200
VDW; torsion: refined_atoms                     713     0.170     0.200
VDW; torsion.others                             778     0.083     0.200
HBOND: refined_atoms                            230     0.206     0.200
HBOND.others                                      1     0.072     0.200
VDW repulsions: symmetry: refined_atoms           7     0.268     0.200
VDW repulsions: symmetry: others                 23     0.202     0.200
HBOND: symmetry: refined_atoms                   19     0.214     0.200
HBOND: symmetry: others                           1     0.094     0.200
M. chain bond B values: refined atoms           745     1.599     1.214
M. chain bond B values: others                  745     1.598     1.214
M. chain angle B values: refined atoms          926     2.523     1.802
M. chain angle B values: others                 927     2.522     1.801
S. chain bond B values: refined atoms           812     2.654     1.564
S. chain bond B values: others                  811     2.651     1.564
S. chain angle B values: refined atoms         1177     4.179     2.197
S. chain angle B values: others                1178     4.177     2.196
Long range B values: refined atoms             1848     6.801    17.052
Long range B values: others                    1750     6.506    15.641
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0403, B  =   -0.0786
Partial structure    1: scale =     0.3804, B  =   46.9136
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2196 100.00   479.0   484.0  0.16  0.17     115   494.2   489.9  0.19  0.19
 0.104    3716 100.00   386.0   368.3  0.15  0.14     208   372.1   372.0  0.21  0.19
 0.173    4687  99.96   246.8   241.6  0.16  0.14     255   263.3   256.5  0.22  0.18
 0.242    5527 100.00   188.1   188.8  0.16  0.13     277   189.5   198.2  0.21  0.16
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1515   0.924    681   0.813   2196   0.890  0.958  0.9599  0.9715  0.8894  0.9416
  0.1042   3032   0.904    684   0.803   3716   0.886  1.002  0.9576  0.9696  0.8945  0.9490
  0.1733   3995   0.869    692   0.769   4687   0.854  0.977  0.9502  0.9578  0.8987  0.9376
  0.2425   4821   0.883    709   0.769   5530   0.869  0.957  0.9522  0.9603  0.9059  0.9389
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16129
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0341
Overall R factor                     =     0.1582
Free R factor                        =     0.2050
Average Fourier shell correlation    =     0.9632
AverageFree Fourier shell correlation=     0.9540
Overall weighted R factor            =     0.1484
Free weighted R factor               =     0.1839
Overall weighted R2 factor           =     0.1825
Free weighted R2 factor              =     0.2118
Average correlation coefficient      =     0.9412
Overall correlation coefficient      =     0.9562
Free correlation coefficient         =     0.9190
Cruickshanks DPI for coordinate error=     0.1398
DPI based on free R factor           =     0.1337
Overall figure of merit              =     0.8712
ML based su of positional parameters =     0.0808
ML based su of thermal parameters    =     2.6932
-----------------------------------------------------------------------------
  Time in seconds: CPU =        13.14
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1635   0.2083   0.861       88018.    4846.7   0.0135  1.038   1.831  1.059   0.087
       1   0.1612   0.2063   0.869       87509.    4836.1   0.0116  0.838   1.755  1.009   0.086
       2   0.1597   0.2052   0.870       87332.    4830.8   0.0121  0.877   1.766  1.017   0.087
       3   0.1591   0.2048   0.871       87258.    4828.4   0.0122  0.884   1.771  1.020   0.086
       4   0.1587   0.2049   0.871       87211.    4826.1   0.0122  0.889   1.774  1.022   0.086
       5   0.1585   0.2049   0.871       87183.    4826.4   0.0122  0.891   1.776  1.024   0.086
       6   0.1584   0.2049   0.871       87171.    4826.4   0.0122  0.892   1.778  1.025   0.086
       7   0.1583   0.2050   0.871       87164.    4826.5   0.0122  0.892   1.779  1.026   0.086
       8   0.1582   0.2050   0.871       87163.    4826.6   0.0122  0.893   1.780  1.026   0.086
       9   0.1582   0.2051   0.871       87167.    4827.1   0.0122  0.893   1.781  1.027   0.086
      10   0.1582   0.2050   0.871       87162.    4826.9   0.0122  0.893   1.780  1.027   0.085
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1635   0.1582
             R free    0.2083   0.2050
     Rms BondLength    0.0135   0.0122
      Rms BondAngle    1.8313   1.7804
     Rms ChirVolume    0.0865   0.0855
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      45.3s System:    0.1s Elapsed:     0:45