###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 15:26:21 


 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 1.80     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 6
  Data line--- END

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

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R06_1-90A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R06_1-80A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R06_1-80A.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       0.0772
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.8000
  Estimated number of reflections :      25918
  Free R exclusion - flag equals:     6
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.8000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R06_1-90A.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=   2.005 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=   1.821 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=   2.164 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=   2.353 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=   2.445 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=   2.095 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

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

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


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


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


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


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


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

FreeR flag                            6
Number of "free" reflections       1016
Number of   all  reflections      19877
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          19877

   Current auto weighting coefficient =    6.9995613    

 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.= 0.886 id.= 3.000 dev= -2.11 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.26318923    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                38.2
Norm of Geom. positional gradient                78.7
Norm of X_ray B-factor gradient                  128.
Norm of Geom. B-factor gradient                 0.218E+05
Product of X_ray and Geom posit. gradients     -0.103E+08
 Cosine of angle between them                      -0.355
Product of X_ray and Geom B-fact gradients     -0.409E+08
 Cosine of angle between them                      -0.005


Residuals: XRAY=     0.7066E+06 GEOM=     0.2615E+05 TOTAL=     0.7327E+06
 function value    732734.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.746     1.644
Bond angles  : others                          3242     2.340     1.582
Torsion angles, period  1. refined              184     6.995     5.000
Torsion angles, period  2. refined               90    36.489    22.778
Torsion angles, period  3. refined              268    14.021    15.000
Torsion angles, period  4. refined                9    10.858    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.017     0.020
VDW repulsions: refined_atoms                   311     0.259     0.200
VDW repulsions.others                          1332     0.232     0.200
VDW; torsion: refined_atoms                     708     0.172     0.200
VDW; torsion.others                             697     0.081     0.200
HBOND: refined_atoms                            238     0.194     0.200
VDW repulsions: symmetry: refined_atoms           7     0.243     0.200
VDW repulsions: symmetry: others                 28     0.176     0.200
HBOND: symmetry: refined_atoms                   22     0.184     0.200
M. chain bond B values: refined atoms           745     1.581     1.206
M. chain bond B values: others                  745     1.581     1.206
M. chain angle B values: refined atoms          926     2.464     1.789
M. chain angle B values: others                 927     2.463     1.789
S. chain bond B values: refined atoms           812     2.590     1.553
S. chain bond B values: others                  811     2.587     1.553
S. chain angle B values: refined atoms         1177     4.054     2.183
S. chain angle B values: others                1178     4.052     2.183
Long range B values: refined atoms             1864     6.990    17.206
Long range B values: others                    1766     6.688    15.796
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =    0.8491
Partial structure    1: scale =     0.3789, B  =   50.2650
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2545 100.00   472.9   480.2  0.16  0.17     148   477.3   501.2  0.21  0.23
 0.116    4359 100.00   340.7   326.1  0.16  0.15     220   363.0   349.3  0.19  0.18
 0.193    5517  99.97   226.5   215.8  0.16  0.13     291   220.1   207.3  0.22  0.19
 0.270    6431 100.00   147.7   154.7  0.21  0.16     356   152.9   159.7  0.25  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1787   0.890    758   0.794   2545   0.861  0.941  0.9551  0.9635  0.8918  0.9370
  0.1161   3581   0.889    778   0.790   4359   0.872  0.998  0.9613  0.9649  0.9288  0.9463
  0.1931   4750   0.876    767   0.758   5517   0.860  1.009  0.9440  0.9598  0.8837  0.9414
  0.2701   5662   0.823    776   0.739   6438   0.813  0.895  0.9356  0.9414  0.8758  0.9093
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18859
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1119
Overall R factor                     =     0.1696
Free R factor                        =     0.2129
Average Fourier shell correlation    =     0.9552
AverageFree Fourier shell correlation=     0.9464
Overall weighted R factor            =     0.1540
Free weighted R factor               =     0.1987
Overall weighted R2 factor           =     0.1877
Free weighted R2 factor              =     0.2442
Average correlation coefficient      =     0.9310
Overall correlation coefficient      =     0.9551
Free correlation coefficient         =     0.9309
Cruickshanks DPI for coordinate error=     0.1241
DPI based on free R factor           =     0.1217
Overall figure of merit              =     0.8467
ML based su of positional parameters =     0.0791
ML based su of thermal parameters    =     2.5416
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    100946.52       26153.551       732734.94      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.29031906    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    713052.69    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0821
Partial structure    1: scale =     0.3787, B  =   49.5113
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1688
Free R factor                        =     0.2123
Average Fourier shell correlation    =     0.9588
AverageFree Fourier shell correlation=     0.9496
Average correlation coefficient      =     0.9333
Overall figure of merit              =     0.8593
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    100457.48       9894.4473       713052.69       732734.94    


     CGMAT cycle number =      3

 Weight matrix   0.29392219    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710963.75    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0410
Partial structure    1: scale =     0.3780, B  =   47.1965
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1675
Free R factor                        =     0.2114
Average Fourier shell correlation    =     0.9595
AverageFree Fourier shell correlation=     0.9502
Average correlation coefficient      =     0.9351
Overall figure of merit              =     0.8605
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    100272.03       9103.4688       710963.75       713052.69    


     CGMAT cycle number =      4

 Weight matrix   0.29494098    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710273.88    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0297
Partial structure    1: scale =     0.3785, B  =   46.7893
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1673
Free R factor                        =     0.2110
Average Fourier shell correlation    =     0.9597
AverageFree Fourier shell correlation=     0.9504
Average correlation coefficient      =     0.9357
Overall figure of merit              =     0.8608
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    100207.05       8868.4492       710273.88       710963.75    


     CGMAT cycle number =      5

 Weight matrix   0.29526827    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    710035.88    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0233
Partial structure    1: scale =     0.3787, B  =   46.8809
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1672
Free R factor                        =     0.2108
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9504
Average correlation coefficient      =     0.9360
Overall figure of merit              =     0.8610
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    100174.76       8856.4932       710035.88       710273.88    


     CGMAT cycle number =      6

 Weight matrix   0.29530600    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709914.25    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0157
Partial structure    1: scale =     0.3788, B  =   46.7335
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1671
Free R factor                        =     0.2106
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9504
Average correlation coefficient      =     0.9362
Overall figure of merit              =     0.8610
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    100154.64       8875.6934       709914.25       710035.88    


     CGMAT cycle number =      7

 Weight matrix   0.29585135    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709794.50    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0152
Partial structure    1: scale =     0.3792, B  =   46.4550
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1671
Free R factor                        =     0.2108
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9504
Average correlation coefficient      =     0.9362
Overall figure of merit              =     0.8612
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    100136.55       8882.5352       709794.50       709914.25    


     CGMAT cycle number =      8

 Weight matrix   0.29611468    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709741.88    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0111
Partial structure    1: scale =     0.3791, B  =   46.4565
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1671
Free R factor                        =     0.2108
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9504
Average correlation coefficient      =     0.9363
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    100128.16       8888.6885       709741.88       709794.50    


     CGMAT cycle number =      9

 Weight matrix   0.29623103    
 Actual weight    6.9995613      is applied to the X-ray term


 function value    709695.31    

-------------------------------------------------------------------------------
             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 =     0.0413, B  =   -0.0345
Partial structure    1: scale =     0.3789, B  =   46.3739
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1671
Free R factor                        =     0.2111
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9504
Average correlation coefficient      =     0.9364
Overall figure of merit              =     0.8613
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    100123.62       8873.9102       709695.31       709741.88    


     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.= 0.906 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   120  120  240
 Maximuum H,K,L                 :    33   33   69
 Minimum acceptable grid spacing:    76   76  160
 Weight matrix   0.29629439    
 Actual weight    6.9995613      is applied to the X-ray term
Norm of X_ray positional gradient                37.2
Norm of Geom. positional gradient                37.2
Norm of X_ray B-factor gradient                  121.
Norm of Geom. B-factor gradient                  123.
Product of X_ray and Geom posit. gradients     -0.134E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.479E+08
 Cosine of angle between them                      -0.996


Residuals: XRAY=     0.7008E+06 GEOM=      8885.     TOTAL=     0.7097E+06
 function value    709711.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.780     1.644
Bond angles  : others                          3242     1.474     1.582
Torsion angles, period  1. refined              184     7.011     5.000
Torsion angles, period  2. refined               90    36.166    22.778
Torsion angles, period  3. refined              268    14.059    15.000
Torsion angles, period  4. refined                9    11.205    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                   313     0.258     0.200
VDW repulsions.others                          1358     0.204     0.200
VDW; torsion: refined_atoms                     707     0.173     0.200
VDW; torsion.others                             784     0.084     0.200
HBOND: refined_atoms                            230     0.189     0.200
HBOND.others                                      1     0.029     0.200
VDW repulsions: symmetry: refined_atoms           9     0.196     0.200
VDW repulsions: symmetry: others                 29     0.159     0.200
HBOND: symmetry: refined_atoms                   22     0.184     0.200
M. chain bond B values: refined atoms           745     1.632     1.284
M. chain bond B values: others                  745     1.631     1.284
M. chain angle B values: refined atoms          926     2.503     1.907
M. chain angle B values: others                 927     2.501     1.907
S. chain bond B values: refined atoms           811     2.792     1.656
S. chain bond B values: others                  810     2.789     1.656
S. chain angle B values: refined atoms         1177     4.328     2.329
S. chain angle B values: others                1178     4.327     2.328
Long range B values: refined atoms             1859     7.048    18.162
Long range B values: others                    1762     6.781    16.678
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0270
Partial structure    1: scale =     0.3790, B  =   46.3444
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.49 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2545 100.00   472.6   480.5  0.16  0.17     148   477.1   499.5  0.21  0.23
 0.116    4359 100.00   340.5   324.9  0.16  0.15     220   362.8   349.1  0.18  0.18
 0.193    5517  99.97   226.4   215.4  0.16  0.13     291   219.9   206.8  0.21  0.18
 0.270    6431 100.00   147.6   154.0  0.19  0.15     356   152.9   159.4  0.25  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1787   0.909    758   0.817   2545   0.881  0.945  0.9585  0.9676  0.8906  0.9371
  0.1161   3581   0.891    778   0.792   4359   0.873  0.998  0.9612  0.9649  0.9284  0.9457
  0.1931   4750   0.883    767   0.765   5517   0.867  1.009  0.9476  0.9615  0.8892  0.9407
  0.2701   5662   0.851    776   0.768   6438   0.841  0.909  0.9425  0.9524  0.8782  0.9263
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18859
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1119
Overall R factor                     =     0.1670
Free R factor                        =     0.2113
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9503
Overall weighted R factor            =     0.1538
Free weighted R factor               =     0.1978
Overall weighted R2 factor           =     0.1881
Free weighted R2 factor              =     0.2438
Average correlation coefficient      =     0.9365
Overall correlation coefficient      =     0.9560
Free correlation coefficient         =     0.9313
Cruickshanks DPI for coordinate error=     0.1222
DPI based on free R factor           =     0.1208
Overall figure of merit              =     0.8614
ML based su of positional parameters =     0.0744
ML based su of thermal parameters    =     2.3689
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02

 fvalues    100121.37       8885.0977       709690.75       709695.31    

    ****                              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.= 0.906 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R06_1-80A.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     1.473     1.582
Torsion angles, period  1. refined              184     7.009     5.000
Torsion angles, period  2. refined               90    36.139    22.778
Torsion angles, period  3. refined              268    14.051    15.000
Torsion angles, period  4. refined                9    11.179    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                   311     0.258     0.200
VDW repulsions.others                          1358     0.203     0.200
VDW; torsion: refined_atoms                     707     0.173     0.200
VDW; torsion.others                             783     0.084     0.200
HBOND: refined_atoms                            231     0.189     0.200
HBOND.others                                      1     0.029     0.200
VDW repulsions: symmetry: refined_atoms           9     0.196     0.200
VDW repulsions: symmetry: others                 29     0.159     0.200
HBOND: symmetry: refined_atoms                   22     0.185     0.200
M. chain bond B values: refined atoms           745     1.631     1.285
M. chain bond B values: others                  745     1.630     1.285
M. chain angle B values: refined atoms          926     2.501     1.908
M. chain angle B values: others                 927     2.500     1.908
S. chain bond B values: refined atoms           811     2.793     1.657
S. chain bond B values: others                  810     2.789     1.657
S. chain angle B values: refined atoms         1177     4.327     2.330
S. chain angle B values: others                1178     4.325     2.329
Long range B values: refined atoms             1858     7.064    18.173
Long range B values: others                    1761     6.799    16.689
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0413, B  =   -0.0433
Partial structure    1: scale =     0.3792, B  =   46.3508
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -0.25 B33 =   0.50 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.039    2545 100.00   472.6   480.4  0.16  0.17     148   477.1   499.3  0.21  0.23
 0.116    4359 100.00   340.5   325.0  0.16  0.15     220   362.8   349.1  0.18  0.18
 0.193    5517  99.97   226.4   215.5  0.16  0.13     291   219.9   206.9  0.21  0.18
 0.270    6431 100.00   147.6   154.0  0.19  0.15     356   152.9   159.5  0.25  0.19
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0391   1787   0.909    758   0.817   2545   0.881  0.945  0.9584  0.9676  0.8902  0.9370
  0.1161   3581   0.891    778   0.792   4359   0.873  0.998  0.9611  0.9648  0.9283  0.9456
  0.1931   4750   0.883    767   0.765   5517   0.867  1.009  0.9477  0.9615  0.8891  0.9408
  0.2701   5662   0.851    776   0.768   6438   0.841  0.909  0.9425  0.9524  0.8782  0.9265
 $$
Resolution limits                    =     41.964     1.800
Number of used reflections           =      18859
Percentage observed                  =    99.9849
Percentage of free reflections       =     5.1119
Overall R factor                     =     0.1670
Free R factor                        =     0.2114
Average Fourier shell correlation    =     0.9600
AverageFree Fourier shell correlation=     0.9503
Overall weighted R factor            =     0.1538
Free weighted R factor               =     0.1978
Overall weighted R2 factor           =     0.1881
Free weighted R2 factor              =     0.2438
Average correlation coefficient      =     0.9365
Overall correlation coefficient      =     0.9560
Free correlation coefficient         =     0.9311
Cruickshanks DPI for coordinate error=     0.1222
DPI based on free R factor           =     0.1208
Overall figure of merit              =     0.8614
ML based su of positional parameters =     0.0744
ML based su of thermal parameters    =     2.3689
-----------------------------------------------------------------------------
  Time in seconds: CPU =        14.25
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1696   0.2129   0.847      100947.    5606.8   0.0118  0.880   1.746  1.012   0.083
       1   0.1688   0.2123   0.859      100457.    5596.8   0.0116  0.864   1.728  1.001   0.084
       2   0.1675   0.2114   0.860      100272.    5592.2   0.0122  0.907   1.753  1.014   0.086
       3   0.1673   0.2110   0.861      100207.    5590.4   0.0123  0.913   1.763  1.020   0.086
       4   0.1672   0.2108   0.861      100175.    5589.6   0.0123  0.915   1.769  1.023   0.086
       5   0.1671   0.2106   0.861      100155.    5589.1   0.0123  0.915   1.773  1.025   0.085
       6   0.1671   0.2108   0.861      100137.    5588.8   0.0123  0.915   1.776  1.026   0.085
       7   0.1671   0.2108   0.861      100128.    5588.9   0.0122  0.915   1.778  1.027   0.085
       8   0.1671   0.2111   0.861      100124.    5589.5   0.0122  0.915   1.779  1.027   0.086
       9   0.1670   0.2113   0.861      100124.    5590.2   0.0122  0.916   1.780  1.028   0.086
      10   0.1670   0.2114   0.861      100124.    5590.6   0.0122  0.915   1.780  1.028   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1696   0.1670
             R free    0.2129   0.2114
     Rms BondLength    0.0118   0.0122
      Rms BondAngle    1.7456   1.7805
     Rms ChirVolume    0.0832   0.0856
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      46.2s System:    0.1s Elapsed:     0:47