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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 26/ 5/2020 Run time: 21:01:26 


 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 1.42     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 7
  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_R07_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R07_1-42A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R07_1-42A.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       0.1240
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.4200
  Estimated number of reflections :      51186
  Free R exclusion - flag equals:     7
  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  1.4200

  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_R07_1-50A.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=   2.060 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=   2.189 ideal_dist=   2.090
            ch:AAA  res:  88  HIS              at:NE2 .->ch:AaA  res: 501  FE               at:FE  .
  INFO:     link is found (not be used) dist=   1.829 ideal_dist=   1.720
            ch:AAA  res:  93  CYS              at:SG  .->ch:AAA  res: 157  TYR              at:CE1 .
  INFO:     link is found (not be used) dist=   2.209 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=   2.402 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=   2.382 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=   2.066 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                            7
Number of "free" reflections       1995
Number of   all  reflections      39817
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          39817

   Current auto weighting coefficient =    6.0498405    

 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.= 0.899 id.= 3.000 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.25055072    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                38.5
Norm of Geom. positional gradient                79.9
Norm of X_ray B-factor gradient                  100.
Norm of Geom. B-factor gradient                 0.238E+05
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -0.463
Product of X_ray and Geom B-fact gradients     -0.296E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1067E+07 GEOM=     0.2694E+05 TOTAL=     0.1094E+07
 function value    1094016.6    

-------------------------------------------------------------------------------
             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     1.756     1.644
Bond angles  : others                          3242     2.343     1.582
Torsion angles, period  1. refined              184     6.939     5.000
Torsion angles, period  2. refined               90    36.282    22.778
Torsion angles, period  3. refined              268    13.306    15.000
Torsion angles, period  4. refined                9    11.782    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.015     0.020
VDW repulsions: refined_atoms                   305     0.265     0.200
VDW repulsions.others                          1349     0.229     0.200
VDW; torsion: refined_atoms                     727     0.172     0.200
VDW; torsion.others                             710     0.081     0.200
HBOND: refined_atoms                            222     0.197     0.200
HBOND.others                                      2     0.081     0.200
VDW repulsions: symmetry: refined_atoms          10     0.185     0.200
VDW repulsions: symmetry: others                 25     0.228     0.200
HBOND: symmetry: refined_atoms                   22     0.275     0.200
HBOND: symmetry: others                           1     0.000     0.200
M. chain bond B values: refined atoms           745     1.722     1.619
M. chain bond B values: others                  745     1.719     1.619
M. chain angle B values: refined atoms          926     2.707     2.418
M. chain angle B values: others                 927     2.706     2.418
S. chain bond B values: refined atoms           811     3.105     2.026
S. chain bond B values: others                  810     3.101     2.025
S. chain angle B values: refined atoms         1177     4.765     2.871
S. chain angle B values: others                1178     4.763     2.870
Long range B values: refined atoms             1858     7.503    22.483
Long range B values: others                    1761     7.079    20.910
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =    0.7691
Partial structure    1: scale =     0.3918, B  =   46.3894
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5070 100.00   382.5   392.1  0.18  0.18     259   341.9   354.2  0.22  0.22
 0.186    8686  99.98   206.1   181.9  0.19  0.17     457   208.5   185.8  0.23  0.20
 0.310   11055 100.00    92.0    88.8  0.23  0.20     592    92.1    87.2  0.26  0.23
 0.434   12822  98.63    38.8    48.2  0.47  0.46     673    38.4    47.1  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3847   0.912   1223   0.807   5070   0.886  0.948  0.9553  0.9683  0.9019  0.9340
  0.1863   7439   0.859   1247   0.759   8686   0.845  1.093  0.9475  0.9562  0.8972  0.9369
  0.3102   9807   0.798   1248   0.733  11055   0.791  0.948  0.9232  0.9311  0.8887  0.9126
  0.4340  11564   0.373   1258   0.332  12822   0.369  0.365  0.5928  0.6099  0.6245  0.6417
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37633
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0008
Overall R factor                     =     0.2194
Free R factor                        =     0.2569
Average Fourier shell correlation    =     0.8325
AverageFree Fourier shell correlation=     0.8207
Overall weighted R factor            =     0.1834
Free weighted R factor               =     0.2203
Overall weighted R2 factor           =     0.2116
Free weighted R2 factor              =     0.2629
Average correlation coefficient      =     0.8288
Overall correlation coefficient      =     0.9595
Free correlation coefficient         =     0.9403
Cruickshanks DPI for coordinate error=     0.0782
DPI based on free R factor           =     0.0821
Overall figure of merit              =     0.6724
ML based su of positional parameters =     0.0753
ML based su of thermal parameters    =     2.1894
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176380.98       26939.789       1094016.6      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.32574189    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1070681.9    

-------------------------------------------------------------------------------
             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 =     0.0466, B  =   -0.0647
Partial structure    1: scale =     0.3917, B  =   45.5751
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2192
Free R factor                        =     0.2566
Average Fourier shell correlation    =     0.8529
AverageFree Fourier shell correlation=     0.8411
Average correlation coefficient      =     0.8283
Overall figure of merit              =     0.7168
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175310.73       10079.910       1070681.9       1094016.6    


     CGMAT cycle number =      3

 Weight matrix   0.32908028    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068506.4    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0258
Partial structure    1: scale =     0.3918, B  =   42.4618
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2183
Free R factor                        =     0.2562
Average Fourier shell correlation    =     0.8545
AverageFree Fourier shell correlation=     0.8424
Average correlation coefficient      =     0.8297
Overall figure of merit              =     0.7181
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    175097.08       9197.0293       1068506.4       1070681.9    


     CGMAT cycle number =      4

 Weight matrix   0.32975373    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067930.8    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0209
Partial structure    1: scale =     0.3920, B  =   39.0601
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2180
Free R factor                        =     0.2560
Average Fourier shell correlation    =     0.8549
AverageFree Fourier shell correlation=     0.8429
Average correlation coefficient      =     0.8301
Overall figure of merit              =     0.7187
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    175058.58       8854.2529       1067930.8       1068506.4    


     CGMAT cycle number =      5

 Weight matrix   0.29982173    
 Actual weight    5.4998550      is applied to the X-ray term


 function value    971515.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0000
Partial structure    1: scale =     0.3920, B  =   39.0601
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2179
Free R factor                        =     0.2556
Average Fourier shell correlation    =     0.8551
AverageFree Fourier shell correlation=     0.8430
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.7191
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    175041.67       8811.2637       971515.06       1067930.8    


     CGMAT cycle number =      6

 Weight matrix   0.27229404    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    884008.06    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0152
Partial structure    1: scale =     0.3922, B  =   39.0347
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2182
Free R factor                        =     0.2556
Average Fourier shell correlation    =     0.8548
AverageFree Fourier shell correlation=     0.8427
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.7185
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    175099.59       8533.2295       884008.06       971515.06    


     CGMAT cycle number =      7

 Weight matrix   0.27202931    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    884104.88    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0223
Partial structure    1: scale =     0.3924, B  =   38.9171
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2186
Free R factor                        =     0.2555
Average Fourier shell correlation    =     0.8549
AverageFree Fourier shell correlation=     0.8429
Average correlation coefficient      =     0.8295
Overall figure of merit              =     0.7191
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05


 fvalues    175189.38       8207.2520       884207.38       884008.06    

 fvalues    175189.38       8207.2520       884168.00       884131.00    
 fvalues    175189.38       8207.2520       884168.00       884131.00    


     CGMAT cycle number =      8

 Weight matrix   0.27109945    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    884171.50    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0185
Partial structure    1: scale =     0.3925, B  =   38.9249
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2187
Free R factor                        =     0.2555
Average Fourier shell correlation    =     0.8545
AverageFree Fourier shell correlation=     0.8424
Average correlation coefficient      =     0.8294
Overall figure of merit              =     0.7182
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    175203.55       8187.3403       884193.13       884131.00    

 fvalues    175203.55       8187.3403       884190.69       884181.88    
 fvalues    175203.55       8187.3403       884190.69       884181.88    


     CGMAT cycle number =      9

 Weight matrix   0.27187148    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    884153.94    

-------------------------------------------------------------------------------
             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 =     0.0465, B  =   -0.0230
Partial structure    1: scale =     0.3925, B  =   38.9481
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2187
Free R factor                        =     0.2555
Average Fourier shell correlation    =     0.8548
AverageFree Fourier shell correlation=     0.8428
Average correlation coefficient      =     0.8294
Overall figure of merit              =     0.7190
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    175199.14       8181.3789       884153.94       884181.88    


     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.= 0.916 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        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   144  144  288
 Maximuum H,K,L                 :    41   41   87
 Minimum acceptable grid spacing:    91   91  192
 Weight matrix   0.27140340    
 Actual weight    4.9998679      is applied to the X-ray term
Norm of X_ray positional gradient                37.4
Norm of Geom. positional gradient                37.6
Norm of X_ray B-factor gradient                  91.8
Norm of Geom. B-factor gradient                  94.4
Product of X_ray and Geom posit. gradients     -0.136E+08
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.279E+08
 Cosine of angle between them                      -0.998


Residuals: XRAY=     0.8760E+06 GEOM=      8172.     TOTAL=     0.8841E+06
 function value    884137.19    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.012     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.756     1.644
Bond angles  : others                          3242     1.489     1.582
Torsion angles, period  1. refined              184     6.936     5.000
Torsion angles, period  2. refined               90    36.285    22.778
Torsion angles, period  3. refined              268    13.330    15.000
Torsion angles, period  4. refined                9    11.735    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                   304     0.265     0.200
VDW repulsions.others                          1368     0.204     0.200
VDW; torsion: refined_atoms                     726     0.172     0.200
VDW; torsion.others                             766     0.084     0.200
HBOND: refined_atoms                            214     0.198     0.200
HBOND.others                                      1     0.127     0.200
VDW repulsions: symmetry: refined_atoms          10     0.182     0.200
VDW repulsions: symmetry: others                 25     0.208     0.200
HBOND: symmetry: refined_atoms                   22     0.275     0.200
HBOND: symmetry: others                           1     0.005     0.200
M. chain bond B values: refined atoms           745     1.754     1.696
M. chain bond B values: others                  745     1.751     1.696
M. chain angle B values: refined atoms          926     2.745     2.533
M. chain angle B values: others                 927     2.744     2.533
S. chain bond B values: refined atoms           811     3.158     2.109
S. chain bond B values: others                  810     3.153     2.109
S. chain angle B values: refined atoms         1177     4.848     2.993
S. chain angle B values: others                1178     4.846     2.993
Long range B values: refined atoms             1847     7.742    23.269
Long range B values: others                    1753     7.355    21.713
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0220
Partial structure    1: scale =     0.3926, B  =   38.9490
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5070 100.00   382.9   392.3  0.18  0.18     259   342.3   354.6  0.21  0.22
 0.186    8686  99.98   206.3   182.2  0.19  0.17     457   208.8   186.3  0.23  0.20
 0.310   11055 100.00    92.1    89.0  0.23  0.20     592    92.2    87.4  0.26  0.23
 0.434   12822  98.63    38.8    48.2  0.47  0.46     673    38.5    47.1  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3847   0.921   1223   0.827   5070   0.898  0.949  0.9584  0.9711  0.9018  0.9340
  0.1863   7439   0.884   1247   0.785   8686   0.870  1.099  0.9542  0.9625  0.8986  0.9378
  0.3102   9807   0.822   1248   0.758  11055   0.815  0.954  0.9328  0.9404  0.8895  0.9134
  0.4340  11564   0.466   1258   0.414  12822   0.461  0.427  0.6425  0.6611  0.6264  0.6423
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37633
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0008
Overall R factor                     =     0.2187
Free R factor                        =     0.2555
Average Fourier shell correlation    =     0.8545
AverageFree Fourier shell correlation=     0.8425
Overall weighted R factor            =     0.1829
Free weighted R factor               =     0.2191
Overall weighted R2 factor           =     0.2111
Free weighted R2 factor              =     0.2634
Average correlation coefficient      =     0.8294
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9406
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0817
Overall figure of merit              =     0.7183
ML based su of positional parameters =     0.0657
ML based su of thermal parameters    =     1.8942
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    175197.59       8172.3813       884137.19       884153.94    

    ****                              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.= 0.916 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
          28          24          36  0.70425701      2.37302221E-02  0.70425248    
          36           8          36  0.70425701      2.37302221E-02  0.70425248    

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R07_1-42A.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     1.755     1.644
Bond angles  : others                          3242     1.488     1.582
Torsion angles, period  1. refined              184     6.937     5.000
Torsion angles, period  2. refined               90    36.287    22.778
Torsion angles, period  3. refined              268    13.330    15.000
Torsion angles, period  4. refined                9    11.730    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                   304     0.265     0.200
VDW repulsions.others                          1370     0.203     0.200
VDW; torsion: refined_atoms                     726     0.172     0.200
VDW; torsion.others                             766     0.084     0.200
HBOND: refined_atoms                            215     0.197     0.200
HBOND.others                                      1     0.126     0.200
VDW repulsions: symmetry: refined_atoms          10     0.182     0.200
VDW repulsions: symmetry: others                 25     0.208     0.200
HBOND: symmetry: refined_atoms                   22     0.275     0.200
HBOND: symmetry: others                           1     0.005     0.200
M. chain bond B values: refined atoms           745     1.753     1.696
M. chain bond B values: others                  745     1.750     1.696
M. chain angle B values: refined atoms          926     2.744     2.533
M. chain angle B values: others                 927     2.742     2.533
S. chain bond B values: refined atoms           811     3.156     2.109
S. chain bond B values: others                  810     3.151     2.109
S. chain angle B values: refined atoms         1177     4.844     2.993
S. chain angle B values: others                1178     4.842     2.993
Long range B values: refined atoms             1848     7.750    23.283
Long range B values: others                    1754     7.359    21.727
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0465, B  =   -0.0205
Partial structure    1: scale =     0.3926, B  =   38.9968
Overall anisotropic scale factors
   B11 =  -0.17 B22 =  -0.17 B33 =   0.34 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5070 100.00   382.9   392.3  0.18  0.18     259   342.3   354.6  0.21  0.22
 0.186    8686  99.98   206.3   182.2  0.19  0.17     457   208.8   186.3  0.23  0.20
 0.310   11055 100.00    92.2    89.0  0.23  0.20     592    92.2    87.4  0.26  0.23
 0.434   12822  98.63    38.8    48.2  0.47  0.46     673    38.5    47.1  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3847   0.921   1223   0.827   5070   0.898  0.950  0.9584  0.9711  0.9019  0.9340
  0.1863   7439   0.884   1247   0.784   8686   0.870  1.099  0.9542  0.9625  0.8986  0.9378
  0.3102   9807   0.822   1248   0.758  11055   0.815  0.954  0.9328  0.9404  0.8895  0.9134
  0.4340  11564   0.468   1258   0.416  12822   0.463  0.428  0.6434  0.6621  0.6264  0.6423
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37633
Percentage observed                  =    99.4927
Percentage of free reflections       =     5.0008
Overall R factor                     =     0.2187
Free R factor                        =     0.2555
Average Fourier shell correlation    =     0.8548
AverageFree Fourier shell correlation=     0.8428
Overall weighted R factor            =     0.1829
Free weighted R factor               =     0.2191
Overall weighted R2 factor           =     0.2111
Free weighted R2 factor              =     0.2633
Average correlation coefficient      =     0.8294
Overall correlation coefficient      =     0.9596
Free correlation coefficient         =     0.9406
Cruickshanks DPI for coordinate error=     0.0779
DPI based on free R factor           =     0.0817
Overall figure of merit              =     0.7190
ML based su of positional parameters =     0.0657
ML based su of thermal parameters    =     1.8942
-----------------------------------------------------------------------------
  Time in seconds: CPU =        29.39
             Elapsed =         128.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2194   0.2569   0.672      176381.    9423.5   0.0123  0.920   1.756  1.020   0.087
       1   0.2192   0.2566   0.717      175311.    9396.2   0.0122  0.911   1.745  1.014   0.087
       2   0.2183   0.2562   0.718      175097.    9392.5   0.0133  0.996   1.799  1.047   0.090
       3   0.2180   0.2560   0.719      175059.    9391.7   0.0134  1.003   1.817  1.057   0.091
       4   0.2179   0.2556   0.719      175042.    9390.8   0.0134  1.006   1.826  1.062   0.091
       5   0.2182   0.2556   0.718      175100.    9392.5   0.0128  0.961   1.798  1.045   0.089
       6   0.2186   0.2555   0.719      175184.    9394.9   0.0122  0.916   1.761  1.023   0.087
       7   0.2187   0.2555   0.718      175201.    9395.9   0.0122  0.915   1.758  1.022   0.086
       8   0.2187   0.2555   0.719      175199.    9395.9   0.0121  0.915   1.757  1.021   0.086
       9   0.2187   0.2555   0.718      175198.    9396.0   0.0121  0.914   1.756  1.020   0.086
      10   0.2187   0.2555   0.719      175205.    9396.5   0.0121  0.914   1.755  1.020   0.086
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2194   0.2187
             R free    0.2569   0.2555
     Rms BondLength    0.0123   0.0121
      Rms BondAngle    1.7560   1.7548
     Rms ChirVolume    0.0867   0.0863
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      61.5s System:    0.2s Elapsed:     1:02