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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: 21:40:04 


 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 14
  Data line--- END

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

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - CDO_complete_R14_1-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R14_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_R14_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:    14
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.4200

  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_R14_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=   2.056 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=   2.194 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=   1.816 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=   2.220 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=   2.425 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=   2.372 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=   2.079 ideal_dist=   1.870
            ch:AaA  res: 501  FE               at:FE  .->ch:AbA  res: 901  2CO              at:OD  .
  --------------------------------
  --- title of input coord file ---

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

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


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


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


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


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


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

FreeR flag                           14
Number of "free" reflections       1939
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.= 0.880 id.= 3.000 dev= -2.12 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   0.25656095    
 Actual weight    6.0498405      is applied to the X-ray term
Norm of X_ray positional gradient                38.6
Norm of Geom. positional gradient                80.3
Norm of X_ray B-factor gradient                  102.
Norm of Geom. B-factor gradient                 0.238E+05
Product of X_ray and Geom posit. gradients     -0.140E+08
 Cosine of angle between them                      -0.465
Product of X_ray and Geom B-fact gradients     -0.300E+08
 Cosine of angle between them                      -0.004


Residuals: XRAY=     0.1067E+07 GEOM=     0.2706E+05 TOTAL=     0.1094E+07
 function value    1093684.9    

-------------------------------------------------------------------------------
             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     1.784     1.644
Bond angles  : others                          3242     2.349     1.582
Torsion angles, period  1. refined              184     6.879     5.000
Torsion angles, period  2. refined               90    35.703    22.778
Torsion angles, period  3. refined              268    13.590    15.000
Torsion angles, period  4. refined                9    12.247    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                   306     0.266     0.200
VDW repulsions.others                          1350     0.229     0.200
VDW; torsion: refined_atoms                     720     0.173     0.200
VDW; torsion.others                             729     0.080     0.200
HBOND: refined_atoms                            215     0.201     0.200
HBOND.others                                      2     0.061     0.200
VDW repulsions: symmetry: refined_atoms           9     0.201     0.200
VDW repulsions: symmetry: others                 23     0.190     0.200
HBOND: symmetry: refined_atoms                   20     0.190     0.200
M. chain bond B values: refined atoms           745     1.745     1.624
M. chain bond B values: others                  745     1.741     1.624
M. chain angle B values: refined atoms          926     2.730     2.421
M. chain angle B values: others                 927     2.729     2.421
S. chain bond B values: refined atoms           811     3.147     2.036
S. chain bond B values: others                  810     3.142     2.036
S. chain angle B values: refined atoms         1177     4.817     2.885
S. chain angle B values: others                1178     4.815     2.885
Long range B values: refined atoms             1845     7.129    22.318
Long range B values: others                    1756     6.846    20.893
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =    0.7642
Partial structure    1: scale =     0.3962, B  =   45.7776
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5069 100.00   378.7   388.5  0.18  0.18     260   397.9   404.3  0.18  0.20
 0.186    8702  99.98   205.4   181.7  0.19  0.17     441   212.6   186.7  0.21  0.18
 0.310   11097 100.00    91.8    88.5  0.23  0.20     550    92.3    90.4  0.26  0.22
 0.434   12813  98.63    38.6    48.0  0.47  0.46     682    39.2    48.5  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3835   0.910   1234   0.804   5069   0.884  0.948  0.9691  0.9685  0.9367  0.9327
  0.1863   7442   0.871   1260   0.773   8702   0.857  1.097  0.9562  0.9593  0.9227  0.9381
  0.3102   9849   0.790   1248   0.714  11097   0.782  0.945  0.9217  0.9326  0.8837  0.9111
  0.4340  11563   0.384   1250   0.338  12813   0.380  0.376  0.6224  0.6184  0.6157  0.6428
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37681
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.8796
Overall R factor                     =     0.2199
Free R factor                        =     0.2343
Average Fourier shell correlation    =     0.8368
AverageFree Fourier shell correlation=     0.8304
Overall weighted R factor            =     0.1836
Free weighted R factor               =     0.1990
Overall weighted R2 factor           =     0.2122
Free weighted R2 factor              =     0.2259
Average correlation coefficient      =     0.8290
Overall correlation coefficient      =     0.9591
Free correlation coefficient         =     0.9572
Cruickshanks DPI for coordinate error=     0.0782
DPI based on free R factor           =     0.0748
Overall figure of merit              =     0.6761
ML based su of positional parameters =     0.0745
ML based su of thermal parameters    =     2.1727
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    176305.47       27064.930       1093684.9      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.30933329    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1070846.0    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0916
Partial structure    1: scale =     0.3960, B  =   44.9294
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                     =     0.2198
Free R factor                        =     0.2343
Average Fourier shell correlation    =     0.8436
AverageFree Fourier shell correlation=     0.8358
Average correlation coefficient      =     0.8294
Overall figure of merit              =     0.6804
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    175320.09       10187.411       1070846.0       1093684.9    


     CGMAT cycle number =      3

 Weight matrix   0.31115860    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1068676.5    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =    0.0012
Partial structure    1: scale =     0.3960, B  =   41.5906
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                     =     0.2188
Free R factor                        =     0.2344
Average Fourier shell correlation    =     0.8427
AverageFree Fourier shell correlation=     0.8340
Average correlation coefficient      =     0.8303
Overall figure of merit              =     0.6766
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    175103.48       9328.3496       1068676.5       1070846.0    


     CGMAT cycle number =      4

 Weight matrix   0.31656072    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067905.8    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =    0.0008
Partial structure    1: scale =     0.3963, B  =   38.4872
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                        =     0.2345
Average Fourier shell correlation    =     0.8464
AverageFree Fourier shell correlation=     0.8382
Average correlation coefficient      =     0.8306
Overall figure of merit              =     0.6836
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    175035.22       8970.5967       1067905.8       1068676.5    


     CGMAT cycle number =      5

 Weight matrix   0.31742048    
 Actual weight    6.0498405      is applied to the X-ray term


 function value    1067746.3    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0033
Partial structure    1: scale =     0.3965, B  =   38.3209
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                        =     0.2346
Average Fourier shell correlation    =     0.8467
AverageFree Fourier shell correlation=     0.8385
Average correlation coefficient      =     0.8308
Overall figure of merit              =     0.6841
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    175016.25       8925.8535       1067746.3       1067905.8    


     CGMAT cycle number =      6

 Weight matrix   0.28871381    
 Actual weight    5.4998550      is applied to the X-ray term


 function value    971472.88    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0130
Partial structure    1: scale =     0.3965, B  =   38.2994
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                     =     0.2185
Free R factor                        =     0.2347
Average Fourier shell correlation    =     0.8469
AverageFree Fourier shell correlation=     0.8387
Average correlation coefficient      =     0.8309
Overall figure of merit              =     0.6844
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    175010.00       8943.2617       971472.88       1067746.3    


     CGMAT cycle number =      7

 Weight matrix   0.26229998    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    883988.19    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0149
Partial structure    1: scale =     0.3965, B  =   38.2368
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                     =     0.2189
Free R factor                        =     0.2348
Average Fourier shell correlation    =     0.8468
AverageFree Fourier shell correlation=     0.8388
Average correlation coefficient      =     0.8305
Overall figure of merit              =     0.6846
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    175072.73       8647.6357       883988.19       971472.88    


     CGMAT cycle number =      8

 Weight matrix   0.26148650    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    884098.75    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0136
Partial structure    1: scale =     0.3966, B  =   38.2979
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                     =     0.2193
Free R factor                        =     0.2350
Average Fourier shell correlation    =     0.8466
AverageFree Fourier shell correlation=     0.8386
Average correlation coefficient      =     0.8300
Overall figure of merit              =     0.6844
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02


 fvalues    175167.95       8307.6621       884127.25       883988.19    

 fvalues    175167.95       8307.6621       884120.81       884124.31    
 fvalues    175167.95       8307.6621       884120.81       884124.31    


     CGMAT cycle number =      9

 Weight matrix   0.26127687    
 Actual weight    4.9998679      is applied to the X-ray term


 function value    884124.00    

-------------------------------------------------------------------------------
             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 =     0.0467, B  =   -0.0111
Partial structure    1: scale =     0.3967, B  =   38.2708
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                     =     0.2193
Free R factor                        =     0.2351
Average Fourier shell correlation    =     0.8466
AverageFree Fourier shell correlation=     0.8386
Average correlation coefficient      =     0.8299
Overall figure of merit              =     0.6844
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    175175.50       8269.6006       884124.00       884124.31    


     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.= 0.902 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   0.26107025    
 Actual weight    4.9998679      is applied to the X-ray term
Norm of X_ray positional gradient                37.6
Norm of Geom. positional gradient                37.8
Norm of X_ray B-factor gradient                  92.9
Norm of Geom. B-factor gradient                  94.3
Product of X_ray and Geom posit. gradients     -0.138E+08
 Cosine of angle between them                      -1.000
Product of X_ray and Geom B-fact gradients     -0.283E+08
 Cosine of angle between them                      -1.000


Residuals: XRAY=     0.8759E+06 GEOM=      8237.     TOTAL=     0.8841E+06
 function value    884133.88    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                   2103     1.779     1.644
Bond angles  : others                          3242     1.484     1.582
Torsion angles, period  1. refined              184     6.881     5.000
Torsion angles, period  2. refined               90    35.548    22.778
Torsion angles, period  3. refined              268    13.540    15.000
Torsion angles, period  4. refined                9    12.218    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   308     0.264     0.200
VDW repulsions.others                          1365     0.202     0.200
VDW; torsion: refined_atoms                     723     0.172     0.200
VDW; torsion.others                             787     0.083     0.200
HBOND: refined_atoms                            217     0.199     0.200
HBOND.others                                      1     0.083     0.200
VDW repulsions: symmetry: refined_atoms          10     0.195     0.200
VDW repulsions: symmetry: others                 27     0.165     0.200
HBOND: symmetry: refined_atoms                   21     0.192     0.200
M. chain bond B values: refined atoms           745     1.779     1.701
M. chain bond B values: others                  745     1.775     1.701
M. chain angle B values: refined atoms          926     2.763     2.537
M. chain angle B values: others                 927     2.761     2.537
S. chain bond B values: refined atoms           811     3.204     2.121
S. chain bond B values: others                  810     3.199     2.121
S. chain angle B values: refined atoms         1177     4.903     3.010
S. chain angle B values: others                1178     4.901     3.009
Long range B values: refined atoms             1853     7.252    23.334
Long range B values: others                    1762     6.953    21.875
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0467, B  =   -0.0078
Partial structure    1: scale =     0.3967, B  =   38.2396
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5069 100.00   379.0   388.6  0.18  0.18     260   398.2   404.8  0.19  0.20
 0.186    8702  99.98   205.5   181.9  0.19  0.17     441   212.7   187.2  0.21  0.18
 0.310   11097 100.00    91.9    88.6  0.23  0.20     550    92.4    90.5  0.26  0.22
 0.434   12813  98.63    38.7    48.0  0.47  0.46     682    39.2    48.6  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3835   0.921   1234   0.821   5069   0.897  0.950  0.9716  0.9714  0.9365  0.9328
  0.1863   7442   0.899   1260   0.802   8702   0.885  1.104  0.9621  0.9659  0.9223  0.9390
  0.3102   9849   0.804   1248   0.729  11097   0.796  0.945  0.9263  0.9375  0.8841  0.9114
  0.4340  11563   0.371   1250   0.335  12813   0.368  0.354  0.6373  0.6374  0.6162  0.6444
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37681
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.8796
Overall R factor                     =     0.2194
Free R factor                        =     0.2351
Average Fourier shell correlation    =     0.8466
AverageFree Fourier shell correlation=     0.8386
Overall weighted R factor            =     0.1831
Free weighted R factor               =     0.1996
Overall weighted R2 factor           =     0.2115
Free weighted R2 factor              =     0.2256
Average correlation coefficient      =     0.8299
Overall correlation coefficient      =     0.9594
Free correlation coefficient         =     0.9571
Cruickshanks DPI for coordinate error=     0.0781
DPI based on free R factor           =     0.0751
Overall figure of merit              =     0.6844
ML based su of positional parameters =     0.0670
ML based su of thermal parameters    =     1.9693
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02


 fvalues    175185.48       8236.7744       884136.31       884124.00    
 fvalues    175185.48       8236.7744       884136.31       884141.06    

    ****                              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.= 0.902 id.= 3.000 dev= -2.10 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_R14_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     1.776     1.644
Bond angles  : others                          3242     1.483     1.582
Torsion angles, period  1. refined              184     6.881     5.000
Torsion angles, period  2. refined               90    35.543    22.778
Torsion angles, period  3. refined              268    13.534    15.000
Torsion angles, period  4. refined                9    12.201    15.000
Chiral centres: refined atoms                   196     0.087     0.200
Planar groups: refined atoms                   1736     0.010     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   310     0.262     0.200
VDW repulsions.others                          1369     0.202     0.200
VDW; torsion: refined_atoms                     723     0.172     0.200
VDW; torsion.others                             789     0.083     0.200
HBOND: refined_atoms                            218     0.198     0.200
HBOND.others                                      1     0.083     0.200
VDW repulsions: symmetry: refined_atoms          10     0.195     0.200
VDW repulsions: symmetry: others                 26     0.168     0.200
HBOND: symmetry: refined_atoms                   21     0.192     0.200
M. chain bond B values: refined atoms           745     1.776     1.702
M. chain bond B values: others                  745     1.772     1.702
M. chain angle B values: refined atoms          926     2.760     2.538
M. chain angle B values: others                 927     2.758     2.537
S. chain bond B values: refined atoms           811     3.198     2.121
S. chain bond B values: others                  810     3.193     2.120
S. chain angle B values: refined atoms         1177     4.894     3.009
S. chain angle B values: others                1178     4.892     3.009
Long range B values: refined atoms             1856     7.290    23.384
Long range B values: others                    1765     6.995    21.929
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0466, B  =   -0.0066
Partial structure    1: scale =     0.3967, B  =   38.2630
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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.062    5069 100.00   379.0   388.6  0.18  0.18     260   398.3   404.9  0.19  0.20
 0.186    8702  99.98   205.5   181.9  0.19  0.17     441   212.7   187.2  0.21  0.18
 0.310   11097 100.00    91.9    88.6  0.23  0.20     550    92.4    90.5  0.26  0.22
 0.434   12813  98.63    38.7    48.0  0.47  0.46     682    39.2    48.6  0.47  0.46
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0625   3835   0.921   1234   0.821   5069   0.897  0.950  0.9716  0.9714  0.9365  0.9328
  0.1863   7442   0.898   1260   0.802   8702   0.885  1.104  0.9621  0.9659  0.9223  0.9389
  0.3102   9849   0.804   1248   0.729  11097   0.796  0.945  0.9263  0.9375  0.8841  0.9114
  0.4340  11563   0.371   1250   0.335  12813   0.368  0.354  0.6372  0.6374  0.6162  0.6444
 $$
Resolution limits                    =     41.964     1.420
Number of used reflections           =      37681
Percentage observed                  =    99.4927
Percentage of free reflections       =     4.8796
Overall R factor                     =     0.2194
Free R factor                        =     0.2350
Average Fourier shell correlation    =     0.8466
AverageFree Fourier shell correlation=     0.8386
Overall weighted R factor            =     0.1832
Free weighted R factor               =     0.1995
Overall weighted R2 factor           =     0.2115
Free weighted R2 factor              =     0.2255
Average correlation coefficient      =     0.8298
Overall correlation coefficient      =     0.9593
Free correlation coefficient         =     0.9571
Cruickshanks DPI for coordinate error=     0.0781
DPI based on free R factor           =     0.0750
Overall figure of merit              =     0.6844
ML based su of positional parameters =     0.0670
ML based su of thermal parameters    =     1.9693
-----------------------------------------------------------------------------
  Time in seconds: CPU =        26.56
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2199   0.2343   0.676      176305.    9175.5   0.0121  0.915   1.784  1.035   0.087
       1   0.2198   0.2343   0.680      175320.    9153.1   0.0119  0.902   1.766  1.025   0.088
       2   0.2188   0.2344   0.677      175103.    9149.2   0.0131  0.991   1.822  1.058   0.091
       3   0.2187   0.2345   0.684      175035.    9145.5   0.0132  0.998   1.843  1.069   0.091
       4   0.2186   0.2346   0.684      175016.    9145.1   0.0132  1.002   1.853  1.075   0.092
       5   0.2185   0.2347   0.684      175010.    9145.3   0.0133  1.004   1.859  1.078   0.092
       6   0.2189   0.2348   0.685      175073.    9146.2   0.0126  0.958   1.828  1.059   0.090
       7   0.2193   0.2350   0.684      175163.    9148.7   0.0120  0.912   1.788  1.036   0.088
       8   0.2193   0.2351   0.684      175176.    9149.2   0.0120  0.909   1.783  1.033   0.087
       9   0.2194   0.2351   0.684      175184.    9149.5   0.0120  0.907   1.779  1.031   0.087
      10   0.2194   0.2350   0.684      175193.    9149.6   0.0119  0.906   1.776  1.029   0.087
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2199   0.2194
             R free    0.2343   0.2350
     Rms BondLength    0.0121   0.0119
      Rms BondAngle    1.7841   1.7755
     Rms ChirVolume    0.0873   0.0873
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      58.5s System:    0.3s Elapsed:     0:59