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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: 14:19:28 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference3:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 41.96 1.90     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 4
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  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_R00_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R00_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - CDO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R00_1-90A.mtz

Cell from mtz :    57.632    57.632   122.391    90.000    90.000    90.000
Space group from mtz: number -   96; name - P 43 21 2

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Rice Maximum Likelihood for Fs

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.200
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:     4       0.0693
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    41.9635  1.9000
  Estimated number of reflections :      21862
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    41.9635  1.9000

  Damping factors:     1.0000  1.0000  1.0000


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


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

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

 Chiral centers
          Weight= 1.00

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

 TORSION ANGLES
          Weight= 1.00

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

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

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

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

 Input file :CDO_complete_R00_2-00A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1836
  Number of residues :     502
  Number of chains   :       4
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   2.028 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=   2.234 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=   1.847 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=   2.244 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=   2.379 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=   2.453 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=   2.070 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                            0
Number of "free" reflections        864
Number of   all  reflections      16986
--------------------------------------------------------------------------------
 Number of reflections in file      39842
 Number of reflections read          16986

   Current auto weighting coefficient =    7.2495699    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

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

A     10 ARG C   . - A     11 THR N   . mod.= 1.554 id.= 1.337 dev= -0.217 sig.= 0.011
A    125 LEU C   . - A    126 ARG N   . mod.= 1.610 id.= 1.337 dev= -0.273 sig.= 0.011
A    164 CYS C   . - A    165 HIS N   . mod.= 1.475 id.= 1.337 dev= -0.138 sig.= 0.011

    ****                          Bond angle outliers                           ****

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

A     10 ARG O     - A     11 THR N     mod.= 104.57 id.= 123.47 dev= 18.896 sig.=  1.500

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

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     10 ARG C     deviation=   0.29 sigma.=   0.02

    ****                              VDW outliers                              ****

VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored

A     93 CYS SG  . - A    157 TYR HE1 . mod.= 0.911 id.= 3.000 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.19745646    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                37.7
Norm of Geom. positional gradient                93.7
Norm of X_ray B-factor gradient                  128.
Norm of Geom. B-factor gradient                 0.224E+05
Product of X_ray and Geom posit. gradients     -0.438E+07
 Cosine of angle between them                      -0.128
Product of X_ray and Geom B-fact gradients     -0.306E+08
 Cosine of angle between them                      -0.003


Residuals: XRAY=     0.6430E+06 GEOM=     0.2628E+05 TOTAL=     0.6693E+06
 function value    669309.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.014     0.013
Bond distances: others                         1393     0.035     0.017
Bond angles  : refined atoms                   2103     1.739     1.644
Bond angles  : others                          3242     2.337     1.582
Torsion angles, period  1. refined              184     7.296     5.000
Torsion angles, period  2. refined               90    36.758    22.778
Torsion angles, period  3. refined              268    14.702    15.000
Torsion angles, period  4. refined                9    11.390    15.000
Chiral centres: refined atoms                   196     0.081     0.200
Planar groups: refined atoms                   1736     0.013     0.020
Planar groups: others                           331     0.014     0.020
VDW repulsions: refined_atoms                   311     0.253     0.200
VDW repulsions.others                          1346     0.225     0.200
VDW; torsion: refined_atoms                     702     0.169     0.200
VDW; torsion.others                             697     0.078     0.200
HBOND: refined_atoms                            229     0.215     0.200
HBOND.others                                      2     0.039     0.200
VDW repulsions: symmetry: refined_atoms           9     0.223     0.200
VDW repulsions: symmetry: others                 27     0.172     0.200
HBOND: symmetry: refined_atoms                   15     0.247     0.200
HBOND: symmetry: others                           1     0.068     0.200
M. chain bond B values: refined atoms           745     1.460     1.193
M. chain bond B values: others                  745     1.459     1.193
M. chain angle B values: refined atoms          926     2.395     1.772
M. chain angle B values: others                 927     2.393     1.772
S. chain bond B values: refined atoms           811     2.174     1.490
S. chain bond B values: others                  810     2.170     1.489
S. chain angle B values: refined atoms         1177     3.490     2.103
S. chain angle B values: others                1178     3.489     2.103
Long range B values: refined atoms             1852     6.422    16.539
Long range B values: others                    1754     6.100    15.181
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =    0.3130
Partial structure    1: scale =     0.3752, B  =   48.0721
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2213 100.00   481.5   484.1  0.16  0.17      98   477.8   484.5  0.20  0.22
 0.104    3735 100.00   386.5   370.1  0.16  0.15     189   387.6   363.3  0.22  0.21
 0.173    4666  99.96   247.5   241.8  0.16  0.14     276   265.1   257.0  0.23  0.19
 0.242    5503 100.00   188.7   189.1  0.19  0.15     301   190.5   190.2  0.24  0.20
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.903    689   0.797   2213   0.870  0.961  0.9594  0.9670  0.9123  0.9414
  0.1042   3040   0.874    695   0.763   3735   0.854  0.993  0.9421  0.9603  0.8653  0.9432
  0.1733   3977   0.852    689   0.750   4666   0.837  0.976  0.9386  0.9526  0.8755  0.9376
  0.2425   4801   0.857    705   0.739   5506   0.842  0.949  0.9331  0.9477  0.8526  0.9169
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16120
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0871
Overall R factor                     =     0.1661
Free R factor                        =     0.2234
Average Fourier shell correlation    =     0.9547
AverageFree Fourier shell correlation=     0.9398
Overall weighted R factor            =     0.1531
Free weighted R factor               =     0.2072
Overall weighted R2 factor           =     0.1840
Free weighted R2 factor              =     0.2497
Average correlation coefficient      =     0.9324
Overall correlation coefficient      =     0.9528
Free correlation coefficient         =     0.9067
Cruickshanks DPI for coordinate error=     0.1469
DPI based on free R factor           =     0.1458
Overall figure of merit              =     0.8471
ML based su of positional parameters =     0.0929
ML based su of thermal parameters    =     3.0825
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Trying gamma equal   5.00000007E-02
 Gamma decreased to   3.99999991E-02
 fvalues    88699.680       26275.250       669309.75      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   0.21204986    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    648935.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1295
Partial structure    1: scale =     0.3759, B  =   47.9335
Overall anisotropic scale factors
   B11 =  -0.27 B22 =  -0.27 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1636
Free R factor                        =     0.2197
Average Fourier shell correlation    =     0.9577
AverageFree Fourier shell correlation=     0.9430
Average correlation coefficient      =     0.9367
Overall figure of merit              =     0.8539
-----------------------------------------------------------------------------
 Trying gamma equal   3.99999991E-02
 Gamma decreased to   3.09090894E-02
 fvalues    88153.008       9864.2715       648935.63       669309.75    


     CGMAT cycle number =      3

 Weight matrix   0.21620570    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    646476.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0777
Partial structure    1: scale =     0.3757, B  =   45.9133
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1620
Free R factor                        =     0.2179
Average Fourier shell correlation    =     0.9586
AverageFree Fourier shell correlation=     0.9441
Average correlation coefficient      =     0.9382
Overall figure of merit              =     0.8556
-----------------------------------------------------------------------------
 Trying gamma equal   3.09090894E-02
 Gamma decreased to   2.26446278E-02
 fvalues    87985.867       8616.6670       646476.38       648935.63    


     CGMAT cycle number =      4

 Weight matrix   0.21945444    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    645492.13    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0654
Partial structure    1: scale =     0.3757, B  =   45.7101
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1613
Free R factor                        =     0.2169
Average Fourier shell correlation    =     0.9591
AverageFree Fourier shell correlation=     0.9447
Average correlation coefficient      =     0.9389
Overall figure of merit              =     0.8568
-----------------------------------------------------------------------------
 Trying gamma equal   2.26446278E-02
 Gamma decreased to   1.51314801E-02
 fvalues    87904.422       8222.8594       645492.13       646476.38    


     CGMAT cycle number =      5

 Weight matrix   0.22213063    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644978.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1205
Partial structure    1: scale =     0.3762, B  =   45.6782
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1609
Free R factor                        =     0.2164
Average Fourier shell correlation    =     0.9594
AverageFree Fourier shell correlation=     0.9452
Average correlation coefficient      =     0.9393
Overall figure of merit              =     0.8578
-----------------------------------------------------------------------------
 Trying gamma equal   1.51314801E-02
 Gamma decreased to   8.30134563E-03
 fvalues    87844.180       8145.9780       644978.50       645492.13    


     CGMAT cycle number =      6

 Weight matrix   0.22323401    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644715.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1105
Partial structure    1: scale =     0.3763, B  =   45.7480
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1606
Free R factor                        =     0.2160
Average Fourier shell correlation    =     0.9596
AverageFree Fourier shell correlation=     0.9455
Average correlation coefficient      =     0.9396
Overall figure of merit              =     0.8583
-----------------------------------------------------------------------------
 Trying gamma equal   8.30134563E-03
 Gamma decreased to   2.09213281E-03
 fvalues    87799.789       8205.0771       644715.75       644978.50    


     CGMAT cycle number =      7

 Weight matrix   0.22384563    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644451.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.0912
Partial structure    1: scale =     0.3811, B  =   46.5237
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1604
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9457
Average correlation coefficient      =     0.9397
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   2.09213281E-03
 Gamma decreased to   9.99999975E-05
 fvalues    87759.203       8234.9844       644451.50       644715.75    


     CGMAT cycle number =      8

 Weight matrix   0.22365353    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644402.69    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1174
Partial structure    1: scale =     0.3811, B  =   46.5468
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1603
Free R factor                        =     0.2158
Average Fourier shell correlation    =     0.9598
AverageFree Fourier shell correlation=     0.9457
Average correlation coefficient      =     0.9398
Overall figure of merit              =     0.8586
-----------------------------------------------------------------------------
 Trying gamma equal   9.99999975E-05
 Trying gamma equal   2.57579032E-02
 Gamma decreased to   2.06263214E-02
 fvalues    87751.359       8243.0352       644402.69       644451.50    


     CGMAT cycle number =      9

 Weight matrix   0.22385034    
 Actual weight    7.2495699      is applied to the X-ray term


 function value    644359.00    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1042
Partial structure    1: scale =     0.3813, B  =   46.5203
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1602
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9458
Average correlation coefficient      =     0.9399
Overall figure of merit              =     0.8587
-----------------------------------------------------------------------------
 Trying gamma equal   2.06263214E-02
 Gamma decreased to   1.59612484E-02
 fvalues    87743.992       8252.8340       644359.00       644402.69    


     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.= 0.948 id.= 3.000 dev= -2.05 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Limits of asymmetric unit      : 1.00 1.00 0.13
 Grid spacing to be used        :   112  112  240
 Maximuum H,K,L                 :    31   31   65
 Minimum acceptable grid spacing:    73   73  154
 Weight matrix   0.22384356    
 Actual weight    7.2495699      is applied to the X-ray term
Norm of X_ray positional gradient                31.8
Norm of Geom. positional gradient                31.8
Norm of X_ray B-factor gradient                  106.
Norm of Geom. B-factor gradient                  111.
Product of X_ray and Geom posit. gradients     -0.979E+07
 Cosine of angle between them                      -0.999
Product of X_ray and Geom B-fact gradients     -0.376E+08
 Cosine of angle between them                      -0.987


Residuals: XRAY=     0.6361E+06 GEOM=      8261.     TOTAL=     0.6443E+06
 function value    644340.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.720     1.644
Bond angles  : others                          3242     1.425     1.582
Torsion angles, period  1. refined              184     6.977     5.000
Torsion angles, period  2. refined               90    36.924    22.778
Torsion angles, period  3. refined              268    14.149    15.000
Torsion angles, period  4. refined                9    11.054    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   298     0.263     0.200
VDW repulsions.others                          1372     0.199     0.200
VDW; torsion: refined_atoms                     712     0.171     0.200
VDW; torsion.others                             777     0.083     0.200
HBOND: refined_atoms                            224     0.207     0.200
VDW repulsions: symmetry: refined_atoms           9     0.222     0.200
VDW repulsions: symmetry: others                 24     0.189     0.200
HBOND: symmetry: refined_atoms                   19     0.221     0.200
HBOND: symmetry: others                           1     0.008     0.200
M. chain bond B values: refined atoms           745     1.528     1.216
M. chain bond B values: others                  745     1.527     1.216
M. chain angle B values: refined atoms          926     2.456     1.806
M. chain angle B values: others                 927     2.455     1.805
S. chain bond B values: refined atoms           811     2.482     1.552
S. chain bond B values: others                  810     2.479     1.551
S. chain angle B values: refined atoms         1177     3.925     2.183
S. chain angle B values: others                1178     3.923     2.182
Long range B values: refined atoms             1844     6.614    17.012
Long range B values: others                    1750     6.342    15.690
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1050
Partial structure    1: scale =     0.3814, B  =   46.5888
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2213 100.00   481.2   484.4  0.16  0.17      98   477.5   483.8  0.20  0.22
 0.104    3735 100.00   386.2   369.2  0.16  0.15     189   387.3   361.1  0.21  0.20
 0.173    4666  99.96   247.3   242.1  0.16  0.14     276   264.9   255.9  0.22  0.19
 0.242    5503 100.00   188.6   189.1  0.16  0.13     301   190.4   189.9  0.23  0.19
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   10. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.923    689   0.821   2213   0.891  0.961  0.9643  0.9712  0.9155  0.9402
  0.1042   3040   0.884    695   0.777   3735   0.864  0.995  0.9479  0.9637  0.8796  0.9451
  0.1733   3977   0.864    689   0.764   4666   0.849  0.976  0.9454  0.9563  0.8907  0.9382
  0.2425   4801   0.866    705   0.747   5506   0.850  0.953  0.9388  0.9558  0.8613  0.9378
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16120
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0871
Overall R factor                     =     0.1601
Free R factor                        =     0.2156
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9458
Overall weighted R factor            =     0.1498
Free weighted R factor               =     0.2001
Overall weighted R2 factor           =     0.1822
Free weighted R2 factor              =     0.2409
Average correlation coefficient      =     0.9400
Overall correlation coefficient      =     0.9549
Free correlation coefficient         =     0.9144
Cruickshanks DPI for coordinate error=     0.1416
DPI based on free R factor           =     0.1407
Overall figure of merit              =     0.8588
ML based su of positional parameters =     0.0872
ML based su of thermal parameters    =     2.9020
-----------------------------------------------------------------------------
 Trying gamma equal   1.59612484E-02
 Gamma decreased to   1.17202727E-02
 fvalues    87740.305       8261.0186       644340.50       644359.00    

    ****                              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.= 0.949 id.= 3.000 dev= -2.05 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: CDO_complete_R00_1-90A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1557     0.011     0.013
Bond distances: others                         1393     0.001     0.017
Bond angles  : refined atoms                   2103     1.722     1.644
Bond angles  : others                          3242     1.426     1.582
Torsion angles, period  1. refined              184     6.978     5.000
Torsion angles, period  2. refined               90    36.925    22.778
Torsion angles, period  3. refined              268    14.143    15.000
Torsion angles, period  4. refined                9    11.063    15.000
Chiral centres: refined atoms                   196     0.083     0.200
Planar groups: refined atoms                   1736     0.009     0.020
Planar groups: others                           331     0.001     0.020
VDW repulsions: refined_atoms                   298     0.263     0.200
VDW repulsions.others                          1376     0.199     0.200
VDW; torsion: refined_atoms                     712     0.171     0.200
VDW; torsion.others                             781     0.083     0.200
HBOND: refined_atoms                            224     0.207     0.200
VDW repulsions: symmetry: refined_atoms           9     0.222     0.200
VDW repulsions: symmetry: others                 24     0.189     0.200
HBOND: symmetry: refined_atoms                   19     0.222     0.200
HBOND: symmetry: others                           1     0.006     0.200
M. chain bond B values: refined atoms           745     1.529     1.216
M. chain bond B values: others                  745     1.527     1.216
M. chain angle B values: refined atoms          926     2.457     1.806
M. chain angle B values: others                 927     2.455     1.805
S. chain bond B values: refined atoms           811     2.483     1.552
S. chain bond B values: others                  810     2.480     1.552
S. chain angle B values: refined atoms         1177     3.925     2.183
S. chain angle B values: others                1178     3.923     2.182
Long range B values: refined atoms             1844     6.592    16.991
Long range B values: others                    1749     6.313    15.662
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0402, B  =   -0.1098
Partial structure    1: scale =     0.3807, B  =   46.7973
Overall anisotropic scale factors
   B11 =  -0.26 B22 =  -0.26 B33 =   0.53 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.035    2213 100.00   481.2   484.6  0.16  0.17      98   477.5   484.0  0.20  0.22
 0.104    3735 100.00   386.2   369.2  0.16  0.15     189   387.3   361.1  0.21  0.20
 0.173    4666  99.96   247.3   242.1  0.16  0.13     276   264.9   255.8  0.22  0.19
 0.242    5503 100.00   188.6   189.2  0.16  0.13     301   190.4   189.9  0.23  0.19
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0351   1524   0.923    689   0.821   2213   0.891  0.961  0.9644  0.9712  0.9157  0.9401
  0.1042   3040   0.884    695   0.777   3735   0.864  0.995  0.9479  0.9637  0.8797  0.9451
  0.1733   3977   0.864    689   0.764   4666   0.849  0.976  0.9455  0.9563  0.8905  0.9382
  0.2425   4801   0.866    705   0.747   5506   0.850  0.953  0.9388  0.9558  0.8613  0.9379
 $$
Resolution limits                    =     41.964     1.900
Number of used reflections           =      16120
Percentage observed                  =    99.9823
Percentage of free reflections       =     5.0871
Overall R factor                     =     0.1602
Free R factor                        =     0.2157
Average Fourier shell correlation    =     0.9599
AverageFree Fourier shell correlation=     0.9458
Overall weighted R factor            =     0.1499
Free weighted R factor               =     0.2004
Overall weighted R2 factor           =     0.1825
Free weighted R2 factor              =     0.2409
Average correlation coefficient      =     0.9400
Overall correlation coefficient      =     0.9549
Free correlation coefficient         =     0.9144
Cruickshanks DPI for coordinate error=     0.1417
DPI based on free R factor           =     0.1408
Overall figure of merit              =     0.8588
ML based su of positional parameters =     0.0872
ML based su of thermal parameters    =     2.9020
-----------------------------------------------------------------------------
  Time in seconds: CPU =        12.26
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1661   0.2234   0.847       88700.    4915.1   0.0142  1.160   1.739  1.017   0.081
       1   0.1636   0.2197   0.854       88153.    4896.1   0.0106  0.776   1.657  0.960   0.081
       2   0.1620   0.2179   0.856       87986.    4888.4   0.0110  0.807   1.678  0.971   0.082
       3   0.1613   0.2169   0.857       87904.    4883.5   0.0111  0.818   1.690  0.978   0.082
       4   0.1609   0.2164   0.858       87844.    4880.9   0.0112  0.825   1.698  0.983   0.082
       5   0.1606   0.2160   0.858       87800.    4878.8   0.0112  0.830   1.706  0.986   0.083
       6   0.1604   0.2158   0.859       87759.    4876.7   0.0113  0.832   1.711  0.989   0.083
       7   0.1603   0.2158   0.859       87751.    4876.6   0.0113  0.832   1.716  0.992   0.083
       8   0.1602   0.2156   0.859       87744.    4875.9   0.0113  0.833   1.718  0.993   0.083
       9   0.1601   0.2156   0.859       87740.    4875.7   0.0113  0.833   1.720  0.994   0.083
      10   0.1602   0.2157   0.859       87740.    4875.8   0.0113  0.833   1.722  0.995   0.083
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1661   0.1602
             R free    0.2234   0.2157
     Rms BondLength    0.0142   0.0113
      Rms BondAngle    1.7388   1.7218
     Rms ChirVolume    0.0810   0.0831
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created

 Refmac:  End of Refmac_5.8.0258   
Times: User:      44.3s System:    0.3s Elapsed:     0:45