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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: maly  Run date: 28/ 5/2020 Run time: 12:05:16 


 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--- make     hydrogen ALL     hout NO     peptide NO     cispeptide YES     ssbridge YES     symmetry YES     sugar YES     connectivity NO     link NO
  Data line--- refi     type REST     resi MLKF     meth CGMAT     bref ISOT
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- weight     MATRIX 0.048
  Data line--- monitor MEDIUM     torsion 10.0     distance 10.0     angle 10.0     plane 10.0     chiral 10.0     bfactor 10.0     bsphere 10.0     rbond 10.0     ncsr 10.0
  Data line--- PNAME BO+Fe
  Data line--- DNAME BF19
  Data line--- RSIZE 80
  Data line--- refi reso 47.35 2.50
  Data line--- bins 9
  Data line--- ncyc 10
  Data line--- weight matrix 0.0480
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

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

 LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - BO_from2-80A_R00_2-59A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - BO_from2-80A_R00_2-50A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - BO_R.mtz
Output reflection file. Logical name - HKLOUT actual file name - BO_from2-80A_R00_2-50A.mtz

Cell from mtz :   134.507   204.057   226.976    90.000    90.000    90.000
Space group from mtz: number -   22; name - F 2 2 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
User supplied dictionary entries: merge_TRP-HIS_FC6.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
    All links to sugar 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:     9       0.0178
  Refinement of individual isotropic Bfactors
  Refinement resln        :    47.3545  2.5000
  Estimated number of reflections :      70515
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.0480
  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:    47.3545  2.5000

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

 Input file :BO_from2-80A_R00_2-59A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         ?
 _lib_version      ?
 _lib_update       ?
  ------------------------------
  WARNING: duplicated name of monomer FC6
           Last entry will be used.
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    72
  NUMBER OF LINKS                            :    78
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    9511
  Number of residues :    1660
  Number of chains   :      49
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : link: NAG<-->NA  is without link_id
 Atoms O6  NA           544         554
            link will be created with covalent bond only. Bond=     2.430
  WARNING : description of link:NAG-NA   is not in the dictionary
            link will be created with bond_length =   2.430
  WARNING : link: NAG<-->NA  is without link_id
 Atoms O6  NA          1101        1110
            link will be created with covalent bond only. Bond=     2.430
  WARNING : CIS peptide bond is found, angle =      3.20
            ch:AAA  res: 465  HIS              --> 466  ASP
  INFO:     link is found (not be used) dist=   2.543 ideal_dist=   2.275
            ch:AAA  res:  63  ASP              at:OD2 .->ch:AuA  res:1002  NA               at:NA  .
  INFO:     link is found (not be used) dist=   2.944 ideal_dist=   2.305
            ch:AAA  res:  86  ASN              at:O   .->ch:AvA  res:1003  NA               at:NA  .
  INFO:     link is found (not be used) dist=   1.830 ideal_dist=   2.075
            ch:AAA  res:  94  HIS              at:NE2 .->ch:AdA  res: 604  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.032 ideal_dist=   2.075
            ch:AAA  res:  96  HIS              at:ND1 .->ch:AcA  res: 603  CU               at:CU  .
  INFO:     link is found (not be used) dist=   1.987 ideal_dist=   2.075
            ch:AAA  res: 134  HIS              at:NE2 .->ch:AcA  res: 603  CU               at:CU  .
  INFO:     link is found (not be used) dist=   1.916 ideal_dist=   2.075
            ch:AAA  res: 136  HIS              at:NE2 .->ch:AbA  res: 602  CU               at:CU  .
  INFO:     link is found (not be used) dist=   3.153 ideal_dist=   2.434
            ch:AAA  res: 284  SER              at:OG  .->ch:AwA  res:1004  NA               at:NA  .
  INFO:     link is found (not be used) dist=   2.545 ideal_dist=   2.305
            ch:AAA  res: 285  ASP              at:OD1 .->ch:AwA  res:1004  NA               at:NA  .
  INFO:     link is found (not be used) dist=   1.695 ideal_dist=   1.410
            ch:AAA  res: 396  TRP              at:CD1 .->ch:AAA  res: 398  HIS              at:NE2 .
  INFO:     link is found (not be used) dist=   1.972 ideal_dist=   2.075
            ch:AAA  res: 398  HIS              at:ND1 .->ch:AaA  res: 601  CU               at:CU  .
  INFO:     link is found (not be used) dist=   1.760 ideal_dist=   2.075
            ch:AAA  res: 401  HIS              at:NE2 .->ch:AdA  res: 604  CU               at:CU  .
  INFO:     link is found (not be used) dist=   1.977 ideal_dist=   2.075
            ch:AAA  res: 403  HIS              at:NE2 .->ch:AbA  res: 602  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.883 ideal_dist=   2.305
            ch:AAA  res: 404  LEU              at:O   .->ch:AxA  res:1005  NA               at:NA  .
  INFO:     link is found (not be used) dist=   2.679 ideal_dist=   2.305
            ch:AAA  res: 447  ALA              at:O   .->ch:AxA  res:1005  NA               at:NA  .
  INFO:     link is found (not be used) dist=   2.047 ideal_dist=   2.075
            ch:AAA  res: 456  HIS              at:NE2 .->ch:AbA  res: 602  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.172 ideal_dist=   2.400
            ch:AAA  res: 457  CYS              at:SG  .->ch:AaA  res: 601  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.193 ideal_dist=   2.075
            ch:AAA  res: 458  HIS              at:NE2 .->ch:AcA  res: 603  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.144 ideal_dist=   2.075
            ch:AAA  res: 462  HIS              at:ND1 .->ch:AaA  res: 601  CU               at:CU  .
  WARNING : link:NAG-ASN  is found dist =     1.428 ideal_dist=     1.439
            ch:AAA  res: 472  ASN              at:ND2 .->AeA  res: 701  NAG              at:C1  .
  WARNING : link:NAG-ASN  is found dist =     1.444 ideal_dist=     1.439
            ch:AAA  res: 482  ASN              at:ND2 .->AjA  res: 711  NAG              at:C1  .
  INFO:     link is found (not be used) dist=   3.092 ideal_dist=   2.305
            ch:AAA  res: 525  GLU              at:OE1 .->ch:AtA  res:1001  NA               at:NA  .
  WARNING : link:BETA1-4  is found dist =     1.427 ideal_dist=     1.439
            ch:AeA  res: 701  NAG              at:O4  .->AfA  res: 702  NAG              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.432 ideal_dist=     1.439
            ch:AfA  res: 702  NAG              at:O4  .->AgA  res: 703  BMA              at:C1  .
  WARNING : link:ALPHA1-3 is found dist =     1.451 ideal_dist=     1.439
            ch:AgA  res: 703  BMA              at:O3  .->AhA  res: 704  MAN              at:C1  .
  WARNING : link:ALPHA1-6 is found dist =     1.461 ideal_dist=     1.439
            ch:AgA  res: 703  BMA              at:O6  .->AiA  res: 705  MAN              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.427 ideal_dist=     1.439
            ch:AjA  res: 711  NAG              at:O4  .->AkA  res: 712  NAG              at:C1  .
  WARNING : link:NAG-NA   is found dist =     2.454 ideal_dist=     2.430
            ch:AjA  res: 711  NAG              at:O6  .->AtA  res:1001  NA               at:NA  .
  WARNING : link:BETA1-4  is found dist =     1.442 ideal_dist=     1.439
            ch:AkA  res: 712  NAG              at:O4  .->AlA  res: 713  BMA              at:C1  .
  INFO:     link is found (not be used) dist=   1.857 ideal_dist=   2.075
            ch:BBB  res:  94  HIS              at:NE2 .->ch:BdB  res: 604  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.186 ideal_dist=   2.075
            ch:BBB  res:  96  HIS              at:ND1 .->ch:BcB  res: 603  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.124 ideal_dist=   2.075
            ch:BBB  res: 134  HIS              at:NE2 .->ch:BcB  res: 603  CU               at:CU  .
  INFO:     link is found (not be used) dist=   1.930 ideal_dist=   2.075
            ch:BBB  res: 136  HIS              at:NE2 .->ch:BbB  res: 602  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.441 ideal_dist=   2.275
            ch:BBB  res: 261  GLU              at:OE2 .->ch:BtB  res:1003  NA               at:NA  .
  INFO:     link is found (not be used) dist=   2.614 ideal_dist=   2.305
            ch:BBB  res: 285  ASP              at:OD1 .->ch:BsB  res:1002  NA               at:NA  .
  INFO:     link is found (not be used) dist=   2.677 ideal_dist=   2.305
            ch:BBB  res: 338  ASP              at:OD1 .->ch:BtB  res:1003  NA               at:NA  .
  INFO:     link is found (not be used) dist=   1.656 ideal_dist=   1.410
            ch:BBB  res: 396  TRP              at:CD1 .->ch:BBB  res: 398  HIS              at:NE2 .
  INFO:     link is found (not be used) dist=   1.996 ideal_dist=   2.075
            ch:BBB  res: 398  HIS              at:ND1 .->ch:BaB  res: 601  CU               at:CU  .
  INFO:     link is found (not be used) dist=   1.870 ideal_dist=   2.075
            ch:BBB  res: 401  HIS              at:NE2 .->ch:BdB  res: 604  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.037 ideal_dist=   2.075
            ch:BBB  res: 403  HIS              at:NE2 .->ch:BbB  res: 602  CU               at:CU  .
  INFO:     link is found (not be used) dist=   1.961 ideal_dist=   2.075
            ch:BBB  res: 456  HIS              at:NE2 .->ch:BbB  res: 602  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.117 ideal_dist=   2.400
            ch:BBB  res: 457  CYS              at:SG  .->ch:BaB  res: 601  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.380 ideal_dist=   2.075
            ch:BBB  res: 458  HIS              at:NE2 .->ch:BcB  res: 603  CU               at:CU  .
  INFO:     link is found (not be used) dist=   2.099 ideal_dist=   2.075
            ch:BBB  res: 462  HIS              at:ND1 .->ch:BaB  res: 601  CU               at:CU  .
  WARNING : link:NAG-ASN  is found dist =     1.435 ideal_dist=     1.439
            ch:BBB  res: 472  ASN              at:ND2 .->BeB  res: 701  NAG              at:C1  .
  WARNING : link:NAG-ASN  is found dist =     1.435 ideal_dist=     1.439
            ch:BBB  res: 482  ASN              at:ND2 .->BiB  res: 711  NAG              at:C1  .
  INFO:     link is found (not be used) dist=   3.018 ideal_dist=   2.305
            ch:BBB  res: 522  THR              at:O   .->ch:BrB  res:1001  NA               at:NA  .
  INFO:     link is found (not be used) dist=   2.940 ideal_dist=   2.305
            ch:BBB  res: 525  GLU              at:OE1 .->ch:BrB  res:1001  NA               at:NA  .
  WARNING : link:BETA1-4  is found dist =     1.424 ideal_dist=     1.439
            ch:BeB  res: 701  NAG              at:O4  .->BfB  res: 702  NAG              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.445 ideal_dist=     1.439
            ch:BfB  res: 702  NAG              at:O4  .->BgB  res: 703  BMA              at:C1  .
  WARNING : link:ALPHA1-3 is found dist =     1.455 ideal_dist=     1.439
            ch:BgB  res: 703  BMA              at:O3  .->BhB  res: 704  MAN              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.454 ideal_dist=     1.439
            ch:BiB  res: 711  NAG              at:O4  .->BjB  res: 712  NAG              at:C1  .
  WARNING : link:NAG-NA   is found dist =     2.436 ideal_dist=     2.430
            ch:BiB  res: 711  NAG              at:O6  .->BrB  res:1001  NA               at:NA  .
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:28-MAY-20
  --------------------------------
  ATTENTION: atom:OXT  ASP               533  BBB  is missing in the structure
  Number of chains                  :      49
  Total number of monomers          :    1660
  Number of atoms                   :   19000
  Number of missing atoms           :       0
  Number of rebuilt atoms           :    8394
  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   1.0317
  CU    13.3445   3.5828   7.1711   0.2470   5.6185  11.3966   1.6743  64.8126   1.2284
  FE    11.7738   4.7611   7.3600   0.3072   3.5235  15.3535   2.3054  76.8805   1.3103
  NA     4.7659   3.2850   3.1758   8.8422   1.2683   0.3136   1.1136 129.4240   0.7258
  CL    11.4601   0.0104   7.1962   1.1662   6.2554  18.5194   1.6455  47.7784  -9.3638



--------------------------------------------------------------------------------
 External restraints group   :            1
 External restraints file    :input_keywords
 Fail if one of the atoms involved in the restraints is missing in the pdb file
 Use restraints for all defined atoms
 Ignore restraints if abs(dmod-drest) >    50.000000     *sigma
 Ignore retraints if input dist >   1.00000003E+32
 Weight scale sigmas         :
       scale bond(dist) sigma :   1.0000000    
       scale angle sigma      :   1.0000000    
       scale torsion sigma    :   1.0000000    
       scale plane sigma      :   1.0000000    
       scale chiral sigma     :   1.0000000    
       scale interval sigma   :   1.0000000    
 Weight min sigma            :   0.0000000    
 Weight max sigma            :   100.00000    
 GM parameter                :  1.99999996E-02
 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:     17143         0     17143
               Angles:     31083         0     31083
              Chirals:      1196         0      1196
               Planes:      2666         0      2666
             Torsions:      9147         0      9147
            Intervals:         0         0         0
--------------------------------------------------------------------------------


    ****                 Harmonic special positions restraints                  ****

 Harmonic restraints: sum 1/sigma^2 (x-x_c)^2
 x - position of atoms, x_c - current positions

 Special positions sum 1/sigma^2(x-sum (R_sym x +t_sym))^2
 x - position of atom, (R_sym,t_sym) are set of symmetry operators for which x =R_sym x +t_sym)

 Data line--- external harmonic residues from 801 A to 804 A sigma 0.03
 Data line--- external harmonic residues from 801 B to 805 B sigma 0.03
 Data line--- external harmonic residues from 139 B to 139 B sigma 0.01
 Data line--- external harmonic residues from 274 B to 274 B sigma 0.01

  Number of harmonic restraints       =          191
  Number of atoms in special position =            0
 -----------------------------------------------------


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

FreeR flag                            0
Number of "free" reflections       2715
Number of   all  reflections      53857
--------------------------------------------------------------------------------
 Number of reflections in file      72569
 Number of reflections read          53857

   Current auto weighting coefficient =    8.7493467    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                          Bond angle outliers                           ****

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

A    701 NAG O4    - A    702 NAG H1    mod.=  57.10 id.= 109.47 dev= 52.369 sig.=  3.000
A    702 NAG H1    - A    702 NAG C2    mod.= 139.52 id.= 108.34 dev=-31.179 sig.=  3.000
A    702 NAG O4    - A    703 BMA H1    mod.=  55.95 id.= 109.47 dev= 53.515 sig.=  3.000
A    703 BMA H1    - A    703 BMA C2    mod.= 146.06 id.= 108.34 dev=-37.719 sig.=  3.000
A    703 BMA O3    - A    704 MAN H1    mod.=  52.84 id.= 109.47 dev= 56.629 sig.=  3.000
A    704 MAN H1    - A    704 MAN C2    mod.= 139.55 id.= 108.34 dev=-31.212 sig.=  3.000
A    711 NAG O4    - A    712 NAG H1    mod.=  56.29 id.= 109.47 dev= 53.179 sig.=  3.000
A    712 NAG O4    - A    713 BMA H1    mod.=  48.50 id.= 109.47 dev= 60.970 sig.=  3.000
A    713 BMA H1    - A    713 BMA C2    mod.= 142.69 id.= 108.34 dev=-34.354 sig.=  3.000
B    701 NAG O4    - B    702 NAG H1    mod.=  56.84 id.= 109.47 dev= 52.631 sig.=  3.000
B    702 NAG H1    - B    702 NAG C2    mod.= 141.75 id.= 108.34 dev=-33.413 sig.=  3.000
B    702 NAG O4    - B    703 BMA H1    mod.=  50.87 id.= 109.47 dev= 58.601 sig.=  3.000
B    703 BMA H1    - B    703 BMA C2    mod.= 142.02 id.= 108.34 dev=-33.682 sig.=  3.000
B    703 BMA O3    - B    704 MAN H1    mod.=  52.50 id.= 109.47 dev= 56.974 sig.=  3.000
B    704 MAN H1    - B    704 MAN C2    mod.= 139.76 id.= 108.34 dev=-31.417 sig.=  3.000
B    711 NAG O4    - B    712 NAG H1    mod.=  50.96 id.= 109.47 dev= 58.508 sig.=  3.000
B    712 NAG H1    - B    712 NAG C2    mod.= 138.45 id.= 108.34 dev=-30.113 sig.=  3.000

    ****                              VDW outliers                              ****

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

A    396 TRP HD1 . - A    398 HIS NE2 . mod.= 0.833 id.= 2.750 dev= -1.92 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.748 id.= 2.750 dev= -2.00 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   216  320  360
 Maximuum H,K,L                 :    54   82   92
 Minimum acceptable grid spacing:   140  213  237
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   216  320  360
 Maximuum H,K,L                 :    54   82   92
 Minimum acceptable grid spacing:   140  213  237
 Weight matrix   4.80000004E-02
 Actual weight    14.110626      is applied to the X-ray term
Norm of X_ray positional gradient                19.7
Norm of Geom. positional gradient                78.5
Norm of X_ray B-factor gradient                  27.3
Norm of Geom. B-factor gradient                  22.7
Product of X_ray and Geom posit. gradients     -0.193E+08
 Cosine of angle between them                      -0.238
Product of X_ray and Geom B-fact gradients     -0.100E+08
 Cosine of angle between them                      -0.928


Residuals: XRAY=     0.5041E+07 GEOM=     0.5508E+05 TOTAL=     0.5096E+07
 function value    5095882.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.035     0.017
Bond angles  : refined atoms                  12685     1.649     1.702
Bond angles  : others                         18398     2.755     1.594
Torsion angles, period  1. refined             1092     8.016     5.000
Torsion angles, period  2. refined              517    31.865    21.915
Torsion angles, period  3. refined             1292    14.756    15.000
Torsion angles, period  4. refined               63    19.412    15.000
Chiral centres: refined atoms                  1196     0.063     0.200
Planar groups: refined atoms                  10355     0.007     0.020
Planar groups: others                          2034     0.009     0.020
VDW repulsions: refined_atoms                  1758     0.212     0.200
VDW repulsions.others                          7799     0.219     0.200
VDW; torsion: refined_atoms                    4236     0.168     0.200
VDW; torsion.others                            3712     0.090     0.200
HBOND: refined_atoms                            477     0.152     0.200
HBOND.others                                      3     0.116     0.200
Metal-ion: refined_atoms                         12     0.134     0.200
VDW repulsions: symmetry: refined_atoms          20     0.197     0.200
VDW repulsions: symmetry: others                 49     0.181     0.200
HBOND: symmetry: refined_atoms                    6     0.155     0.200
M. chain bond B values: refined atoms          4328     3.079     4.649
M. chain bond B values: others                 4327     3.077     4.648
M. chain angle B values: refined atoms         5426     4.547     6.967
M. chain angle B values: others                5427     4.547     6.969
S. chain bond B values: refined atoms          4896     3.843     5.089
S. chain bond B values: others                 4897     3.842     5.089
S. chain angle B values: refined atoms         7255     5.470     7.575
S. chain angle B values: others                7256     5.469     7.575
Long range B values: refined atoms             9971     7.041    54.590
Long range B values: others                    9897     7.035    54.554
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =    2.4191
Partial structure    1: scale =     0.3849, B  =   47.5929
Overall anisotropic scale factors
   B11 =  -1.15 B22 =  -1.47 B33 =   2.62 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.009    2076  99.68  2782.1  2730.4  0.19  0.19      99  2933.5  2813.4  0.24  0.21
 0.027    3528 100.00  2149.6  2310.4  0.15  0.14     197  2166.2  2320.2  0.22  0.20
 0.045    4551 100.00  2444.2  2503.9  0.12  0.11     237  2428.8  2540.2  0.19  0.17
 0.062    5303 100.00  2245.5  2097.1  0.13  0.12     282  2280.4  2113.0  0.19  0.17
 0.080    5999  99.98  1696.7  1485.1  0.17  0.16     331  1609.2  1411.7  0.24  0.22
 0.098    6611 100.00  1229.4  1075.2  0.20  0.18     338  1277.1  1115.8  0.27  0.25
 0.116    7179 100.00   845.2   806.1  0.21  0.18     393   868.6   835.6  0.30  0.27
 0.133    7686  99.99   563.2   637.0  0.30  0.28     412   534.8   628.2  0.38  0.35
 0.151    8177  99.90   349.4   505.4  0.62  0.61     423   347.9   500.2  0.62  0.61
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0093   1740   0.856    336   0.738   2076   0.837  0.939  0.9169  0.9368  0.7730  0.8963
  0.0270   3190   0.880    338   0.811   3528   0.874  0.896  0.9516  0.9635  0.9089  0.9589
  0.0448   4201   0.896    350   0.869   4551   0.894  0.949  0.9600  0.9707  0.9303  0.9669
  0.0625   4967   0.887    336   0.808   5303   0.882  1.031  0.9545  0.9660  0.9170  0.9623
  0.0802   5649   0.865    350   0.778   5999   0.860  1.088  0.9287  0.9540  0.8644  0.9514
  0.0980   6264   0.808    347   0.707   6611   0.803  1.063  0.9055  0.9307  0.8188  0.9296
  0.1157   6834   0.754    345   0.617   7179   0.747  0.953  0.8763  0.9012  0.8122  0.9055
  0.1334   7332   0.651    354   0.518   7686   0.645  0.725  0.7915  0.8310  0.7358  0.8511
  0.1511   7861   0.317    332   0.262   8193   0.315  0.271  0.4505  0.4846  0.5114  0.6107
 $$
Resolution limits                    =     47.354     2.500
Number of used reflections           =      51126
Percentage observed                  =    99.9425
Percentage of free reflections       =     5.0391
Overall R factor                     =     0.1894
Free R factor                        =     0.2513
Average Fourier shell correlation    =     0.8525
AverageFree Fourier shell correlation=     0.8293
Overall weighted R factor            =     0.1564
Free weighted R factor               =     0.2106
Overall weighted R2 factor           =     0.1692
Free weighted R2 factor              =     0.2184
Average correlation coefficient      =     0.8733
Overall correlation coefficient      =     0.9578
Free correlation coefficient         =     0.9232
Cruickshanks DPI for coordinate error=     0.4107
DPI based on free R factor           =     0.2758
Overall figure of merit              =     0.7223
ML based su of positional parameters =     0.2470
ML based su of thermal parameters    =    12.2670
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Not converging with gamma equal    0.0000000    
 Trying gamma equal   5.24999984E-02
 Gamma decreased to   4.19999994E-02
 fvalues    357234.25       55083.625       5095882.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   4.80000041E-02
 Actual weight    12.341332      is applied to the X-ray term


 function value    4420700.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.009     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =   -0.1441
Partial structure    1: scale =     0.3849, B  =   47.2837
Overall anisotropic scale factors
   B11 =  -1.15 B22 =  -1.45 B33 =   2.59 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1888
Free R factor                        =     0.2509
Average Fourier shell correlation    =     0.8643
AverageFree Fourier shell correlation=     0.8417
Average correlation coefficient      =     0.8750
Overall figure of merit              =     0.7404
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    355899.34       28428.523       4420700.5       5095882.5    


     CGMAT cycle number =      3

 Weight matrix   4.80000004E-02
 Actual weight    12.193597      is applied to the X-ray term


 function value    4365680.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.005     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =    0.1018
Partial structure    1: scale =     0.3850, B  =   47.2406
Overall anisotropic scale factors
   B11 =  -1.14 B22 =  -1.44 B33 =   2.58 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1883
Free R factor                        =     0.2510
Average Fourier shell correlation    =     0.8679
AverageFree Fourier shell correlation=     0.8454
Average correlation coefficient      =     0.8762
Overall figure of merit              =     0.7445
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    355801.59       27179.586       4365680.5       4420700.5    


     CGMAT cycle number =      4

 Weight matrix   4.79999967E-02
 Actual weight    12.188026      is applied to the X-ray term


 function value    4363104.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =    0.1554
Partial structure    1: scale =     0.3852, B  =   47.0486
Overall anisotropic scale factors
   B11 =  -1.14 B22 =  -1.43 B33 =   2.57 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1882
Free R factor                        =     0.2511
Average Fourier shell correlation    =     0.8691
AverageFree Fourier shell correlation=     0.8466
Average correlation coefficient      =     0.8771
Overall figure of merit              =     0.7455
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02
 fvalues    355774.41       26916.348       4363104.5       4365680.5    


     CGMAT cycle number =      5

 Weight matrix   4.79999967E-02
 Actual weight    12.162270      is applied to the X-ray term


 function value    4353343.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =    0.2022
Partial structure    1: scale =     0.3850, B  =   47.0594
Overall anisotropic scale factors
   B11 =  -1.13 B22 =  -1.43 B33 =   2.56 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1883
Free R factor                        =     0.2508
Average Fourier shell correlation    =     0.8693
AverageFree Fourier shell correlation=     0.8467
Average correlation coefficient      =     0.8778
Overall figure of merit              =     0.7458
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03
 fvalues    355726.56       26900.469       4353343.0       4363104.5    


     CGMAT cycle number =      6

 Weight matrix   4.80000004E-02
 Actual weight    12.201730      is applied to the X-ray term


 function value    4367794.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =    0.1706
Partial structure    1: scale =     0.3852, B  =   46.9075
Overall anisotropic scale factors
   B11 =  -1.13 B22 =  -1.43 B33 =   2.56 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1881
Free R factor                        =     0.2510
Average Fourier shell correlation    =     0.8693
AverageFree Fourier shell correlation=     0.8466
Average correlation coefficient      =     0.8782
Overall figure of merit              =     0.7456
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Not converging with gamma equal   8.71641375E-03
 Trying gamma equal   4.29446921E-02
 Gamma decreased to   3.60990353E-02


 fvalues    355754.66       26852.443       4367508.0       4353343.0    
 fvalues    355754.66       26852.443       4367508.0       4367674.5    


     CGMAT cycle number =      7

 Weight matrix   4.80000004E-02
 Actual weight    12.196074      is applied to the X-ray term


 function value    4365661.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =    0.1873
Partial structure    1: scale =     0.3852, B  =   46.8317
Overall anisotropic scale factors
   B11 =  -1.13 B22 =  -1.42 B33 =   2.55 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1881
Free R factor                        =     0.2509
Average Fourier shell correlation    =     0.8694
AverageFree Fourier shell correlation=     0.8466
Average correlation coefficient      =     0.8785
Overall figure of merit              =     0.7457
-----------------------------------------------------------------------------
 Trying gamma equal   3.60990353E-02
 Gamma decreased to   2.98757106E-02
 fvalues    355753.31       26867.631       4365661.0       4367674.5    


     CGMAT cycle number =      8

 Weight matrix   4.80000004E-02
 Actual weight    12.175582      is applied to the X-ray term


 function value    4358003.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =    0.2083
Partial structure    1: scale =     0.3850, B  =   46.8261
Overall anisotropic scale factors
   B11 =  -1.13 B22 =  -1.42 B33 =   2.55 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1882
Free R factor                        =     0.2508
Average Fourier shell correlation    =     0.8695
AverageFree Fourier shell correlation=     0.8467
Average correlation coefficient      =     0.8786
Overall figure of merit              =     0.7458
-----------------------------------------------------------------------------
 Trying gamma equal   2.98757106E-02
 Gamma decreased to   2.42181439E-02
 fvalues    355723.84       26858.436       4358003.5       4365661.0    


     CGMAT cycle number =      9

 Weight matrix   4.80000004E-02
 Actual weight    12.207973      is applied to the X-ray term


 function value    4369720.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =    0.1867
Partial structure    1: scale =     0.3849, B  =   46.7513
Overall anisotropic scale factors
   B11 =  -1.13 B22 =  -1.42 B33 =   2.55 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1881
Free R factor                        =     0.2512
Average Fourier shell correlation    =     0.8694
AverageFree Fourier shell correlation=     0.8465
Average correlation coefficient      =     0.8787
Overall figure of merit              =     0.7456
-----------------------------------------------------------------------------
 Trying gamma equal   2.42181439E-02
 Gamma decreased to   1.90749019E-02


 fvalues    355748.91       26842.031       4369662.5       4358003.5    
 fvalues    355748.91       26842.031       4369662.5       4369815.0    


     CGMAT cycle number =     10

    ****                              VDW outliers                              ****

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

A    396 TRP HD1 . - A    398 HIS NE2 . mod.= 0.903 id.= 2.750 dev= -1.85 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.792 id.= 2.750 dev= -1.96 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   216  320  360
 Maximuum H,K,L                 :    54   82   92
 Minimum acceptable grid spacing:   140  213  237
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   216  320  360
 Maximuum H,K,L                 :    54   82   92
 Minimum acceptable grid spacing:   140  213  237
 Weight matrix   4.80000004E-02
 Actual weight    12.180618      is applied to the X-ray term
Norm of X_ray positional gradient                18.2
Norm of Geom. positional gradient                18.2
Norm of X_ray B-factor gradient                  24.9
Norm of Geom. B-factor gradient                  24.3
Product of X_ray and Geom posit. gradients     -0.173E+08
 Cosine of angle between them                      -0.996
Product of X_ray and Geom B-fact gradients     -0.105E+08
 Cosine of angle between them                      -0.992


Residuals: XRAY=     0.4333E+07 GEOM=     0.2684E+05 TOTAL=     0.4360E+07
 function value    4359622.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.001     0.017
Bond angles  : refined atoms                  12685     1.674     1.702
Bond angles  : others                         18398     1.227     1.594
Torsion angles, period  1. refined             1092     8.036     5.000
Torsion angles, period  2. refined              517    31.892    21.915
Torsion angles, period  3. refined             1292    14.728    15.000
Torsion angles, period  4. refined               63    19.525    15.000
Chiral centres: refined atoms                  1196     0.064     0.200
Planar groups: refined atoms                  10355     0.007     0.020
Planar groups: others                          2034     0.001     0.020
VDW repulsions: refined_atoms                  1763     0.212     0.200
VDW repulsions.others                          7924     0.187     0.200
VDW; torsion: refined_atoms                    4238     0.168     0.200
VDW; torsion.others                            3941     0.076     0.200
HBOND: refined_atoms                            484     0.153     0.200
HBOND.others                                      1     0.094     0.200
Metal-ion: refined_atoms                         12     0.139     0.200
VDW repulsions: symmetry: refined_atoms          19     0.204     0.200
VDW repulsions: symmetry: others                 43     0.165     0.200
HBOND: symmetry: refined_atoms                    6     0.155     0.200
M. chain bond B values: refined atoms          4328     3.326     4.855
M. chain bond B values: others                 4327     3.325     4.854
M. chain angle B values: refined atoms         5426     4.821     7.276
M. chain angle B values: others                5427     4.821     7.277
S. chain bond B values: refined atoms          4896     4.148     5.306
S. chain bond B values: others                 4897     4.148     5.306
S. chain angle B values: refined atoms         7255     5.811     7.894
S. chain angle B values: others                7256     5.811     7.894
Long range B values: refined atoms             9985     7.279    57.029
Long range B values: others                    9907     7.274    56.982
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =    0.1877
Partial structure    1: scale =     0.3849, B  =   46.8265
Overall anisotropic scale factors
   B11 =  -1.13 B22 =  -1.42 B33 =   2.55 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.009    2076  99.68  2790.1  2737.3  0.19  0.19      99  2941.9  2831.0  0.23  0.21
 0.027    3528 100.00  2155.8  2316.1  0.15  0.14     197  2172.4  2323.7  0.22  0.20
 0.045    4551 100.00  2451.2  2512.8  0.12  0.11     237  2435.8  2552.7  0.19  0.17
 0.062    5303 100.00  2252.0  2104.3  0.13  0.12     282  2287.0  2124.5  0.19  0.17
 0.080    5999  99.98  1701.6  1491.9  0.17  0.16     331  1613.8  1416.9  0.24  0.22
 0.098    6611 100.00  1232.9  1078.9  0.20  0.18     338  1280.8  1119.6  0.26  0.24
 0.116    7179 100.00   847.6   807.6  0.20  0.18     393   871.1   836.3  0.30  0.27
 0.133    7686  99.99   564.9   638.2  0.29  0.27     412   536.4   631.1  0.37  0.35
 0.151    8177  99.90   350.4   507.2  0.61  0.61     423   348.9   503.6  0.62  0.61
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0093   1740   0.863    336   0.746   2076   0.844  0.939  0.9198  0.9391  0.7762  0.8976
  0.0270   3190   0.896    338   0.827   3528   0.889  0.896  0.9556  0.9679  0.9090  0.9593
  0.0448   4201   0.905    350   0.876   4551   0.902  0.949  0.9623  0.9730  0.9301  0.9671
  0.0625   4967   0.896    336   0.815   5303   0.891  1.031  0.9570  0.9682  0.9174  0.9620
  0.0802   5649   0.878    350   0.792   5999   0.873  1.088  0.9329  0.9580  0.8644  0.9518
  0.0980   6264   0.815    347   0.716   6611   0.810  1.063  0.9089  0.9342  0.8193  0.9313
  0.1157   6834   0.754    345   0.620   7179   0.747  0.953  0.8768  0.9016  0.8142  0.9079
  0.1334   7332   0.723    354   0.584   7686   0.716  0.756  0.8238  0.8631  0.7359  0.8566
  0.1511   7861   0.363    332   0.296   8193   0.360  0.296  0.5178  0.5489  0.5115  0.6357
 $$
Resolution limits                    =     47.354     2.500
Number of used reflections           =      51126
Percentage observed                  =    99.9425
Percentage of free reflections       =     5.0391
Overall R factor                     =     0.1881
Free R factor                        =     0.2510
Average Fourier shell correlation    =     0.8695
AverageFree Fourier shell correlation=     0.8466
Overall weighted R factor            =     0.1555
Free weighted R factor               =     0.2098
Overall weighted R2 factor           =     0.1684
Free weighted R2 factor              =     0.2170
Average correlation coefficient      =     0.8789
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9236
Cruickshanks DPI for coordinate error=     0.4081
DPI based on free R factor           =     0.2754
Overall figure of merit              =     0.7457
ML based su of positional parameters =     0.2292
ML based su of thermal parameters    =    11.3451
-----------------------------------------------------------------------------
 Trying gamma equal   1.90749019E-02
 Gamma decreased to   1.43992268E-02
 fvalues    355711.28       26838.436       4359622.0       4369815.0    

    ****                              VDW outliers                              ****

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

A    396 TRP HD1 . - A    398 HIS NE2 . mod.= 0.904 id.= 2.750 dev= -1.85 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.791 id.= 2.750 dev= -1.96 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: BO_from2-80A_R00_2-50A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7918     0.001     0.017
Bond angles  : refined atoms                  12685     1.674     1.702
Bond angles  : others                         18398     1.226     1.594
Torsion angles, period  1. refined             1092     8.040     5.000
Torsion angles, period  2. refined              517    31.903    21.915
Torsion angles, period  3. refined             1292    14.724    15.000
Torsion angles, period  4. refined               63    19.536    15.000
Chiral centres: refined atoms                  1196     0.064     0.200
Planar groups: refined atoms                  10355     0.007     0.020
Planar groups: others                          2034     0.001     0.020
VDW repulsions: refined_atoms                  1764     0.212     0.200
VDW repulsions.others                          7921     0.187     0.200
VDW; torsion: refined_atoms                    4237     0.168     0.200
VDW; torsion.others                            3964     0.076     0.200
HBOND: refined_atoms                            488     0.152     0.200
HBOND.others                                      1     0.096     0.200
Metal-ion: refined_atoms                         12     0.139     0.200
VDW repulsions: symmetry: refined_atoms          19     0.203     0.200
VDW repulsions: symmetry: others                 42     0.167     0.200
HBOND: symmetry: refined_atoms                    6     0.152     0.200
M. chain bond B values: refined atoms          4328     3.323     4.855
M. chain bond B values: others                 4327     3.322     4.854
M. chain angle B values: refined atoms         5426     4.817     7.275
M. chain angle B values: others                5427     4.817     7.277
S. chain bond B values: refined atoms          4896     4.151     5.306
S. chain bond B values: others                 4897     4.151     5.306
S. chain angle B values: refined atoms         7255     5.816     7.894
S. chain angle B values: others                7256     5.815     7.894
Long range B values: refined atoms             9988     7.270    57.024
Long range B values: others                    9908     7.265    56.975
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0057, B  =    0.2010
Partial structure    1: scale =     0.3848, B  =   46.8097
Overall anisotropic scale factors
   B11 =  -1.13 B22 =  -1.42 B33 =   2.55 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.009    2076  99.68  2789.1  2734.9  0.19  0.19      99  2940.8  2830.7  0.24  0.21
 0.027    3528 100.00  2155.0  2315.8  0.15  0.14     197  2171.6  2325.5  0.22  0.20
 0.045    4551 100.00  2450.3  2512.1  0.12  0.11     237  2434.9  2551.1  0.19  0.17
 0.062    5303 100.00  2251.1  2103.6  0.13  0.12     282  2286.2  2124.3  0.19  0.17
 0.080    5999  99.98  1700.9  1491.6  0.17  0.16     331  1613.2  1417.0  0.24  0.22
 0.098    6611 100.00  1232.4  1078.5  0.20  0.18     338  1280.3  1119.8  0.26  0.24
 0.116    7179 100.00   847.3   807.2  0.20  0.18     393   870.7   835.8  0.30  0.27
 0.133    7686  99.99   564.6   637.8  0.29  0.27     412   536.2   630.7  0.37  0.35
 0.151    8177  99.90   350.3   507.0  0.61  0.61     423   348.8   503.5  0.62  0.61
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0093   1740   0.863    336   0.746   2076   0.844  0.939  0.9192  0.9390  0.7737  0.8979
  0.0270   3190   0.895    338   0.826   3528   0.889  0.896  0.9555  0.9678  0.9085  0.9592
  0.0448   4201   0.904    350   0.876   4551   0.902  0.949  0.9622  0.9730  0.9301  0.9671
  0.0625   4967   0.895    336   0.815   5303   0.890  1.031  0.9569  0.9682  0.9172  0.9621
  0.0802   5649   0.877    350   0.791   5999   0.872  1.088  0.9326  0.9579  0.8638  0.9518
  0.0980   6264   0.815    347   0.716   6611   0.810  1.063  0.9089  0.9341  0.8195  0.9313
  0.1157   6834   0.754    345   0.621   7179   0.748  0.953  0.8768  0.9016  0.8140  0.9079
  0.1334   7332   0.722    354   0.584   7686   0.716  0.756  0.8237  0.8631  0.7354  0.8566
  0.1511   7861   0.362    332   0.296   8193   0.360  0.296  0.5177  0.5489  0.5114  0.6361
 $$
Resolution limits                    =     47.354     2.500
Number of used reflections           =      51126
Percentage observed                  =    99.9425
Percentage of free reflections       =     5.0391
Overall R factor                     =     0.1882
Free R factor                        =     0.2514
Average Fourier shell correlation    =     0.8694
AverageFree Fourier shell correlation=     0.8465
Overall weighted R factor            =     0.1556
Free weighted R factor               =     0.2104
Overall weighted R2 factor           =     0.1685
Free weighted R2 factor              =     0.2176
Average correlation coefficient      =     0.8789
Overall correlation coefficient      =     0.9583
Free correlation coefficient         =     0.9234
Cruickshanks DPI for coordinate error=     0.4082
DPI based on free R factor           =     0.2758
Overall figure of merit              =     0.7456
ML based su of positional parameters =     0.2292
ML based su of thermal parameters    =    11.3451
-----------------------------------------------------------------------------
  Time in seconds: CPU =       144.10
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1894   0.2513   0.722      357234.   19435.9   0.0077  0.537   1.649  0.920   0.063
       1   0.1888   0.2509   0.740      355899.   19414.5   0.0082  0.569   1.674  0.929   0.066
       2   0.1883   0.2510   0.745      355802.   19413.1   0.0080  0.557   1.670  0.930   0.064
       3   0.1882   0.2511   0.746      355774.   19412.6   0.0080  0.555   1.669  0.930   0.064
       4   0.1883   0.2508   0.746      355727.   19410.0   0.0080  0.555   1.670  0.931   0.064
       5   0.1881   0.2510   0.746      355764.   19413.3   0.0080  0.555   1.671  0.931   0.064
       6   0.1881   0.2509   0.746      355753.   19412.9   0.0080  0.556   1.672  0.932   0.064
       7   0.1882   0.2508   0.746      355724.   19410.8   0.0080  0.556   1.673  0.932   0.064
       8   0.1881   0.2512   0.746      355741.   19413.3   0.0080  0.556   1.673  0.932   0.064
       9   0.1881   0.2510   0.746      355711.   19410.7   0.0080  0.556   1.674  0.932   0.064
      10   0.1882   0.2514   0.746      355717.   19412.1   0.0080  0.555   1.674  0.932   0.064
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1894   0.1882
             R free    0.2513   0.2514
     Rms BondLength    0.0077   0.0080
      Rms BondAngle    1.6492   1.6743
     Rms ChirVolume    0.0631   0.0640
 $$

 Refmac:  End of Refmac_5.8.0258   
Times: User:     217.9s System:    1.1s Elapsed:     3:39