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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: 12:16:24 


 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 2.40
  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_2-50A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - BO_from2-80A_R00_2-40A.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_2-40A.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       0.0193
  Refinement of individual isotropic Bfactors
  Refinement resln        :    47.3545  2.4000
  Estimated number of reflections :      81495
  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  2.4000

  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_2-50A.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 =      3.09
            ch:AAA  res: 465  HIS              --> 466  ASP
  INFO:     link is found (not be used) dist=   2.532 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=   2.894 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=   1.818 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=   2.038 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=   1.972 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=   1.915 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=   3.092 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=   1.704 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=   1.962 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=   1.759 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=   1.971 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=   2.899 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=   2.678 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=   2.051 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=   2.178 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=   2.196 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=   2.146 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 =     1.429 ideal_dist=     1.439
            ch:AAA  res: 472  ASN              at:ND2 .->AeA  res: 701  NAG              at:C1  .
  WARNING : link:NAG-ASN  is found dist =     1.443 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=   3.070 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 =     1.426 ideal_dist=     1.439
            ch:AeA  res: 701  NAG              at:O4  .->AfA  res: 702  NAG              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.433 ideal_dist=     1.439
            ch:AfA  res: 702  NAG              at:O4  .->AgA  res: 703  BMA              at:C1  .
  WARNING : link:ALPHA1-3 is found dist =     1.450 ideal_dist=     1.439
            ch:AgA  res: 703  BMA              at:O3  .->AhA  res: 704  MAN              at:C1  .
  WARNING : link:ALPHA1-6 is found dist =     1.460 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 =     2.456 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=   1.856 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=   2.169 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=   2.129 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=   1.924 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=   2.423 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=   2.604 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=   2.660 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=   1.655 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=   2.011 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=   1.862 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=   2.034 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=   1.963 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=   2.135 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=   2.368 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=   2.105 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 =     1.434 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=   3.024 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=   2.930 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 =     1.423 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 =     1.454 ideal_dist=     1.439
            ch:BgB  res: 703  BMA              at:O3  .->BhB  res: 704  MAN              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.455 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       3052
Number of   all  reflections      60803
--------------------------------------------------------------------------------
 Number of reflections in file      72569
 Number of reflections read          60803

   Current auto weighting coefficient =    8.4993744    

 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.=  57.58 id.= 109.47 dev= 51.892 sig.=  3.000
A    702 NAG H1    - A    702 NAG C2    mod.= 139.26 id.= 108.34 dev=-30.916 sig.=  3.000
A    702 NAG O4    - A    703 BMA H1    mod.=  55.67 id.= 109.47 dev= 53.797 sig.=  3.000
A    703 BMA H1    - A    703 BMA C2    mod.= 146.50 id.= 108.34 dev=-38.162 sig.=  3.000
A    703 BMA O3    - A    704 MAN H1    mod.=  53.13 id.= 109.47 dev= 56.343 sig.=  3.000
A    704 MAN H1    - A    704 MAN C2    mod.= 138.81 id.= 108.34 dev=-30.472 sig.=  3.000
A    711 NAG O4    - A    712 NAG H1    mod.=  55.95 id.= 109.47 dev= 53.517 sig.=  3.000
A    712 NAG H1    - A    712 NAG C2    mod.= 138.46 id.= 108.34 dev=-30.116 sig.=  3.000
A    712 NAG O4    - A    713 BMA H1    mod.=  48.40 id.= 109.47 dev= 61.070 sig.=  3.000
A    713 BMA H1    - A    713 BMA C2    mod.= 142.82 id.= 108.34 dev=-34.481 sig.=  3.000
B    701 NAG O4    - B    702 NAG H1    mod.=  57.32 id.= 109.47 dev= 52.147 sig.=  3.000
B    702 NAG H1    - B    702 NAG C2    mod.= 141.77 id.= 108.34 dev=-33.434 sig.=  3.000
B    702 NAG O4    - B    703 BMA H1    mod.=  50.53 id.= 109.47 dev= 58.941 sig.=  3.000
B    703 BMA H1    - B    703 BMA C2    mod.= 141.67 id.= 108.34 dev=-33.329 sig.=  3.000
B    703 BMA O3    - B    704 MAN H1    mod.=  52.58 id.= 109.47 dev= 56.891 sig.=  3.000
B    704 MAN H1    - B    704 MAN C2    mod.= 139.62 id.= 108.34 dev=-31.277 sig.=  3.000
B    711 NAG O4    - B    712 NAG H1    mod.=  50.96 id.= 109.47 dev= 58.507 sig.=  3.000
B    712 NAG H1    - B    712 NAG C2    mod.= 138.47 id.= 108.34 dev=-30.126 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.= 0.849 id.= 2.750 dev= -1.90 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.738 id.= 2.750 dev= -2.01 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  336  384
 Maximuum H,K,L                 :    57   86   95
 Minimum acceptable grid spacing:   144  218  243
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   216  336  384
 Maximuum H,K,L                 :    57   86   95
 Minimum acceptable grid spacing:   144  218  243
 Weight matrix   4.80000004E-02
 Actual weight    15.437384      is applied to the X-ray term
Norm of X_ray positional gradient                21.1
Norm of Geom. positional gradient                78.7
Norm of X_ray B-factor gradient                  28.9
Norm of Geom. B-factor gradient                  23.2
Product of X_ray and Geom posit. gradients     -0.215E+08
 Cosine of angle between them                      -0.248
Product of X_ray and Geom B-fact gradients     -0.109E+08
 Cosine of angle between them                      -0.929


Residuals: XRAY=     0.6087E+07 GEOM=     0.5591E+05 TOTAL=     0.6142E+07
 function value    6142434.5    

-------------------------------------------------------------------------------
             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     1.675     1.702
Bond angles  : others                         18398     2.757     1.594
Torsion angles, period  1. refined             1092     8.040     5.000
Torsion angles, period  2. refined              517    31.901    21.915
Torsion angles, period  3. refined             1292    14.726    15.000
Torsion angles, period  4. refined               63    19.528    15.000
Chiral centres: refined atoms                  1196     0.064     0.200
Planar groups: refined atoms                  10355     0.007     0.020
Planar groups: others                          2034     0.009     0.020
VDW repulsions: refined_atoms                  1765     0.212     0.200
VDW repulsions.others                          7810     0.219     0.200
VDW; torsion: refined_atoms                    4236     0.168     0.200
VDW; torsion.others                            3707     0.090     0.200
HBOND: refined_atoms                            488     0.152     0.200
HBOND.others                                      2     0.129     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                 45     0.185     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     4.150     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     7.272    57.030
Long range B values: others                    9908     7.267    56.981
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0058, B  =    2.2259
Partial structure    1: scale =     0.3872, B  =   45.2072
Overall anisotropic scale factors
   B11 =  -1.14 B22 =  -1.29 B33 =   2.43 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.010    2334  99.72  2652.8  2672.5  0.19  0.19     116  2780.0  2778.5  0.24  0.21
 0.029    3971 100.00  2150.6  2330.5  0.15  0.14     226  2115.7  2254.4  0.21  0.19
 0.049    5128 100.00  2390.8  2403.2  0.12  0.11     264  2359.3  2445.1  0.20  0.18
 0.068    5989 100.00  2032.2  1835.4  0.15  0.14     325  2032.8  1806.5  0.20  0.18
 0.087    6795  99.99  1483.7  1257.1  0.20  0.18     344  1468.9  1248.1  0.26  0.24
 0.106    7446 100.00  1022.0   896.8  0.21  0.19     412  1065.2   934.7  0.27  0.25
 0.126    8097  99.99   661.5   657.1  0.23  0.21     442   658.5   679.4  0.33  0.31
 0.145    8694 100.00   401.5   508.1  0.44  0.43     441   386.5   497.9  0.49  0.48
 0.164    9107  98.15   279.9   404.0  0.66  0.65     467   280.8   414.1  0.68  0.67
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0101   1970   0.846    364   0.732   2334   0.829  0.910  0.9159  0.9352  0.7787  0.8989
  0.0293   3598   0.882    373   0.832   3971   0.877  0.890  0.9512  0.9649  0.9127  0.9605
  0.0485   4755   0.894    373   0.841   5128   0.890  0.964  0.9569  0.9691  0.9224  0.9644
  0.0678   5624   0.880    365   0.808   5989   0.876  1.062  0.9499  0.9632  0.9158  0.9607
  0.0870   6414   0.835    381   0.736   6795   0.829  1.110  0.9198  0.9439  0.8679  0.9470
  0.1063   7074   0.785    372   0.679   7446   0.780  1.054  0.8925  0.9194  0.8011  0.9217
  0.1255   7713   0.726    384   0.564   8097   0.718  0.891  0.8486  0.8763  0.7732  0.8872
  0.1448   8322   0.525    372   0.429   8694   0.521  0.519  0.6483  0.7091  0.5880  0.7375
  0.1640   8799   0.177    323   0.159   9122   0.177  0.132  0.3181  0.3337  0.5279  0.4677
 $$
Resolution limits                    =     47.354     2.400
Number of used reflections           =      57576
Percentage observed                  =    99.6679
Percentage of free reflections       =     5.0120
Overall R factor                     =     0.2015
Free R factor                        =     0.2625
Average Fourier shell correlation    =     0.8044
AverageFree Fourier shell correlation=     0.7823
Overall weighted R factor            =     0.1660
Free weighted R factor               =     0.2187
Overall weighted R2 factor           =     0.1750
Free weighted R2 factor              =     0.2239
Average correlation coefficient      =     0.8298
Overall correlation coefficient      =     0.9581
Free correlation coefficient         =     0.9251
Cruickshanks DPI for coordinate error=     0.3437
DPI based on free R factor           =     0.2608
Overall figure of merit              =     0.6708
ML based su of positional parameters =     0.2583
ML based su of thermal parameters    =    12.7190
-----------------------------------------------------------------------------
 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    394272.03       55905.770       6142434.5      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   4.80000004E-02
 Actual weight    13.529187      is applied to the X-ray term


 function value    5344182.0    

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

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0058, B  =   -0.0802
Partial structure    1: scale =     0.3869, B  =   44.6610
Overall anisotropic scale factors
   B11 =  -1.14 B22 =  -1.27 B33 =   2.40 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2013
Free R factor                        =     0.2621
Average Fourier shell correlation    =     0.8061
AverageFree Fourier shell correlation=     0.7838
Average correlation coefficient      =     0.8327
Overall figure of merit              =     0.6809
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    392827.00       29552.008       5344182.0       6142434.5    


     CGMAT cycle number =      3

 Weight matrix   4.80000004E-02
 Actual weight    13.292334      is applied to the X-ray term


 function value    5248101.5    

-------------------------------------------------------------------------------
             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 =     0.0058, B  =    0.1587
Partial structure    1: scale =     0.3870, B  =   44.4642
Overall anisotropic scale factors
   B11 =  -1.13 B22 =  -1.25 B33 =   2.38 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2004
Free R factor                        =     0.2624
Average Fourier shell correlation    =     0.8168
AverageFree Fourier shell correlation=     0.7949
Average correlation coefficient      =     0.8332
Overall figure of merit              =     0.6893
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    392687.09       28373.430       5248101.5       5344182.0    


     CGMAT cycle number =      4

 Weight matrix   4.80000004E-02
 Actual weight    13.255833      is applied to the X-ray term


 function value    5233161.0    

-------------------------------------------------------------------------------
             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 =     0.0058, B  =    0.1628
Partial structure    1: scale =     0.3871, B  =   44.2433
Overall anisotropic scale factors
   B11 =  -1.13 B22 =  -1.24 B33 =   2.37 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2004
Free R factor                        =     0.2625
Average Fourier shell correlation    =     0.8177
AverageFree Fourier shell correlation=     0.7957
Average correlation coefficient      =     0.8343
Overall figure of merit              =     0.6900
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02
 fvalues    392665.94       28047.020       5233161.0       5248101.5    


     CGMAT cycle number =      5

 Weight matrix   4.79999967E-02
 Actual weight    13.394234      is applied to the X-ray term


 function value    5288329.5    

-------------------------------------------------------------------------------
             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 =     0.0058, B  =    0.1811
Partial structure    1: scale =     0.3870, B  =   44.0961
Overall anisotropic scale factors
   B11 =  -1.13 B22 =  -1.24 B33 =   2.36 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2002
Free R factor                        =     0.2625
Average Fourier shell correlation    =     0.8116
AverageFree Fourier shell correlation=     0.7892
Average correlation coefficient      =     0.8349
Overall figure of merit              =     0.6856
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03


 fvalues    392765.75       28038.891       5287714.5       5233161.0    
 fvalues    392765.75       28038.891       5287714.5       5288835.0    


     CGMAT cycle number =      6

 Weight matrix   4.80000004E-02
 Actual weight    13.266109      is applied to the X-ray term


 function value    5237215.5    

-------------------------------------------------------------------------------
             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 =     0.0058, B  =    0.1981
Partial structure    1: scale =     0.3870, B  =   43.9388
Overall anisotropic scale factors
   B11 =  -1.12 B22 =  -1.23 B33 =   2.35 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2001
Free R factor                        =     0.2625
Average Fourier shell correlation    =     0.8176
AverageFree Fourier shell correlation=     0.7955
Average correlation coefficient      =     0.8349
Overall figure of merit              =     0.6899
-----------------------------------------------------------------------------
 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    392662.28       28114.965       5237215.5       5288835.0    


     CGMAT cycle number =      7

 Weight matrix   4.80000004E-02
 Actual weight    13.401576      is applied to the X-ray term


 function value    5291390.0    

-------------------------------------------------------------------------------
             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 =     0.0058, B  =    0.1999
Partial structure    1: scale =     0.3871, B  =   43.8528
Overall anisotropic scale factors
   B11 =  -1.12 B22 =  -1.23 B33 =   2.35 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2001
Free R factor                        =     0.2625
Average Fourier shell correlation    =     0.8115
AverageFree Fourier shell correlation=     0.7890
Average correlation coefficient      =     0.8353
Overall figure of merit              =     0.6854
-----------------------------------------------------------------------------
 Trying gamma equal   3.60990353E-02
 Gamma decreased to   2.98757106E-02


 fvalues    392761.78       28039.158       5292183.0       5237215.5    

 fvalues    392761.78       28039.158       5292249.5       5291666.0    
 fvalues    392761.78       28039.158       5292249.5       5291666.0    


     CGMAT cycle number =      8

 Weight matrix   4.80000004E-02
 Actual weight    13.457407      is applied to the X-ray term


 function value    5313784.0    

-------------------------------------------------------------------------------
             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 =     0.0058, B  =    0.1826
Partial structure    1: scale =     0.3871, B  =   43.8620
Overall anisotropic scale factors
   B11 =  -1.12 B22 =  -1.23 B33 =   2.35 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2001
Free R factor                        =     0.2625
Average Fourier shell correlation    =     0.8064
AverageFree Fourier shell correlation=     0.7836
Average correlation coefficient      =     0.8353
Overall figure of merit              =     0.6821
-----------------------------------------------------------------------------
 Trying gamma equal   2.98757106E-02
 Gamma decreased to   2.42181439E-02


 fvalues    392773.00       28060.770       5314052.0       5291666.0    

 fvalues    392773.00       28060.770       5313999.5       5313767.0    
 fvalues    392773.00       28060.770       5313999.5       5313767.0    


     CGMAT cycle number =      9

 Weight matrix   4.80000004E-02
 Actual weight    13.489085      is applied to the X-ray term


 function value    5326563.0    

-------------------------------------------------------------------------------
             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 =     0.0058, B  =    0.1997
Partial structure    1: scale =     0.3871, B  =   43.8421
Overall anisotropic scale factors
   B11 =  -1.12 B22 =  -1.23 B33 =   2.35 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2001
Free R factor                        =     0.2625
Average Fourier shell correlation    =     0.8063
AverageFree Fourier shell correlation=     0.7835
Average correlation coefficient      =     0.8352
Overall figure of merit              =     0.6819
-----------------------------------------------------------------------------
 Trying gamma equal   2.42181439E-02
 Gamma decreased to   1.90749019E-02


 fvalues    392791.31       28071.531       5326656.0       5313767.0    

 fvalues    392791.31       28071.531       5326638.0       5326467.0    
 fvalues    392791.31       28071.531       5326638.0       5326467.0    


     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.= 0.910 id.= 2.750 dev= -1.84 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.781 id.= 2.750 dev= -1.97 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  336  384
 Maximuum H,K,L                 :    57   86   95
 Minimum acceptable grid spacing:   144  218  243
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   216  336  384
 Maximuum H,K,L                 :    57   86   95
 Minimum acceptable grid spacing:   144  218  243
 Weight matrix   4.80000004E-02
 Actual weight    13.484199      is applied to the X-ray term
Norm of X_ray positional gradient                19.7
Norm of Geom. positional gradient                19.5
Norm of X_ray B-factor gradient                  26.2
Norm of Geom. B-factor gradient                  25.2
Product of X_ray and Geom posit. gradients     -0.201E+08
 Cosine of angle between them                      -0.996
Product of X_ray and Geom B-fact gradients     -0.114E+08
 Cosine of angle between them                      -0.993


Residuals: XRAY=     0.5297E+07 GEOM=     0.2808E+05 TOTAL=     0.5325E+07
 function value    5324592.0    

-------------------------------------------------------------------------------
             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     1.711     1.702
Bond angles  : others                         18398     1.237     1.594
Torsion angles, period  1. refined             1092     8.069     5.000
Torsion angles, period  2. refined              517    31.948    21.915
Torsion angles, period  3. refined             1292    14.775    15.000
Torsion angles, period  4. refined               63    19.704    15.000
Chiral centres: refined atoms                  1196     0.066     0.200
Planar groups: refined atoms                  10355     0.007     0.020
Planar groups: others                          2034     0.002     0.020
VDW repulsions: refined_atoms                  1755     0.214     0.200
VDW repulsions.others                          7888     0.190     0.200
VDW; torsion: refined_atoms                    4215     0.169     0.200
VDW; torsion.others                            3907     0.077     0.200
HBOND: refined_atoms                            490     0.152     0.200
HBOND.others                                      1     0.076     0.200
Metal-ion: refined_atoms                         12     0.138     0.200
VDW repulsions: symmetry: refined_atoms          21     0.196     0.200
VDW repulsions: symmetry: others                 46     0.167     0.200
HBOND: symmetry: refined_atoms                    7     0.135     0.200
M. chain bond B values: refined atoms          4328     3.610     5.045
M. chain bond B values: others                 4327     3.608     5.044
M. chain angle B values: refined atoms         5426     5.139     7.560
M. chain angle B values: others                5427     5.139     7.562
S. chain bond B values: refined atoms          4896     4.546     5.506
S. chain bond B values: others                 4897     4.546     5.506
S. chain angle B values: refined atoms         7255     6.266     8.189
S. chain angle B values: others                7256     6.266     8.190
Long range B values: refined atoms             9965     7.556    59.137
Long range B values: others                    9885     7.554    59.081
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0058, B  =    0.1959
Partial structure    1: scale =     0.3871, B  =   43.8555
Overall anisotropic scale factors
   B11 =  -1.12 B22 =  -1.23 B33 =   2.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.010    2334  99.72  2659.7  2675.0  0.19  0.19     116  2787.3  2790.9  0.24  0.21
 0.029    3971 100.00  2156.2  2334.3  0.15  0.14     226  2121.2  2258.9  0.21  0.19
 0.049    5128 100.00  2397.0  2412.3  0.12  0.11     264  2365.4  2454.1  0.20  0.18
 0.068    5989 100.00  2037.5  1841.0  0.15  0.14     325  2038.1  1814.3  0.20  0.18
 0.087    6795  99.99  1487.6  1262.1  0.19  0.18     344  1472.8  1250.1  0.26  0.24
 0.106    7446 100.00  1024.6   898.8  0.21  0.19     412  1068.0   938.4  0.27  0.25
 0.126    8097  99.99   663.2   657.4  0.22  0.20     442   660.2   680.1  0.33  0.31
 0.145    8694 100.00   402.6   509.0  0.44  0.43     441   387.5   499.9  0.50  0.48
 0.164    9107  98.15   280.7   405.0  0.65  0.65     467   281.5   415.9  0.68  0.67
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0101   1970   0.860    364   0.744   2334   0.842  0.913  0.9188  0.9378  0.7786  0.8988
  0.0293   3598   0.897    373   0.848   3971   0.893  0.890  0.9559  0.9695  0.9144  0.9610
  0.0485   4755   0.903    373   0.851   5128   0.899  0.964  0.9597  0.9718  0.9242  0.9653
  0.0678   5624   0.891    365   0.816   5989   0.886  1.062  0.9527  0.9663  0.9150  0.9612
  0.0870   6414   0.854    381   0.753   6795   0.849  1.110  0.9271  0.9505  0.8682  0.9470
  0.1063   7074   0.791    372   0.683   7446   0.786  1.054  0.8953  0.9224  0.8006  0.9236
  0.1255   7713   0.741    384   0.581   8097   0.733  0.899  0.8533  0.8818  0.7722  0.8897
  0.1448   8322   0.572    372   0.471   8694   0.568  0.539  0.6897  0.7463  0.5861  0.7461
  0.1640   8799   0.148    323   0.135   9122   0.147  0.120  0.2682  0.2913  0.5321  0.4890
 $$
Resolution limits                    =     47.354     2.400
Number of used reflections           =      57576
Percentage observed                  =    99.6679
Percentage of free reflections       =     5.0120
Overall R factor                     =     0.2001
Free R factor                        =     0.2625
Average Fourier shell correlation    =     0.8063
AverageFree Fourier shell correlation=     0.7835
Overall weighted R factor            =     0.1649
Free weighted R factor               =     0.2186
Overall weighted R2 factor           =     0.1742
Free weighted R2 factor              =     0.2232
Average correlation coefficient      =     0.8352
Overall correlation coefficient      =     0.9586
Free correlation coefficient         =     0.9254
Cruickshanks DPI for coordinate error=     0.3413
DPI based on free R factor           =     0.2608
Overall figure of merit              =     0.6820
ML based su of positional parameters =     0.2412
ML based su of thermal parameters    =    11.9115
-----------------------------------------------------------------------------
 Trying gamma equal   1.90749019E-02
 Gamma decreased to   1.43992268E-02
 fvalues    392794.28       28075.795       5324592.0       5326467.0    

    ****                              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.= 0.910 id.= 2.750 dev= -1.84 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.781 id.= 2.750 dev= -1.97 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_2-40A.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     1.711     1.702
Bond angles  : others                         18398     1.237     1.594
Torsion angles, period  1. refined             1092     8.069     5.000
Torsion angles, period  2. refined              517    31.949    21.915
Torsion angles, period  3. refined             1292    14.776    15.000
Torsion angles, period  4. refined               63    19.705    15.000
Chiral centres: refined atoms                  1196     0.066     0.200
Planar groups: refined atoms                  10355     0.007     0.020
Planar groups: others                          2034     0.002     0.020
VDW repulsions: refined_atoms                  1756     0.214     0.200
VDW repulsions.others                          7890     0.190     0.200
VDW; torsion: refined_atoms                    4215     0.169     0.200
VDW; torsion.others                            3913     0.077     0.200
HBOND: refined_atoms                            491     0.151     0.200
HBOND.others                                      1     0.076     0.200
Metal-ion: refined_atoms                         12     0.138     0.200
VDW repulsions: symmetry: refined_atoms          21     0.196     0.200
VDW repulsions: symmetry: others                 47     0.165     0.200
HBOND: symmetry: refined_atoms                    7     0.135     0.200
M. chain bond B values: refined atoms          4328     3.611     5.045
M. chain bond B values: others                 4327     3.609     5.044
M. chain angle B values: refined atoms         5426     5.141     7.560
M. chain angle B values: others                5427     5.140     7.562
S. chain bond B values: refined atoms          4896     4.548     5.506
S. chain bond B values: others                 4897     4.548     5.506
S. chain angle B values: refined atoms         7255     6.268     8.189
S. chain angle B values: others                7256     6.268     8.189
Long range B values: refined atoms             9967     7.557    59.142
Long range B values: others                    9887     7.555    59.086
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0058, B  =    0.1912
Partial structure    1: scale =     0.3871, B  =   43.8414
Overall anisotropic scale factors
   B11 =  -1.12 B22 =  -1.23 B33 =   2.35 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.010    2334  99.72  2659.6  2675.2  0.19  0.19     116  2787.2  2790.8  0.24  0.21
 0.029    3971 100.00  2156.2  2334.5  0.15  0.14     226  2121.2  2259.0  0.21  0.19
 0.049    5128 100.00  2397.0  2412.5  0.12  0.11     264  2365.4  2454.4  0.20  0.18
 0.068    5989 100.00  2037.4  1841.2  0.15  0.14     325  2038.1  1814.4  0.20  0.18
 0.087    6795  99.99  1487.5  1262.2  0.19  0.18     344  1472.7  1250.2  0.26  0.24
 0.106    7446 100.00  1024.6   899.0  0.21  0.19     412  1068.0   938.6  0.27  0.25
 0.126    8097  99.99   663.2   657.5  0.22  0.20     442   660.2   680.2  0.33  0.31
 0.145    8694 100.00   402.6   509.1  0.44  0.43     441   387.5   499.9  0.50  0.48
 0.164    9107  98.15   280.6   405.1  0.65  0.65     467   281.5   416.1  0.68  0.67
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0101   1970   0.860    364   0.744   2334   0.842  0.913  0.9188  0.9379  0.7788  0.8988
  0.0293   3598   0.897    373   0.848   3971   0.893  0.890  0.9559  0.9695  0.9144  0.9610
  0.0485   4755   0.903    373   0.851   5128   0.899  0.964  0.9597  0.9718  0.9242  0.9654
  0.0678   5624   0.891    365   0.816   5989   0.886  1.062  0.9528  0.9664  0.9151  0.9612
  0.0870   6414   0.854    381   0.753   6795   0.849  1.110  0.9271  0.9505  0.8682  0.9470
  0.1063   7074   0.791    372   0.683   7446   0.786  1.054  0.8953  0.9224  0.8005  0.9236
  0.1255   7713   0.741    384   0.581   8097   0.733  0.899  0.8533  0.8818  0.7721  0.8897
  0.1448   8322   0.573    372   0.471   8694   0.568  0.539  0.6898  0.7464  0.5862  0.7461
  0.1640   8799   0.148    323   0.135   9122   0.147  0.120  0.2683  0.2913  0.5323  0.4889
 $$
Resolution limits                    =     47.354     2.400
Number of used reflections           =      57576
Percentage observed                  =    99.6679
Percentage of free reflections       =     5.0120
Overall R factor                     =     0.2001
Free R factor                        =     0.2625
Average Fourier shell correlation    =     0.8063
AverageFree Fourier shell correlation=     0.7835
Overall weighted R factor            =     0.1649
Free weighted R factor               =     0.2185
Overall weighted R2 factor           =     0.1742
Free weighted R2 factor              =     0.2232
Average correlation coefficient      =     0.8352
Overall correlation coefficient      =     0.9586
Free correlation coefficient         =     0.9254
Cruickshanks DPI for coordinate error=     0.3413
DPI based on free R factor           =     0.2607
Overall figure of merit              =     0.6820
ML based su of positional parameters =     0.2412
ML based su of thermal parameters    =    11.9115
-----------------------------------------------------------------------------
  Time in seconds: CPU =       195.44
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2015   0.2625   0.671      394272.   21306.9   0.0080  0.556   1.675  0.933   0.064
       1   0.2013   0.2621   0.681      392827.   21291.9   0.0087  0.599   1.704  0.944   0.068
       2   0.2004   0.2624   0.689      392687.   21289.2   0.0085  0.590   1.705  0.949   0.065
       3   0.2004   0.2625   0.690      392666.   21288.4   0.0084  0.585   1.704  0.948   0.066
       4   0.2002   0.2625   0.686      392728.   21291.2   0.0084  0.585   1.706  0.949   0.066
       5   0.2001   0.2625   0.690      392662.   21288.8   0.0085  0.589   1.710  0.951   0.066
       6   0.2001   0.2625   0.685      392741.   21291.7   0.0084  0.586   1.710  0.951   0.066
       7   0.2001   0.2625   0.682      392774.   21293.8   0.0084  0.587   1.711  0.951   0.066
       8   0.2001   0.2625   0.682      392798.   21294.5   0.0084  0.588   1.711  0.951   0.066
       9   0.2001   0.2625   0.682      392794.   21294.5   0.0084  0.588   1.711  0.952   0.066
      10   0.2001   0.2625   0.682      392789.   21294.3   0.0084  0.588   1.711  0.952   0.066
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2015   0.2001
             R free    0.2625   0.2625
     Rms BondLength    0.0080   0.0084
      Rms BondAngle    1.6748   1.7114
     Rms ChirVolume    0.0640   0.0662
 $$

 Refmac:  End of Refmac_5.8.0258   
Times: User:     269.6s System:    0.9s Elapsed:     4:31