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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: 11:46:59 


 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 2.70
  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_2-80A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - BO_from2-80A_R00_2-70A.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_2-70A.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       0.0152
  Refinement of individual isotropic Bfactors
  Refinement resln        :    47.3545  2.7000
  Estimated number of reflections :      56525
  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  2.7000

  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_2-80A.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 =      2.43
            ch:AAA  res: 465  HIS              --> 466  ASP
  INFO:     link is found (not be used) dist=   2.592 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=   2.772 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=   1.806 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=   2.061 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=   1.910 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=   3.136 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=   2.554 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=   1.680 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=   1.992 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=   1.803 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=   1.981 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=   2.834 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=   2.671 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=   2.040 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=   2.163 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=   2.191 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=   2.112 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 =     1.433 ideal_dist=     1.439
            ch:AAA  res: 472  ASN              at:ND2 .->AeA  res: 701  NAG              at:C1  .
  WARNING : link:NAG-ASN  is found dist =     1.452 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=   2.994 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 =     1.430 ideal_dist=     1.439
            ch:AeA  res: 701  NAG              at:O4  .->AfA  res: 702  NAG              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.430 ideal_dist=     1.439
            ch:AfA  res: 702  NAG              at:O4  .->AgA  res: 703  BMA              at:C1  .
  WARNING : link:ALPHA1-3 is found dist =     1.449 ideal_dist=     1.439
            ch:AgA  res: 703  BMA              at:O3  .->AhA  res: 704  MAN              at:C1  .
  WARNING : link:ALPHA1-6 is found dist =     1.464 ideal_dist=     1.439
            ch:AgA  res: 703  BMA              at:O6  .->AiA  res: 705  MAN              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.416 ideal_dist=     1.439
            ch:AjA  res: 711  NAG              at:O4  .->AkA  res: 712  NAG              at:C1  .
  WARNING : link:NAG-NA   is found dist =     2.453 ideal_dist=     2.430
            ch:AjA  res: 711  NAG              at:O6  .->AtA  res:1001  NA               at:NA  .
  WARNING : link:BETA1-4  is found dist =     1.438 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=   1.852 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=   2.198 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=   2.089 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=   1.888 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=   2.400 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=   2.659 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=   2.657 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=   1.652 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=   1.990 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=   1.934 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=   2.013 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=   1.992 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=   2.101 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=   2.391 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=   2.115 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 =     1.432 ideal_dist=     1.439
            ch:BBB  res: 472  ASN              at:ND2 .->BeB  res: 701  NAG              at:C1  .
  WARNING : link:NAG-ASN  is found dist =     1.430 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=   3.022 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=   2.954 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 =     1.422 ideal_dist=     1.439
            ch:BeB  res: 701  NAG              at:O4  .->BfB  res: 702  NAG              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.443 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 =     1.451 ideal_dist=     1.439
            ch:BiB  res: 711  NAG              at:O4  .->BjB  res: 712  NAG              at:C1  .
  WARNING : link:NAG-NA   is found dist =     2.433 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       2170
Number of   all  reflections      42864
--------------------------------------------------------------------------------
 Number of reflections in file      72569
 Number of reflections read          42864

   Current auto weighting coefficient =    9.2493343    

 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.=  56.54 id.= 109.47 dev= 52.930 sig.=  3.000
A    702 NAG H1    - A    702 NAG C2    mod.= 140.52 id.= 108.34 dev=-32.181 sig.=  3.000
A    702 NAG O4    - A    703 BMA H1    mod.=  56.87 id.= 109.47 dev= 52.603 sig.=  3.000
A    703 BMA H1    - A    703 BMA C2    mod.= 145.48 id.= 108.34 dev=-37.137 sig.=  3.000
A    703 BMA O3    - A    704 MAN H1    mod.=  52.25 id.= 109.47 dev= 57.221 sig.=  3.000
A    704 MAN H1    - A    704 MAN C2    mod.= 139.30 id.= 108.34 dev=-30.959 sig.=  3.000
A    711 NAG O4    - A    712 NAG H1    mod.=  57.77 id.= 109.47 dev= 51.697 sig.=  3.000
A    712 NAG O4    - A    713 BMA H1    mod.=  49.29 id.= 109.47 dev= 60.182 sig.=  3.000
A    713 BMA H1    - A    713 BMA C2    mod.= 141.23 id.= 108.34 dev=-32.894 sig.=  3.000
B    701 NAG O4    - B    702 NAG H1    mod.=  57.05 id.= 109.47 dev= 52.423 sig.=  3.000
B    702 NAG H1    - B    702 NAG C2    mod.= 143.50 id.= 108.34 dev=-35.160 sig.=  3.000
B    702 NAG O4    - B    703 BMA H1    mod.=  49.77 id.= 109.47 dev= 59.702 sig.=  3.000
B    703 BMA H1    - B    703 BMA C2    mod.= 141.00 id.= 108.34 dev=-32.665 sig.=  3.000
B    703 BMA O3    - B    704 MAN H1    mod.=  52.54 id.= 109.47 dev= 56.925 sig.=  3.000
B    704 MAN H1    - B    704 MAN C2    mod.= 139.89 id.= 108.34 dev=-31.554 sig.=  3.000
B    711 NAG O4    - B    712 NAG H1    mod.=  51.39 id.= 109.47 dev= 58.085 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.= 0.787 id.= 2.750 dev= -1.96 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.745 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  308  352
 Maximuum H,K,L                 :    50   76   85
 Minimum acceptable grid spacing:   134  203  226
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   216  308  352
 Maximuum H,K,L                 :    50   76   85
 Minimum acceptable grid spacing:   134  203  226
 Weight matrix   4.80000041E-02
 Actual weight    13.474351      is applied to the X-ray term
Norm of X_ray positional gradient                18.8
Norm of Geom. positional gradient                78.6
Norm of X_ray B-factor gradient                  27.1
Norm of Geom. B-factor gradient                  22.7
Product of X_ray and Geom posit. gradients     -0.172E+08
 Cosine of angle between them                      -0.223
Product of X_ray and Geom B-fact gradients     -0.906E+07
 Cosine of angle between them                      -0.846


Residuals: XRAY=     0.3962E+07 GEOM=     0.5497E+05 TOTAL=     0.4017E+07
 function value    4017098.8    

-------------------------------------------------------------------------------
             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     1.659     1.702
Bond angles  : others                         18398     2.756     1.594
Torsion angles, period  1. refined             1092     7.952     5.000
Torsion angles, period  2. refined              517    31.705    21.915
Torsion angles, period  3. refined             1292    15.121    15.000
Torsion angles, period  4. refined               63    19.963    15.000
Chiral centres: refined atoms                  1196     0.064     0.200
Planar groups: refined atoms                  10355     0.007     0.020
Planar groups: others                          2034     0.008     0.020
VDW repulsions: refined_atoms                  1807     0.210     0.200
VDW repulsions.others                          7841     0.221     0.200
VDW; torsion: refined_atoms                    4236     0.169     0.200
VDW; torsion.others                            3733     0.091     0.200
HBOND: refined_atoms                            515     0.154     0.200
HBOND.others                                      3     0.109     0.200
Metal-ion: refined_atoms                         14     0.118     0.200
VDW repulsions: symmetry: refined_atoms          21     0.204     0.200
VDW repulsions: symmetry: others                 45     0.186     0.200
HBOND: symmetry: refined_atoms                    5     0.186     0.200
M. chain bond B values: refined atoms          4328     2.702     4.234
M. chain bond B values: others                 4327     2.701     4.232
M. chain angle B values: refined atoms         5426     4.118     6.345
M. chain angle B values: others                5427     4.118     6.346
S. chain bond B values: refined atoms          4896     3.394     4.632
S. chain bond B values: others                 4897     3.393     4.632
S. chain angle B values: refined atoms         7255     4.917     6.898
S. chain angle B values: others                7256     4.917     6.899
Long range B values: refined atoms            10057     6.560    49.761
Long range B values: others                    9975     6.547    49.753
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0054, B  =    1.8612
Partial structure    1: scale =     0.3795, B  =   49.7038
Overall anisotropic scale factors
   B11 =  -1.23 B22 =  -1.67 B33 =   2.90 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.008    1667  99.60  3089.3  2871.7  0.20  0.20      79  3167.4  2865.3  0.25  0.22
 0.023    2823 100.00  2237.5  2344.4  0.14  0.13     160  2297.1  2378.8  0.22  0.20
 0.038    3606 100.00  2523.1  2614.7  0.12  0.11     189  2518.1  2640.0  0.19  0.17
 0.054    4228 100.00  2574.1  2537.4  0.12  0.11     225  2490.7  2496.7  0.20  0.18
 0.069    4787 100.00  2144.6  1998.3  0.14  0.12     254  2161.4  1989.8  0.19  0.17
 0.084    5216  99.98  1703.7  1536.2  0.16  0.14     290  1696.4  1546.8  0.22  0.20
 0.099    5732 100.00  1259.9  1177.1  0.18  0.16     286  1295.4  1198.3  0.28  0.25
 0.114    6103 100.00   920.6   946.0  0.21  0.17     339   924.4   947.3  0.31  0.26
 0.130    6517  99.99   657.3   788.8  0.36  0.32     346   652.2   821.3  0.42  0.37
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0080   1376   0.842    291   0.733   1667   0.823  0.991  0.9029  0.9331  0.7406  0.8952
  0.0232   2541   0.877    282   0.803   2823   0.870  0.920  0.9490  0.9608  0.8968  0.9556
  0.0384   3303   0.899    303   0.866   3606   0.896  0.939  0.9616  0.9723  0.9305  0.9672
  0.0536   3937   0.884    291   0.807   4228   0.879  0.977  0.9485  0.9661  0.9053  0.9654
  0.0688   4491   0.889    296   0.816   4787   0.884  1.031  0.9555  0.9662  0.9255  0.9619
  0.0840   4922   0.868    294   0.752   5216   0.861  1.056  0.9322  0.9544  0.8629  0.9513
  0.0992   5432   0.806    300   0.717   5732   0.802  0.997  0.8985  0.9298  0.8021  0.9296
  0.1144   5804   0.744    299   0.620   6103   0.738  0.887  0.8685  0.9002  0.8040  0.9101
  0.1296   6231   0.600    294   0.466   6525   0.594  0.665  0.7843  0.7892  0.7684  0.8052
 $$
Resolution limits                    =     47.354     2.700
Number of used reflections           =      40686
Percentage observed                  =    99.9487
Percentage of free reflections       =     5.0590
Overall R factor                     =     0.1640
Free R factor                        =     0.2365
Average Fourier shell correlation    =     0.9201
AverageFree Fourier shell correlation=     0.9014
Overall weighted R factor            =     0.1388
Free weighted R factor               =     0.2009
Overall weighted R2 factor           =     0.1586
Free weighted R2 factor              =     0.2150
Average correlation coefficient      =     0.9208
Overall correlation coefficient      =     0.9579
Free correlation coefficient         =     0.9127
Cruickshanks DPI for coordinate error=     0.8552
DPI based on free R factor           =     0.3142
Overall figure of merit              =     0.7982
ML based su of positional parameters =     0.2413
ML based su of thermal parameters    =    12.4165
-----------------------------------------------------------------------------
 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    294049.44       54973.547       4017098.8      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   4.80000041E-02
 Actual weight    12.016417      is applied to the X-ray term


 function value    3547645.5    

-------------------------------------------------------------------------------
             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 =     0.0054, B  =   -0.0626
Partial structure    1: scale =     0.3791, B  =   48.7209
Overall anisotropic scale factors
   B11 =  -1.21 B22 =  -1.67 B33 =   2.88 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1632
Free R factor                        =     0.2362
Average Fourier shell correlation    =     0.9309
AverageFree Fourier shell correlation=     0.9105
Average correlation coefficient      =     0.9245
Overall figure of merit              =     0.8194
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    292925.56       27730.063       3547645.5       4017098.8    


     CGMAT cycle number =      3

 Weight matrix   4.80000004E-02
 Actual weight    11.820968      is applied to the X-ray term


 function value    3485837.3    

-------------------------------------------------------------------------------
             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 =     0.0054, B  =    0.0897
Partial structure    1: scale =     0.3796, B  =   48.5485
Overall anisotropic scale factors
   B11 =  -1.20 B22 =  -1.67 B33 =   2.87 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1626
Free R factor                        =     0.2356
Average Fourier shell correlation    =     0.9328
AverageFree Fourier shell correlation=     0.9117
Average correlation coefficient      =     0.9272
Overall figure of merit              =     0.8224
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    292656.59       26352.910       3485837.3       3547645.5    


     CGMAT cycle number =      4

 Weight matrix   4.80000004E-02
 Actual weight    11.760046      is applied to the X-ray term


 function value    3466382.8    

-------------------------------------------------------------------------------
             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 =     0.0054, B  =    0.1161
Partial structure    1: scale =     0.3797, B  =   48.3596
Overall anisotropic scale factors
   B11 =  -1.19 B22 =  -1.68 B33 =   2.87 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1626
Free R factor                        =     0.2350
Average Fourier shell correlation    =     0.9332
AverageFree Fourier shell correlation=     0.9120
Average correlation coefficient      =     0.9283
Overall figure of merit              =     0.8229
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02
 fvalues    292542.34       26071.293       3466382.8       3485837.3    


     CGMAT cycle number =      5

 Weight matrix   4.80000004E-02
 Actual weight    11.759189      is applied to the X-ray term


 function value    3465645.8    

-------------------------------------------------------------------------------
             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 =     0.0054, B  =    0.1322
Partial structure    1: scale =     0.3798, B  =   48.2857
Overall anisotropic scale factors
   B11 =  -1.18 B22 =  -1.68 B33 =   2.86 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1626
Free R factor                        =     0.2348
Average Fourier shell correlation    =     0.9333
AverageFree Fourier shell correlation=     0.9120
Average correlation coefficient      =     0.9289
Overall figure of merit              =     0.8229
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03
 fvalues    292505.84       26014.211       3465645.8       3466382.8    


     CGMAT cycle number =      6

 Weight matrix   4.80000041E-02
 Actual weight    11.767811      is applied to the X-ray term


 function value    3467885.3    

-------------------------------------------------------------------------------
             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 =     0.0054, B  =    0.1524
Partial structure    1: scale =     0.3799, B  =   48.2776
Overall anisotropic scale factors
   B11 =  -1.18 B22 =  -1.68 B33 =   2.86 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1626
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9333
AverageFree Fourier shell correlation=     0.9120
Average correlation coefficient      =     0.9292
Overall figure of merit              =     0.8228
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Gamma decreased to   2.19674082E-03


 fvalues    292481.41       25952.033       3467381.3       3465645.8    
 fvalues    292481.41       25952.033       3467381.3       3467817.8    


     CGMAT cycle number =      7

 Weight matrix   4.79999967E-02
 Actual weight    11.777449      is applied to the X-ray term


 function value    3470423.3    

-------------------------------------------------------------------------------
             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 =     0.0054, B  =    0.1663
Partial structure    1: scale =     0.3799, B  =   48.2362
Overall anisotropic scale factors
   B11 =  -1.17 B22 =  -1.68 B33 =   2.86 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1625
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9334
AverageFree Fourier shell correlation=     0.9119
Average correlation coefficient      =     0.9294
Overall figure of merit              =     0.8228
-----------------------------------------------------------------------------
 Trying gamma equal   2.19674082E-03
 Not converging with gamma equal   2.19674082E-03
 Trying gamma equal   3.33133601E-02
 Gamma decreased to   2.70900354E-02


 fvalues    292467.38       25901.914       3470235.0       3467817.8    
 fvalues    292467.38       25901.914       3470235.0       3470421.5    


     CGMAT cycle number =      8

 Weight matrix   4.80000004E-02
 Actual weight    11.753582      is applied to the X-ray term


 function value    3463146.3    

-------------------------------------------------------------------------------
             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 =     0.0054, B  =    0.1646
Partial structure    1: scale =     0.3799, B  =   48.2288
Overall anisotropic scale factors
   B11 =  -1.17 B22 =  -1.69 B33 =   2.86 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1625
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9335
AverageFree Fourier shell correlation=     0.9121
Average correlation coefficient      =     0.9295
Overall figure of merit              =     0.8230
-----------------------------------------------------------------------------
 Trying gamma equal   2.70900354E-02
 Gamma decreased to   2.14324687E-02
 fvalues    292444.00       25881.699       3463146.3       3470421.5    


     CGMAT cycle number =      9

 Weight matrix   4.79999967E-02
 Actual weight    11.764475      is applied to the X-ray term


 function value    3466474.5    

-------------------------------------------------------------------------------
             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 =     0.0054, B  =    0.1105
Partial structure    1: scale =     0.3799, B  =   48.3140
Overall anisotropic scale factors
   B11 =  -1.17 B22 =  -1.69 B33 =   2.86 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1624
Free R factor                        =     0.2349
Average Fourier shell correlation    =     0.9335
AverageFree Fourier shell correlation=     0.9121
Average correlation coefficient      =     0.9296
Overall figure of merit              =     0.8229
-----------------------------------------------------------------------------
 Trying gamma equal   2.14324687E-02
 Gamma decreased to   1.62892267E-02


 fvalues    292456.41       25846.668       3466439.3       3463146.3    
 fvalues    292456.41       25846.668       3466439.3       3466442.8    


     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.= 0.892 id.= 2.750 dev= -1.86 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.789 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  308  352
 Maximuum H,K,L                 :    50   76   85
 Minimum acceptable grid spacing:   134  203  226
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   216  308  352
 Maximuum H,K,L                 :    50   76   85
 Minimum acceptable grid spacing:   134  203  226
 Weight matrix   4.80000004E-02
 Actual weight    11.784975      is applied to the X-ray term
Norm of X_ray positional gradient                17.2
Norm of Geom. positional gradient                17.3
Norm of X_ray B-factor gradient                  24.2
Norm of Geom. B-factor gradient                  23.8
Product of X_ray and Geom posit. gradients     -0.155E+08
 Cosine of angle between them                      -0.996
Product of X_ray and Geom B-fact gradients     -0.998E+07
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.3447E+07 GEOM=     0.2585E+05 TOTAL=     0.3473E+07
 function value    3472653.5    

-------------------------------------------------------------------------------
             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
Bond angles  : refined atoms                  12685     1.647     1.702
Bond angles  : others                         18398     1.220     1.594
Torsion angles, period  1. refined             1092     7.976     5.000
Torsion angles, period  2. refined              517    31.911    21.915
Torsion angles, period  3. refined             1292    14.930    15.000
Torsion angles, period  4. refined               63    19.874    15.000
Chiral centres: refined atoms                  1196     0.064     0.200
Planar groups: refined atoms                  10355     0.006     0.020
Planar groups: others                          2034     0.001     0.020
VDW repulsions: refined_atoms                  1788     0.211     0.200
VDW repulsions.others                          7910     0.186     0.200
VDW; torsion: refined_atoms                    4228     0.169     0.200
VDW; torsion.others                            3980     0.076     0.200
HBOND: refined_atoms                            480     0.155     0.200
HBOND.others                                      1     0.117     0.200
Metal-ion: refined_atoms                         13     0.124     0.200
VDW repulsions: symmetry: refined_atoms          20     0.199     0.200
VDW repulsions: symmetry: others                 42     0.167     0.200
HBOND: symmetry: refined_atoms                    7     0.154     0.200
M. chain bond B values: refined atoms          4328     2.866     4.421
M. chain bond B values: others                 4327     2.864     4.420
M. chain angle B values: refined atoms         5426     4.313     6.626
M. chain angle B values: others                5427     4.313     6.627
S. chain bond B values: refined atoms          4896     3.635     4.850
S. chain bond B values: others                 4897     3.635     4.850
S. chain angle B values: refined atoms         7255     5.208     7.219
S. chain angle B values: others                7256     5.208     7.220
Long range B values: refined atoms            10001     6.813    51.913
Long range B values: others                    9923     6.797    51.892
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0054, B  =    0.1163
Partial structure    1: scale =     0.3799, B  =   48.3537
Overall anisotropic scale factors
   B11 =  -1.17 B22 =  -1.69 B33 =   2.86 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.008    1667  99.60  3087.9  2864.4  0.20  0.20      79  3165.9  2840.6  0.25  0.22
 0.023    2823 100.00  2236.4  2340.9  0.14  0.13     160  2296.0  2375.5  0.21  0.20
 0.038    3606 100.00  2521.9  2617.8  0.12  0.11     189  2516.9  2636.8  0.18  0.16
 0.054    4228 100.00  2572.9  2544.5  0.12  0.11     225  2489.5  2500.5  0.21  0.19
 0.069    4787 100.00  2143.6  1997.7  0.14  0.12     254  2160.4  2000.8  0.19  0.17
 0.084    5216  99.98  1702.9  1532.6  0.16  0.15     290  1695.6  1545.0  0.23  0.20
 0.099    5732 100.00  1259.3  1174.6  0.18  0.16     286  1294.7  1193.8  0.27  0.24
 0.114    6103 100.00   920.1   940.2  0.21  0.18     339   924.0   944.8  0.31  0.26
 0.130    6517  99.99   657.0   778.7  0.32  0.28     346   651.9   816.2  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0080   1376   0.845    291   0.733   1667   0.825  0.991  0.9045  0.9331  0.7444  0.8926
  0.0232   2541   0.889    282   0.816   2823   0.882  0.920  0.9524  0.9639  0.8979  0.9544
  0.0384   3303   0.914    303   0.882   3606   0.912  0.939  0.9664  0.9761  0.9358  0.9688
  0.0536   3937   0.892    291   0.818   4228   0.887  0.977  0.9512  0.9681  0.9066  0.9646
  0.0688   4491   0.895    296   0.825   4787   0.891  1.031  0.9573  0.9682  0.9253  0.9625
  0.0840   4922   0.870    294   0.758   5216   0.864  1.056  0.9328  0.9546  0.8613  0.9494
  0.0992   5432   0.803    300   0.712   5732   0.798  0.997  0.8967  0.9278  0.8010  0.9270
  0.1144   5804   0.742    299   0.620   6103   0.736  0.887  0.8653  0.8970  0.7981  0.9050
  0.1296   6231   0.733    294   0.576   6525   0.726  0.740  0.8475  0.8712  0.7752  0.8695
 $$
Resolution limits                    =     47.354     2.700
Number of used reflections           =      40686
Percentage observed                  =    99.9487
Percentage of free reflections       =     5.0590
Overall R factor                     =     0.1625
Free R factor                        =     0.2350
Average Fourier shell correlation    =     0.9335
AverageFree Fourier shell correlation=     0.9120
Overall weighted R factor            =     0.1387
Free weighted R factor               =     0.1994
Overall weighted R2 factor           =     0.1589
Free weighted R2 factor              =     0.2132
Average correlation coefficient      =     0.9296
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9138
Cruickshanks DPI for coordinate error=     0.8471
DPI based on free R factor           =     0.3122
Overall figure of merit              =     0.8228
ML based su of positional parameters =     0.2255
ML based su of thermal parameters    =    11.5010
-----------------------------------------------------------------------------
 Trying gamma equal   1.62892267E-02
 Gamma decreased to   1.16135515E-02


 fvalues    292472.66       25849.535       3472650.8       3466442.8    

 fvalues    292472.66       25849.535       3472687.3       3472632.5    
 fvalues    292472.66       25849.535       3472687.3       3472632.5    

    ****                              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.= 0.893 id.= 2.750 dev= -1.86 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.789 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_2-70A.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     1.647     1.702
Bond angles  : others                         18398     1.219     1.594
Torsion angles, period  1. refined             1092     7.978     5.000
Torsion angles, period  2. refined              517    31.913    21.915
Torsion angles, period  3. refined             1292    14.924    15.000
Torsion angles, period  4. refined               63    19.860    15.000
Chiral centres: refined atoms                  1196     0.064     0.200
Planar groups: refined atoms                  10355     0.006     0.020
Planar groups: others                          2034     0.001     0.020
VDW repulsions: refined_atoms                  1786     0.211     0.200
VDW repulsions.others                          7912     0.186     0.200
VDW; torsion: refined_atoms                    4228     0.169     0.200
VDW; torsion.others                            3986     0.076     0.200
HBOND: refined_atoms                            482     0.155     0.200
HBOND.others                                      1     0.119     0.200
Metal-ion: refined_atoms                         13     0.124     0.200
VDW repulsions: symmetry: refined_atoms          20     0.199     0.200
VDW repulsions: symmetry: others                 42     0.167     0.200
HBOND: symmetry: refined_atoms                    7     0.154     0.200
M. chain bond B values: refined atoms          4328     2.866     4.421
M. chain bond B values: others                 4327     2.864     4.420
M. chain angle B values: refined atoms         5426     4.313     6.626
M. chain angle B values: others                5427     4.314     6.627
S. chain bond B values: refined atoms          4896     3.636     4.850
S. chain bond B values: others                 4897     3.636     4.850
S. chain angle B values: refined atoms         7255     5.210     7.219
S. chain angle B values: others                7256     5.209     7.220
Long range B values: refined atoms            10001     6.826    51.916
Long range B values: others                    9923     6.810    51.896
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0054, B  =    0.1059
Partial structure    1: scale =     0.3798, B  =   48.3634
Overall anisotropic scale factors
   B11 =  -1.17 B22 =  -1.69 B33 =   2.86 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.008    1667  99.60  3087.8  2864.8  0.20  0.20      79  3165.9  2840.8  0.25  0.22
 0.023    2823 100.00  2236.4  2340.9  0.14  0.13     160  2296.0  2376.1  0.21  0.20
 0.038    3606 100.00  2521.9  2618.2  0.12  0.11     189  2516.9  2637.0  0.18  0.16
 0.054    4228 100.00  2572.9  2545.0  0.12  0.11     225  2489.5  2500.8  0.21  0.19
 0.069    4787 100.00  2143.5  1998.0  0.14  0.12     254  2160.3  2001.3  0.19  0.17
 0.084    5216  99.98  1702.9  1533.1  0.16  0.15     290  1695.6  1545.7  0.23  0.20
 0.099    5732 100.00  1259.3  1175.0  0.18  0.16     286  1294.7  1194.5  0.27  0.24
 0.114    6103 100.00   920.1   940.4  0.21  0.18     339   923.9   945.2  0.31  0.26
 0.130    6517  99.99   657.0   779.0  0.32  0.29     346   651.9   816.5  0.41  0.36
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0080   1376   0.845    291   0.733   1667   0.825  0.991  0.9045  0.9331  0.7441  0.8925
  0.0232   2541   0.890    282   0.816   2823   0.882  0.920  0.9526  0.9640  0.8983  0.9544
  0.0384   3303   0.914    303   0.882   3606   0.912  0.939  0.9664  0.9761  0.9360  0.9688
  0.0536   3937   0.892    291   0.818   4228   0.887  0.977  0.9512  0.9681  0.9065  0.9646
  0.0688   4491   0.895    296   0.825   4787   0.891  1.031  0.9573  0.9681  0.9253  0.9625
  0.0840   4922   0.870    294   0.758   5216   0.864  1.056  0.9329  0.9546  0.8613  0.9494
  0.0992   5432   0.803    300   0.713   5732   0.798  0.997  0.8968  0.9279  0.8011  0.9269
  0.1144   5804   0.742    299   0.620   6103   0.736  0.887  0.8654  0.8971  0.7980  0.9050
  0.1296   6231   0.733    294   0.576   6525   0.726  0.740  0.8475  0.8713  0.7755  0.8698
 $$
Resolution limits                    =     47.354     2.700
Number of used reflections           =      40686
Percentage observed                  =    99.9487
Percentage of free reflections       =     5.0590
Overall R factor                     =     0.1625
Free R factor                        =     0.2350
Average Fourier shell correlation    =     0.9335
AverageFree Fourier shell correlation=     0.9120
Overall weighted R factor            =     0.1387
Free weighted R factor               =     0.1993
Overall weighted R2 factor           =     0.1589
Free weighted R2 factor              =     0.2131
Average correlation coefficient      =     0.9297
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9139
Cruickshanks DPI for coordinate error=     0.8472
DPI based on free R factor           =     0.3122
Overall figure of merit              =     0.8228
ML based su of positional parameters =     0.2255
ML based su of thermal parameters    =    11.5010
-----------------------------------------------------------------------------
  Time in seconds: CPU =       158.66
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1640   0.2365   0.798      294049.   16147.0   0.0078  0.545   1.659  0.928   0.064
       1   0.1632   0.2362   0.819      292926.   16129.1   0.0080  0.552   1.662  0.924   0.067
       2   0.1626   0.2356   0.822      292657.   16123.6   0.0078  0.541   1.649  0.921   0.064
       3   0.1626   0.2350   0.823      292542.   16118.0   0.0077  0.538   1.646  0.920   0.064
       4   0.1626   0.2348   0.823      292506.   16117.8   0.0077  0.537   1.646  0.920   0.064
       5   0.1626   0.2349   0.823      292487.   16117.6   0.0077  0.536   1.646  0.920   0.064
       6   0.1625   0.2349   0.823      292468.   16117.3   0.0077  0.536   1.647  0.920   0.064
       7   0.1625   0.2349   0.823      292444.   16116.7   0.0077  0.535   1.647  0.920   0.064
       8   0.1624   0.2349   0.823      292459.   16118.9   0.0077  0.534   1.647  0.920   0.064
       9   0.1625   0.2350   0.823      292474.   16120.6   0.0076  0.534   1.647  0.920   0.064
      10   0.1625   0.2350   0.823      292468.   16120.5   0.0076  0.534   1.647  0.920   0.064
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1640   0.1625
             R free    0.2365   0.2350
     Rms BondLength    0.0078   0.0076
      Rms BondAngle    1.6594   1.6474
     Rms ChirVolume    0.0644   0.0637
 $$

 Refmac:  End of Refmac_5.8.0258   
Times: User:     231.7s System:    0.9s Elapsed:     3:53