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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: 12:30:00 


 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 2.30
  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_2-40A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - BO_from2-80A_R00_2-30A.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_2-30A.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       0.0210
  Refinement of individual isotropic Bfactors
  Refinement resln        :    47.3545  2.3000
  Estimated number of reflections :      90973
  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  2.3000

  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_2-40A.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 =      2.31
            ch:AAA  res: 465  HIS              --> 466  ASP
  INFO:     link is found (not be used) dist=   2.523 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=   2.910 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=   1.833 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=   2.033 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=   1.973 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=   1.909 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=   3.108 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=   2.550 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=   1.706 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=   1.950 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=   1.762 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=   2.909 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=   2.697 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=   2.052 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=   2.184 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=   2.200 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=   2.150 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 =     1.430 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=   3.043 ideal_dist=   2.305
            ch:AAA  res: 525  GLU              at:OE1 .->ch:AtA  res:1001  NA               at:NA  .
  WARNING : link:BETA1-4  is found dist =     1.427 ideal_dist=     1.439
            ch:AeA  res: 701  NAG              at:O4  .->AfA  res: 702  NAG              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.431 ideal_dist=     1.439
            ch:AfA  res: 702  NAG              at:O4  .->AgA  res: 703  BMA              at:C1  .
  WARNING : link:ALPHA1-3 is found dist =     1.452 ideal_dist=     1.439
            ch:AgA  res: 703  BMA              at:O3  .->AhA  res: 704  MAN              at:C1  .
  WARNING : link:ALPHA1-6 is found dist =     1.461 ideal_dist=     1.439
            ch:AgA  res: 703  BMA              at:O6  .->AiA  res: 705  MAN              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.425 ideal_dist=     1.439
            ch:AjA  res: 711  NAG              at:O4  .->AkA  res: 712  NAG              at:C1  .
  WARNING : link:NAG-NA   is found dist =     2.457 ideal_dist=     2.430
            ch:AjA  res: 711  NAG              at:O6  .->AtA  res:1001  NA               at:NA  .
  WARNING : link:BETA1-4  is found dist =     1.444 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=   1.867 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=   2.168 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=   2.146 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=   1.916 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=   2.448 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=   2.565 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=   2.668 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=   1.646 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=   2.025 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=   1.849 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=   2.048 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=   1.956 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=   2.141 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=   2.352 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=   2.101 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 =     1.434 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=   3.019 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=   2.942 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 =     1.421 ideal_dist=     1.439
            ch:BeB  res: 701  NAG              at:O4  .->BfB  res: 702  NAG              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.444 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 =     1.456 ideal_dist=     1.439
            ch:BiB  res: 711  NAG              at:O4  .->BjB  res: 712  NAG              at:C1  .
  WARNING : link:NAG-NA   is found dist =     2.440 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       3466
Number of   all  reflections      69005
--------------------------------------------------------------------------------
 Number of reflections in file      72569
 Number of reflections read          69005

   Current auto weighting coefficient =    8.2494106    

 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.=  57.55 id.= 109.47 dev= 51.916 sig.=  3.000
A    702 NAG H1    - A    702 NAG C2    mod.= 139.52 id.= 108.34 dev=-31.185 sig.=  3.000
A    702 NAG O4    - A    703 BMA H1    mod.=  55.61 id.= 109.47 dev= 53.859 sig.=  3.000
A    703 BMA H1    - A    703 BMA C2    mod.= 145.94 id.= 108.34 dev=-37.597 sig.=  3.000
A    703 BMA O3    - A    704 MAN H1    mod.=  52.39 id.= 109.47 dev= 57.078 sig.=  3.000
A    704 MAN H1    - A    704 MAN C2    mod.= 139.00 id.= 108.34 dev=-30.659 sig.=  3.000
A    711 NAG O4    - A    712 NAG H1    mod.=  55.98 id.= 109.47 dev= 53.495 sig.=  3.000
A    712 NAG H1    - A    712 NAG C2    mod.= 139.26 id.= 108.34 dev=-30.920 sig.=  3.000
A    712 NAG O4    - A    713 BMA H1    mod.=  47.67 id.= 109.47 dev= 61.797 sig.=  3.000
A    713 BMA H1    - A    713 BMA C2    mod.= 142.90 id.= 108.34 dev=-34.557 sig.=  3.000
B    701 NAG O4    - B    702 NAG H1    mod.=  57.59 id.= 109.47 dev= 51.876 sig.=  3.000
B    702 NAG H1    - B    702 NAG C2    mod.= 142.26 id.= 108.34 dev=-33.915 sig.=  3.000
B    702 NAG O4    - B    703 BMA H1    mod.=  49.79 id.= 109.47 dev= 59.677 sig.=  3.000
B    703 BMA H1    - B    703 BMA C2    mod.= 141.20 id.= 108.34 dev=-32.860 sig.=  3.000
B    703 BMA O3    - B    704 MAN H1    mod.=  52.50 id.= 109.47 dev= 56.972 sig.=  3.000
B    704 MAN H1    - B    704 MAN C2    mod.= 139.06 id.= 108.34 dev=-30.717 sig.=  3.000
B    711 NAG O4    - B    712 NAG H1    mod.=  51.05 id.= 109.47 dev= 58.419 sig.=  3.000
B    712 NAG H1    - B    712 NAG C2    mod.= 138.57 id.= 108.34 dev=-30.227 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.= 0.857 id.= 2.750 dev= -1.89 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.729 id.= 2.750 dev= -2.02 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        :   224  336  384
 Maximuum H,K,L                 :    59   89   99
 Minimum acceptable grid spacing:   148  224  250
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   224  336  384
 Maximuum H,K,L                 :    59   89   99
 Minimum acceptable grid spacing:   148  224  250
 Weight matrix   4.80000004E-02
 Actual weight    17.891365      is applied to the X-ray term
Norm of X_ray positional gradient                23.5
Norm of Geom. positional gradient                79.1
Norm of X_ray B-factor gradient                  31.0
Norm of Geom. B-factor gradient                  24.1
Product of X_ray and Geom posit. gradients     -0.254E+08
 Cosine of angle between them                      -0.262
Product of X_ray and Geom B-fact gradients     -0.123E+08
 Cosine of angle between them                      -0.941


Residuals: XRAY=     0.7751E+07 GEOM=     0.5720E+05 TOTAL=     0.7808E+07
 function value    7808343.0    

-------------------------------------------------------------------------------
             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     1.712     1.702
Bond angles  : others                         18398     2.765     1.594
Torsion angles, period  1. refined             1092     8.067     5.000
Torsion angles, period  2. refined              517    31.950    21.915
Torsion angles, period  3. refined             1292    14.777    15.000
Torsion angles, period  4. refined               63    19.713    15.000
Chiral centres: refined atoms                  1196     0.066     0.200
Planar groups: refined atoms                  10355     0.007     0.020
Planar groups: others                          2034     0.010     0.020
VDW repulsions: refined_atoms                  1758     0.214     0.200
VDW repulsions.others                          7813     0.220     0.200
VDW; torsion: refined_atoms                    4219     0.169     0.200
VDW; torsion.others                            3718     0.091     0.200
HBOND: refined_atoms                            491     0.151     0.200
HBOND.others                                      2     0.120     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                 48     0.182     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     5.141     7.562
S. chain bond B values: refined atoms          4896     4.548     5.506
S. chain bond B values: others                 4897     4.547     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             9973     7.558    59.163
Long range B values: others                    9893     7.556    59.106
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0059, B  =    1.8798
Partial structure    1: scale =     0.3887, B  =   42.2554
Overall anisotropic scale factors
   B11 =  -1.05 B22 =  -1.17 B33 =   2.22 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.011    2630  99.75  2543.9  2621.6  0.20  0.19     128  2661.1  2710.4  0.24  0.21
 0.032    4522 100.00  2152.6  2329.0  0.15  0.14     256  2093.8  2241.1  0.21  0.19
 0.053    5791 100.00  2337.4  2281.5  0.12  0.11     305  2337.1  2347.0  0.19  0.18
 0.074    6816  99.99  1806.2  1579.6  0.17  0.16     361  1790.8  1545.8  0.23  0.20
 0.095    7713 100.00  1259.8  1047.0  0.21  0.20     397  1273.2  1064.2  0.27  0.25
 0.116    8469 100.00   812.0   726.6  0.21  0.20     460   856.2   766.0  0.30  0.29
 0.137    9183  99.99   492.8   536.9  0.29  0.28     496   473.6   531.8  0.37  0.35
 0.158    9844  99.33   303.9   406.7  0.55  0.55     490   308.0   422.1  0.59  0.58
 0.179    9522  90.96   230.1   320.1  0.64  0.64     517   227.5   311.2  0.63  0.64
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0109   2236   0.846    394   0.740   2630   0.830  0.890  0.9163  0.9359  0.7884  0.9012
  0.0319   4113   0.882    409   0.837   4522   0.878  0.893  0.9520  0.9663  0.9156  0.9630
  0.0528   5391   0.894    400   0.830   5791   0.890  0.990  0.9574  0.9689  0.9172  0.9624
  0.0738   6407   0.869    409   0.786   6816   0.864  1.093  0.9421  0.9577  0.9085  0.9566
  0.0947   7302   0.798    411   0.691   7713   0.793  1.115  0.9017  0.9295  0.8239  0.9378
  0.1157   8058   0.750    411   0.620   8469   0.743  1.014  0.8778  0.9011  0.8052  0.9111
  0.1367   8769   0.637    414   0.509   9183   0.631  0.724  0.7790  0.8225  0.6955  0.8328
  0.1576   9459   0.282    385   0.235   9844   0.280  0.244  0.4176  0.4487  0.5280  0.5748
  0.1786   9323   0.059    220   0.041   9543   0.058  0.042  0.0673  0.0703  0.3174  0.3117
 $$
Resolution limits                    =     47.354     2.300
Number of used reflections           =      64511
Percentage observed                  =    98.4135
Percentage of free reflections       =     5.0233
Overall R factor                     =     0.2104
Free R factor                        =     0.2695
Average Fourier shell correlation    =     0.7194
AverageFree Fourier shell correlation=     0.6978
Overall weighted R factor            =     0.1742
Free weighted R factor               =     0.2261
Overall weighted R2 factor           =     0.1798
Free weighted R2 factor              =     0.2278
Average correlation coefficient      =     0.7759
Overall correlation coefficient      =     0.9592
Free correlation coefficient         =     0.9287
Cruickshanks DPI for coordinate error=     0.2967
DPI based on free R factor           =     0.2434
Overall figure of merit              =     0.6001
ML based su of positional parameters =     0.2781
ML based su of thermal parameters    =    13.6972
-----------------------------------------------------------------------------
 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    433233.78       57199.727       7808343.0      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   4.80000004E-02
 Actual weight    15.359879      is applied to the X-ray term


 function value    6658184.0    

-------------------------------------------------------------------------------
             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 =     0.0059, B  =    0.0067
Partial structure    1: scale =     0.3882, B  =   41.4551
Overall anisotropic scale factors
   B11 =  -1.02 B22 =  -1.15 B33 =   2.16 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2107
Free R factor                        =     0.2696
Average Fourier shell correlation    =     0.7250
AverageFree Fourier shell correlation=     0.7036
Average correlation coefficient      =     0.7761
Overall figure of merit              =     0.6130
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    431429.56       31478.625       6658184.0       7808343.0    


     CGMAT cycle number =      3

 Weight matrix   4.80000041E-02
 Actual weight    15.345380      is applied to the X-ray term


 function value    6651261.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7918     0.005     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0059, B  =    0.2783
Partial structure    1: scale =     0.3884, B  =   40.8194
Overall anisotropic scale factors
   B11 =  -1.00 B22 =  -1.13 B33 =   2.14 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2100
Free R factor                        =     0.2699
Average Fourier shell correlation    =     0.7253
AverageFree Fourier shell correlation=     0.7039
Average correlation coefficient      =     0.7758
Overall figure of merit              =     0.6143
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    431472.50       30151.820       6651261.5       6658184.0    


     CGMAT cycle number =      4

 Weight matrix   4.80000004E-02
 Actual weight    15.318084      is applied to the X-ray term


 function value    6638188.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7918     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0059, B  =    0.3030
Partial structure    1: scale =     0.3883, B  =   40.6637
Overall anisotropic scale factors
   B11 =  -0.99 B22 =  -1.13 B33 =   2.12 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2100
Free R factor                        =     0.2702
Average Fourier shell correlation    =     0.7255
AverageFree Fourier shell correlation=     0.7040
Average correlation coefficient      =     0.7758
Overall figure of merit              =     0.6145
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02
 fvalues    431395.03       30042.855       6638188.0       6651261.5    


     CGMAT cycle number =      5

 Weight matrix   4.80000004E-02
 Actual weight    15.367706      is applied to the X-ray term


 function value    6659824.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7918     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0059, B  =    0.2817
Partial structure    1: scale =     0.3882, B  =   40.5999
Overall anisotropic scale factors
   B11 =  -0.99 B22 =  -1.12 B33 =   2.11 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2099
Free R factor                        =     0.2701
Average Fourier shell correlation    =     0.7254
AverageFree Fourier shell correlation=     0.7039
Average correlation coefficient      =     0.7757
Overall figure of merit              =     0.6143
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03


 fvalues    431411.59       30039.293       6659741.5       6638188.0    
 fvalues    431411.59       30039.293       6659741.5       6659846.0    


     CGMAT cycle number =      6

 Weight matrix   4.80000004E-02
 Actual weight    15.397670      is applied to the X-ray term


 function value    6673081.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7918     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0059, B  =    0.3150
Partial structure    1: scale =     0.3881, B  =   40.5338
Overall anisotropic scale factors
   B11 =  -0.98 B22 =  -1.12 B33 =   2.10 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2099
Free R factor                        =     0.2703
Average Fourier shell correlation    =     0.7254
AverageFree Fourier shell correlation=     0.7038
Average correlation coefficient      =     0.7757
Overall figure of merit              =     0.6142
-----------------------------------------------------------------------------
 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    431427.41       30106.895       6672730.5       6659846.0    
 fvalues    431427.41       30106.895       6672730.5       6673083.5    


     CGMAT cycle number =      7

 Weight matrix   4.80000041E-02
 Actual weight    15.390503      is applied to the X-ray term


 function value    6669869.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7918     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0059, B  =    0.3047
Partial structure    1: scale =     0.3880, B  =   40.4921
Overall anisotropic scale factors
   B11 =  -0.98 B22 =  -1.11 B33 =   2.10 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2099
Free R factor                        =     0.2703
Average Fourier shell correlation    =     0.7254
AverageFree Fourier shell correlation=     0.7039
Average correlation coefficient      =     0.7757
Overall figure of merit              =     0.6143
-----------------------------------------------------------------------------
 Trying gamma equal   3.60990353E-02
 Gamma decreased to   2.98757106E-02
 fvalues    431418.19       30126.088       6669869.0       6673083.5    


     CGMAT cycle number =      8

 Weight matrix   4.80000004E-02
 Actual weight    15.405567      is applied to the X-ray term


 function value    6676507.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7918     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0059, B  =    0.3028
Partial structure    1: scale =     0.3880, B  =   40.5475
Overall anisotropic scale factors
   B11 =  -0.98 B22 =  -1.11 B33 =   2.09 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2099
Free R factor                        =     0.2705
Average Fourier shell correlation    =     0.7254
AverageFree Fourier shell correlation=     0.7038
Average correlation coefficient      =     0.7757
Overall figure of merit              =     0.6142
-----------------------------------------------------------------------------
 Trying gamma equal   2.98757106E-02
 Gamma decreased to   2.42181439E-02


 fvalues    431427.97       30146.426       6676765.5       6669869.0    

 fvalues    431427.97       30146.426       6676523.0       6676539.0    
 fvalues    431427.97       30146.426       6676523.0       6676539.0    


     CGMAT cycle number =      9

 Weight matrix   4.80000004E-02
 Actual weight    15.413110      is applied to the X-ray term


 function value    6679847.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7918     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0059, B  =    0.2992
Partial structure    1: scale =     0.3880, B  =   40.5642
Overall anisotropic scale factors
   B11 =  -0.98 B22 =  -1.11 B33 =   2.09 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2099
Free R factor                        =     0.2706
Average Fourier shell correlation    =     0.7254
AverageFree Fourier shell correlation=     0.7038
Average correlation coefficient      =     0.7757
Overall figure of merit              =     0.6142
-----------------------------------------------------------------------------
 Trying gamma equal   2.42181439E-02
 Gamma decreased to   1.90749019E-02


 fvalues    431430.66       30153.582       6679759.5       6676539.0    
 fvalues    431430.66       30153.582       6679759.5       6679841.5    


     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.= 0.907 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.= 0.756 id.= 2.750 dev= -1.99 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        :   224  336  384
 Maximuum H,K,L                 :    59   89   99
 Minimum acceptable grid spacing:   148  224  250
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   224  336  384
 Maximuum H,K,L                 :    59   89   99
 Minimum acceptable grid spacing:   148  224  250
 Weight matrix   4.80000041E-02
 Actual weight    15.431353      is applied to the X-ray term
Norm of X_ray positional gradient                21.6
Norm of Geom. positional gradient                21.6
Norm of X_ray B-factor gradient                  28.2
Norm of Geom. B-factor gradient                  26.8
Product of X_ray and Geom posit. gradients     -0.243E+08
 Cosine of angle between them                      -0.998
Product of X_ray and Geom B-fact gradients     -0.130E+08
 Cosine of angle between them                      -0.987


Residuals: XRAY=     0.6658E+07 GEOM=     0.3016E+05 TOTAL=     0.6688E+07
 function value    6688031.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7918     0.001     0.017
Bond angles  : refined atoms                  12685     1.782     1.702
Bond angles  : others                         18398     1.254     1.594
Torsion angles, period  1. refined             1092     8.172     5.000
Torsion angles, period  2. refined              517    32.097    21.915
Torsion angles, period  3. refined             1292    14.943    15.000
Torsion angles, period  4. refined               63    19.956    15.000
Chiral centres: refined atoms                  1196     0.069     0.200
Planar groups: refined atoms                  10355     0.008     0.020
Planar groups: others                          2034     0.002     0.020
VDW repulsions: refined_atoms                  1772     0.215     0.200
VDW repulsions.others                          7899     0.191     0.200
VDW; torsion: refined_atoms                    4222     0.170     0.200
VDW; torsion.others                            3957     0.078     0.200
HBOND: refined_atoms                            486     0.154     0.200
HBOND.others                                      2     0.047     0.200
Metal-ion: refined_atoms                         12     0.139     0.200
VDW repulsions: symmetry: refined_atoms          18     0.210     0.200
VDW repulsions: symmetry: others                 50     0.161     0.200
HBOND: symmetry: refined_atoms                    6     0.136     0.200
M. chain bond B values: refined atoms          4328     4.001     5.210
M. chain bond B values: others                 4327     3.999     5.209
M. chain angle B values: refined atoms         5426     5.590     7.807
M. chain angle B values: others                5427     5.590     7.809
S. chain bond B values: refined atoms          4896     5.050     5.686
S. chain bond B values: others                 4897     5.050     5.687
S. chain angle B values: refined atoms         7255     6.829     8.454
S. chain angle B values: others                7256     6.828     8.454
Long range B values: refined atoms             9982     7.994    61.071
Long range B values: others                    9898     7.994    61.007
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0059, B  =    0.2980
Partial structure    1: scale =     0.3881, B  =   40.6031
Overall anisotropic scale factors
   B11 =  -0.98 B22 =  -1.11 B33 =   2.09 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.011    2630  99.75  2544.3  2623.8  0.20  0.19     128  2661.4  2713.9  0.24  0.21
 0.032    4522 100.00  2152.9  2329.6  0.15  0.14     256  2094.1  2241.6  0.21  0.20
 0.053    5791 100.00  2337.8  2283.3  0.12  0.11     305  2337.5  2346.3  0.19  0.18
 0.074    6816  99.99  1806.5  1579.0  0.17  0.16     361  1791.0  1546.4  0.23  0.21
 0.095    7713 100.00  1259.9  1045.4  0.22  0.20     397  1273.4  1059.7  0.27  0.26
 0.116    8469 100.00   812.1   726.1  0.21  0.20     460   856.4   764.5  0.30  0.29
 0.137    9183  99.99   492.9   538.6  0.29  0.28     496   473.7   531.5  0.37  0.36
 0.158    9844  99.33   304.0   407.6  0.56  0.55     490   308.1   424.1  0.59  0.58
 0.179    9522  90.96   230.1   320.5  0.63  0.63     517   227.5   311.3  0.63  0.64
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0109   2236   0.862    394   0.754   2630   0.845  0.893  0.9200  0.9397  0.7888  0.9008
  0.0319   4113   0.900    409   0.854   4522   0.895  0.893  0.9568  0.9711  0.9153  0.9638
  0.0528   5391   0.900    400   0.835   5791   0.896  0.990  0.9591  0.9709  0.9173  0.9634
  0.0738   6407   0.885    409   0.803   6816   0.880  1.095  0.9467  0.9630  0.9064  0.9579
  0.0947   7302   0.817    411   0.708   7713   0.812  1.118  0.9099  0.9375  0.8217  0.9383
  0.1157   8058   0.753    411   0.625   8469   0.747  1.014  0.8791  0.9030  0.8039  0.9123
  0.1367   8769   0.686    414   0.552   9183   0.680  0.741  0.8001  0.8439  0.6944  0.8355
  0.1576   9459   0.284    385   0.236   9844   0.282  0.245  0.4220  0.4517  0.5265  0.5701
  0.1786   9323   0.059    220   0.041   9543   0.058  0.042  0.0675  0.0705  0.3208  0.3087
 $$
Resolution limits                    =     47.354     2.300
Number of used reflections           =      64511
Percentage observed                  =    98.4135
Percentage of free reflections       =     5.0233
Overall R factor                     =     0.2099
Free R factor                        =     0.2707
Average Fourier shell correlation    =     0.7254
AverageFree Fourier shell correlation=     0.7038
Overall weighted R factor            =     0.1736
Free weighted R factor               =     0.2274
Overall weighted R2 factor           =     0.1792
Free weighted R2 factor              =     0.2294
Average correlation coefficient      =     0.7757
Overall correlation coefficient      =     0.9594
Free correlation coefficient         =     0.9282
Cruickshanks DPI for coordinate error=     0.2960
DPI based on free R factor           =     0.2445
Overall figure of merit              =     0.6141
ML based su of positional parameters =     0.2580
ML based su of thermal parameters    =    12.7590
-----------------------------------------------------------------------------
 Trying gamma equal   1.90749019E-02
 Gamma decreased to   1.43992268E-02


 fvalues    431453.41       30160.529       6688124.5       6679841.5    

 fvalues    431453.41       30160.529       6687902.5       6688070.0    
 fvalues    431453.41       30160.529       6687902.5       6688070.0    

    ****                              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.= 0.907 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.= 0.755 id.= 2.750 dev= -1.99 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_2-30A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7918     0.001     0.017
Bond angles  : refined atoms                  12685     1.783     1.702
Bond angles  : others                         18398     1.254     1.594
Torsion angles, period  1. refined             1092     8.175     5.000
Torsion angles, period  2. refined              517    32.102    21.915
Torsion angles, period  3. refined             1292    14.950    15.000
Torsion angles, period  4. refined               63    19.968    15.000
Chiral centres: refined atoms                  1196     0.069     0.200
Planar groups: refined atoms                  10355     0.008     0.020
Planar groups: others                          2034     0.002     0.020
VDW repulsions: refined_atoms                  1774     0.215     0.200
VDW repulsions.others                          7901     0.190     0.200
VDW; torsion: refined_atoms                    4222     0.170     0.200
VDW; torsion.others                            3964     0.078     0.200
HBOND: refined_atoms                            486     0.154     0.200
HBOND.others                                      2     0.047     0.200
Metal-ion: refined_atoms                         12     0.139     0.200
VDW repulsions: symmetry: refined_atoms          18     0.210     0.200
VDW repulsions: symmetry: others                 50     0.161     0.200
HBOND: symmetry: refined_atoms                    6     0.136     0.200
M. chain bond B values: refined atoms          4328     4.003     5.210
M. chain bond B values: others                 4327     4.001     5.209
M. chain angle B values: refined atoms         5426     5.593     7.806
M. chain angle B values: others                5427     5.593     7.808
S. chain bond B values: refined atoms          4896     5.051     5.686
S. chain bond B values: others                 4897     5.051     5.686
S. chain angle B values: refined atoms         7255     6.831     8.453
S. chain angle B values: others                7256     6.830     8.453
Long range B values: refined atoms             9984     7.996    61.076
Long range B values: others                    9900     7.996    61.012
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0059, B  =    0.3011
Partial structure    1: scale =     0.3881, B  =   40.6018
Overall anisotropic scale factors
   B11 =  -0.98 B22 =  -1.11 B33 =   2.09 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.011    2630  99.75  2544.2  2623.8  0.20  0.19     128  2661.3  2714.1  0.24  0.21
 0.032    4522 100.00  2152.8  2329.7  0.15  0.14     256  2094.0  2241.9  0.21  0.20
 0.053    5791 100.00  2337.7  2283.3  0.12  0.11     305  2337.4  2346.1  0.19  0.18
 0.074    6816  99.99  1806.4  1579.2  0.17  0.16     361  1791.0  1546.3  0.23  0.21
 0.095    7713 100.00  1259.9  1045.4  0.22  0.20     397  1273.4  1059.7  0.27  0.26
 0.116    8469 100.00   812.1   726.1  0.21  0.20     460   856.3   764.4  0.30  0.29
 0.137    9183  99.99   492.9   538.6  0.29  0.28     496   473.7   531.5  0.37  0.36
 0.158    9844  99.33   304.0   407.7  0.56  0.55     490   308.1   424.1  0.59  0.58
 0.179    9522  90.96   230.1   320.5  0.63  0.63     517   227.5   311.2  0.63  0.64
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0109   2236   0.862    394   0.754   2630   0.845  0.893  0.9200  0.9397  0.7888  0.9007
  0.0319   4113   0.900    409   0.853   4522   0.895  0.893  0.9568  0.9711  0.9153  0.9638
  0.0528   5391   0.901    400   0.835   5791   0.896  0.990  0.9591  0.9710  0.9174  0.9634
  0.0738   6407   0.885    409   0.803   6816   0.880  1.095  0.9466  0.9630  0.9063  0.9579
  0.0947   7302   0.817    411   0.708   7713   0.812  1.118  0.9099  0.9374  0.8217  0.9384
  0.1157   8058   0.753    411   0.625   8469   0.747  1.014  0.8790  0.9029  0.8039  0.9123
  0.1367   8769   0.686    414   0.552   9183   0.680  0.741  0.8000  0.8439  0.6944  0.8355
  0.1576   9459   0.283    385   0.236   9844   0.282  0.245  0.4220  0.4517  0.5267  0.5702
  0.1786   9323   0.059    220   0.041   9543   0.059  0.042  0.0675  0.0705  0.3207  0.3088
 $$
Resolution limits                    =     47.354     2.300
Number of used reflections           =      64511
Percentage observed                  =    98.4135
Percentage of free reflections       =     5.0233
Overall R factor                     =     0.2099
Free R factor                        =     0.2708
Average Fourier shell correlation    =     0.7254
AverageFree Fourier shell correlation=     0.7037
Overall weighted R factor            =     0.1736
Free weighted R factor               =     0.2275
Overall weighted R2 factor           =     0.1793
Free weighted R2 factor              =     0.2294
Average correlation coefficient      =     0.7757
Overall correlation coefficient      =     0.9594
Free correlation coefficient         =     0.9282
Cruickshanks DPI for coordinate error=     0.2960
DPI based on free R factor           =     0.2446
Overall figure of merit              =     0.6141
ML based su of positional parameters =     0.2580
ML based su of thermal parameters    =    12.7590
-----------------------------------------------------------------------------
  Time in seconds: CPU =       210.35
             Elapsed =         256.00

    ****           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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2104   0.2695   0.600      433234.   23408.4   0.0084  0.588   1.712  0.952   0.066
       1   0.2107   0.2696   0.613      431430.   23382.3   0.0095  0.653   1.756  0.973   0.071
       2   0.2100   0.2699   0.614      431473.   23390.0   0.0092  0.639   1.761  0.979   0.068
       3   0.2100   0.2702   0.614      431395.   23387.5   0.0092  0.640   1.766  0.982   0.069
       4   0.2099   0.2701   0.614      431410.   23388.4   0.0092  0.639   1.771  0.984   0.069
       5   0.2099   0.2703   0.614      431427.   23390.0   0.0092  0.641   1.776  0.986   0.069
       6   0.2099   0.2703   0.614      431418.   23389.9   0.0092  0.641   1.778  0.987   0.069
       7   0.2099   0.2705   0.614      431426.   23390.5   0.0092  0.641   1.780  0.988   0.069
       8   0.2099   0.2706   0.614      431431.   23391.3   0.0092  0.641   1.781  0.989   0.069
       9   0.2099   0.2707   0.614      431451.   23392.3   0.0092  0.641   1.782  0.989   0.069
      10   0.2099   0.2708   0.614      431449.   23392.3   0.0092  0.641   1.783  0.989   0.069
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2104   0.2099
             R free    0.2695   0.2708
     Rms BondLength    0.0084   0.0092
      Rms BondAngle    1.7115   1.7828
     Rms ChirVolume    0.0662   0.0693
 $$

 Refmac:  End of Refmac_5.8.0258   
Times: User:     282.4s System:    2.2s Elapsed:     4:45