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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: 11:43:08 


 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 2.80
  Data line--- ncyc 10
  Data line--- bins 9
  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_2-80A_modified.pdb
Output coordinate file. Logical name - XYZOUT actual file name - BO_from2-80A_R00_2-80A.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_2-80A.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       0.0142
  Refinement of individual isotropic Bfactors
  Refinement resln        :    47.3545  2.8000
  Estimated number of reflections :      51329
  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  2.8000

  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_2-80A_modified.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 : CIS peptide bond is found, angle =      5.25
            ch:AAA  res:  66  SER              -->  67  PRO
  WARNING : CIS peptide bond is found, angle =     10.14
            ch:AAA  res: 447  ALA              --> 448  PRO
  WARNING : CIS peptide bond is found, angle =      4.63
            ch:AAA  res: 465  HIS              --> 466  ASP
  WARNING : CIS peptide bond is found, angle =      0.55
            ch:BBB  res:  66  SER              -->  67  PRO
  WARNING : CIS peptide bond is found, angle =      7.13
            ch:BBB  res: 447  ALA              --> 448  PRO
  WARNING : CIS peptide bond is found, angle =      0.00
            ch:BBB  res: 465  HIS              --> 466  ASP
  INFO:     link is found (not be used) dist=   2.604 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=   2.965 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=   1.836 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=   2.056 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=   2.000 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=   1.922 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=   3.102 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=   2.523 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=   1.396 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=   2.090 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=   1.810 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=   1.960 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=   2.785 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=   2.683 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=   2.036 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=   2.185 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=   2.166 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 =     1.457 ideal_dist=     1.439
            ch:AAA  res: 472  ASN              at:ND2 .->AeA  res: 701  NAG              at:C1  .
  WARNING : link:NAG-ASN  is found dist =     1.448 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=   3.046 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 =     1.451 ideal_dist=     1.439
            ch:AeA  res: 701  NAG              at:O4  .->AfA  res: 702  NAG              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.411 ideal_dist=     1.439
            ch:AfA  res: 702  NAG              at:O4  .->AgA  res: 703  BMA              at:C1  .
  WARNING : link:ALPHA1-3 is found dist =     1.490 ideal_dist=     1.439
            ch:AgA  res: 703  BMA              at:O3  .->AhA  res: 704  MAN              at:C1  .
  WARNING : link:ALPHA1-6 is found dist =     1.471 ideal_dist=     1.439
            ch:AgA  res: 703  BMA              at:O6  .->AiA  res: 705  MAN              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.432 ideal_dist=     1.439
            ch:AjA  res: 711  NAG              at:O4  .->AkA  res: 712  NAG              at:C1  .
  WARNING : link:NAG-NA   is found dist =     2.355 ideal_dist=     2.434
            ch:AjA  res: 711  NAG              at:O6  .->AtA  res:1001  NA               at:NA  .
  WARNING : link:BETA1-4  is found dist =     1.451 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=   1.832 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=   2.174 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=   2.119 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=   1.917 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=   2.508 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=   2.580 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=   2.672 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=   1.388 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=   2.021 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=   1.923 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=   2.078 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=   1.954 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=   2.137 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=   2.311 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=   2.095 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 =     1.440 ideal_dist=     1.439
            ch:BBB  res: 472  ASN              at:ND2 .->BeB  res: 701  NAG              at:C1  .
  WARNING : link:NAG-ASN  is found dist =     1.418 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=   3.021 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=   2.986 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 =     1.449 ideal_dist=     1.439
            ch:BeB  res: 701  NAG              at:O4  .->BfB  res: 702  NAG              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.415 ideal_dist=     1.439
            ch:BfB  res: 702  NAG              at:O4  .->BgB  res: 703  BMA              at:C1  .
  WARNING : link:ALPHA1-3 is found dist =     1.471 ideal_dist=     1.439
            ch:BgB  res: 703  BMA              at:O3  .->BhB  res: 704  MAN              at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.455 ideal_dist=     1.439
            ch:BiB  res: 711  NAG              at:O4  .->BjB  res: 712  NAG              at:C1  .
  WARNING : link:NAG-NA   is found dist =     2.326 ideal_dist=     2.434
            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:XX-XXX-XX
  --------------------------------
  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:     17141         0     17141
               Angles:     31081         0     31081
              Chirals:      1196         0      1196
               Planes:      2666         0      2666
             Torsions:      9145         0      9145
            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       1940
Number of   all  reflections      38477
--------------------------------------------------------------------------------
 Number of reflections in file      72569
 Number of reflections read          38477

   Current auto weighting coefficient =    9.4992666    

 mode : HKRF


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



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

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

B    401 HIS N   . - B    401 HIS CA  . mod.= 1.384 id.= 1.488 dev=  0.104 sig.= 0.010

    ****                          Bond angle outliers                           ****

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

A    701 NAG H1    - A    701 NAG C2    mod.= 144.04 id.= 108.34 dev=-35.698 sig.=  3.000
A    701 NAG O4    - A    702 NAG H1    mod.=  58.78 id.= 109.47 dev= 50.687 sig.=  3.000
A    702 NAG H1    - A    702 NAG C2    mod.= 140.26 id.= 108.34 dev=-31.916 sig.=  3.000
A    702 NAG O4    - A    703 BMA H1    mod.=  54.98 id.= 109.47 dev= 54.494 sig.=  3.000
A    703 BMA H1    - A    703 BMA C2    mod.= 145.24 id.= 108.34 dev=-36.905 sig.=  3.000
A    703 BMA O6    - A    705 MAN H1    mod.=  49.17 id.= 109.47 dev= 60.302 sig.=  3.000
A    703 BMA O3    - A    704 MAN H1    mod.=  52.00 id.= 109.47 dev= 57.469 sig.=  3.000
A    704 MAN H1    - A    704 MAN C2    mod.= 138.91 id.= 108.34 dev=-30.572 sig.=  3.000
A    705 MAN H1    - A    705 MAN C2    mod.= 139.42 id.= 108.34 dev=-31.083 sig.=  3.000
A    711 NAG H1    - A    711 NAG C2    mod.= 142.40 id.= 108.34 dev=-34.063 sig.=  3.000
A    711 NAG O4    - A    712 NAG H1    mod.=  54.50 id.= 109.47 dev= 54.965 sig.=  3.000
A    712 NAG H1    - A    712 NAG C2    mod.= 138.68 id.= 108.34 dev=-30.335 sig.=  3.000
A    712 NAG O4    - A    713 BMA H1    mod.=  53.58 id.= 109.47 dev= 55.894 sig.=  3.000
A    713 BMA H1    - A    713 BMA C2    mod.= 141.03 id.= 108.34 dev=-32.689 sig.=  3.000
B    701 NAG H1    - B    701 NAG C2    mod.= 141.38 id.= 108.34 dev=-33.037 sig.=  3.000
B    701 NAG O4    - B    702 NAG H1    mod.=  57.82 id.= 109.47 dev= 51.655 sig.=  3.000
B    702 NAG H1    - B    702 NAG C2    mod.= 142.67 id.= 108.34 dev=-34.329 sig.=  3.000
B    702 NAG O4    - B    703 BMA H1    mod.=  50.39 id.= 109.47 dev= 59.083 sig.=  3.000
B    703 BMA H1    - B    703 BMA C2    mod.= 141.59 id.= 108.34 dev=-33.255 sig.=  3.000
B    703 BMA O3    - B    704 MAN H1    mod.=  52.23 id.= 109.47 dev= 57.244 sig.=  3.000
B    704 MAN H1    - B    704 MAN C2    mod.= 138.51 id.= 108.34 dev=-30.169 sig.=  3.000
B    711 NAG O4    - B    712 NAG H1    mod.=  53.35 id.= 109.47 dev= 56.115 sig.=  3.000
B    712 NAG H1    - B    712 NAG C2    mod.= 139.09 id.= 108.34 dev=-30.750 sig.=  3.000

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

Deviations from the planarity >10.000Sigma will be monitored
Atom: A     24 ARG CD    deviation=  -0.27 sigma.=   0.02
Atom: A     24 ARG HE    deviation=   0.27 sigma.=   0.02
Atom: A    125 ARG CD    deviation=   0.33 sigma.=   0.02
Atom: A    125 ARG HE    deviation=  -0.32 sigma.=   0.02
Atom: A    317 ARG CD    deviation=   0.24 sigma.=   0.02
Atom: A    317 ARG HE    deviation=  -0.24 sigma.=   0.02
Atom: A    497 ARG CD    deviation=  -0.34 sigma.=   0.02
Atom: A    497 ARG HE    deviation=   0.34 sigma.=   0.02
Atom: B    125 ARG CD  A deviation=  -0.21 sigma.=   0.02
Atom: B    125 ARG HE  A deviation=   0.21 sigma.=   0.02
Atom: B    125 ARG CD  B deviation=  -0.38 sigma.=   0.02
Atom: B    125 ARG HE  B deviation=   0.37 sigma.=   0.02
Atom: B    294 ARG CD    deviation=   0.65 sigma.=   0.02
Atom: B    294 ARG HE    deviation=  -0.64 sigma.=   0.02
Atom: B    356 ARG CD  A deviation=  -0.25 sigma.=   0.02
Atom: B    356 ARG HE  A deviation=   0.25 sigma.=   0.02

    ****                              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.= 0.499 id.= 2.750 dev= -2.25 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.536 id.= 2.750 dev= -2.21 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        :   196  300  336
 Maximuum H,K,L                 :    49   74   82
 Minimum acceptable grid spacing:   131  199  221
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   196  300  336
 Maximuum H,K,L                 :    49   74   82
 Minimum acceptable grid spacing:   131  199  221
 Weight matrix   4.80000041E-02
 Actual weight    16.397293      is applied to the X-ray term
Norm of X_ray positional gradient                35.3
Norm of Geom. positional gradient                148.
Norm of X_ray B-factor gradient                  114.
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients     -0.142E+08
 Cosine of angle between them                      -0.052
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.4486E+07 GEOM=     0.7187E+05 TOTAL=     0.4558E+07
 function value    4558193.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.021     0.013
Bond distances: others                         7916     0.035     0.017
Bond angles  : refined atoms                  12685     1.889     1.702
Bond angles  : others                         18396     2.833     1.594
Torsion angles, period  1. refined             1092     7.574     5.000
Torsion angles, period  2. refined              517    32.094    21.915
Torsion angles, period  3. refined             1292    14.814    15.000
Torsion angles, period  4. refined               63    19.358    15.000
Chiral centres: refined atoms                  1196     0.101     0.200
Planar groups: refined atoms                  10355     0.015     0.020
Planar groups: others                          2034     0.032     0.020
VDW repulsions: refined_atoms                  1745     0.219     0.200
VDW repulsions.others                          7770     0.225     0.200
VDW; torsion: refined_atoms                    4212     0.176     0.200
VDW; torsion.others                            3848     0.105     0.200
HBOND: refined_atoms                            503     0.144     0.200
HBOND.others                                      6     0.086     0.200
Metal-ion: refined_atoms                         11     0.126     0.200
VDW repulsions: symmetry: refined_atoms          16     0.205     0.200
VDW repulsions: symmetry: others                 42     0.191     0.200
HBOND: symmetry: refined_atoms                    7     0.141     0.200
M. chain bond B values: refined atoms          4328     0.000     3.653
M. chain bond B values: others                 4327     0.000     3.653
M. chain angle B values: refined atoms         5426     0.000     5.480
M. chain angle B values: others                5427     0.000     5.480
S. chain bond B values: refined atoms          4896     0.000     3.653
S. chain bond B values: others                 4897     0.000     3.653
S. chain angle B values: refined atoms         7255     0.000     5.480
S. chain angle B values: others                7256     0.000     5.480
Long range B values: refined atoms             9962     0.000    41.983
Long range B values: others                    9872     0.000    41.854
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0051, B  =    4.8855
Partial structure    1: scale =     0.3843, B  =   14.9662
Overall anisotropic scale factors
   B11 =  -1.35 B22 =  -1.58 B33 =   2.93 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.008    1507  99.56  3295.9  2956.7  0.21  0.21      66  3464.9  2920.6  0.26  0.24
 0.022    2541 100.00  2377.1  2470.0  0.17  0.16     140  2386.2  2467.9  0.24  0.21
 0.036    3220 100.00  2566.3  2674.7  0.17  0.15     184  2539.6  2600.1  0.21  0.19
 0.050    3807 100.00  2732.3  2709.8  0.16  0.14     193  2709.8  2781.6  0.22  0.19
 0.064    4297 100.00  2455.0  2316.1  0.17  0.16     226  2572.0  2393.7  0.21  0.19
 0.078    4708  99.98  1941.8  1779.6  0.20  0.18     266  1829.0  1655.7  0.25  0.23
 0.092    5135 100.00  1526.1  1404.0  0.23  0.20     252  1556.7  1438.4  0.24  0.22
 0.106    5479 100.00  1154.5  1154.8  0.26  0.22     307  1197.3  1181.2  0.28  0.24
 0.120    5824 100.00   839.9   914.2  0.30  0.27     304   870.2   966.9  0.36  0.31
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0075   1236   0.839    271   0.734   1507   0.820  1.020  0.9046  0.9325  0.7358  0.8920
  0.0216   2272   0.873    269   0.778   2541   0.863  0.928  0.9409  0.9524  0.8753  0.9278
  0.0358   2948   0.882    272   0.859   3220   0.880  0.934  0.9483  0.9595  0.8998  0.9348
  0.0499   3536   0.874    271   0.804   3807   0.869  0.966  0.9428  0.9544  0.8972  0.9354
  0.0640   4025   0.873    272   0.798   4297   0.868  1.011  0.9439  0.9510  0.8933  0.9262
  0.0781   4433   0.865    275   0.765   4708   0.859  1.031  0.9200  0.9402  0.8467  0.9002
  0.0922   4852   0.831    283   0.727   5135   0.826  1.016  0.9122  0.9232  0.8349  0.8751
  0.1064   5201   0.779    278   0.691   5479   0.774  0.925  0.8812  0.8955  0.7940  0.8421
  0.1205   5565   0.675    272   0.536   5837   0.669  0.797  0.8265  0.8358  0.7516  0.8124
 $$
Resolution limits                    =     47.354     2.800
Number of used reflections           =      36531
Percentage observed                  =    99.9454
Percentage of free reflections       =     5.0378
Overall R factor                     =     0.2002
Free R factor                        =     0.2438
Average Fourier shell correlation    =     0.9194
AverageFree Fourier shell correlation=     0.9069
Overall weighted R factor            =     0.1729
Free weighted R factor               =     0.2114
Overall weighted R2 factor           =     0.1910
Free weighted R2 factor              =     0.2281
Average correlation coefficient      =     0.8853
Overall correlation coefficient      =     0.9313
Free correlation coefficient         =     0.8942
DPI based on free R factor           =     0.3544
Overall figure of merit              =     0.8138
ML based su of positional parameters =     0.2662
ML based su of thermal parameters    =    13.8450
-----------------------------------------------------------------------------
 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    273601.31       71872.250       4558193.0      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   4.80000004E-02
 Actual weight    13.816204      is applied to the X-ray term


 function value    3737672.5    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.014     0.013
Bond distances: others                         7916     0.010     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0052, B  =    0.5416
Partial structure    1: scale =     0.3824, B  =   37.8362
Overall anisotropic scale factors
   B11 =  -1.31 B22 =  -1.61 B33 =   2.92 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1676
Free R factor                        =     0.2313
Average Fourier shell correlation    =     0.9364
AverageFree Fourier shell correlation=     0.9181
Average correlation coefficient      =     0.9266
Overall figure of merit              =     0.8270
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    268330.25       30366.945       3737672.5       4558193.0    


     CGMAT cycle number =      3

 Weight matrix   4.80000004E-02
 Actual weight    13.194399      is applied to the X-ray term


 function value    3550641.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.010     0.013
Bond distances: others                         7916     0.006     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0052, B  =    0.1969
Partial structure    1: scale =     0.3795, B  =   43.0115
Overall anisotropic scale factors
   B11 =  -1.28 B22 =  -1.65 B33 =   2.93 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1599
Free R factor                        =     0.2281
Average Fourier shell correlation    =     0.9396
AverageFree Fourier shell correlation=     0.9205
Average correlation coefficient      =     0.9337
Overall figure of merit              =     0.8308
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    267064.06       26891.203       3550641.0       3737672.5    


     CGMAT cycle number =      4

 Weight matrix   4.80000004E-02
 Actual weight    12.918523      is applied to the X-ray term


 function value    3467341.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7916     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0052, B  =    0.4131
Partial structure    1: scale =     0.3796, B  =   46.2897
Overall anisotropic scale factors
   B11 =  -1.26 B22 =  -1.68 B33 =   2.95 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1568
Free R factor                        =     0.2264
Average Fourier shell correlation    =     0.9406
AverageFree Fourier shell correlation=     0.9213
Average correlation coefficient      =     0.9364
Overall figure of merit              =     0.8321
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02
 fvalues    266365.59       26291.734       3467341.8       3550641.0    


     CGMAT cycle number =      5

 Weight matrix   4.80000004E-02
 Actual weight    12.810681      is applied to the X-ray term


 function value    3433647.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.009     0.013
Bond distances: others                         7916     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0053, B  =    0.2304
Partial structure    1: scale =     0.3800, B  =   48.2377
Overall anisotropic scale factors
   B11 =  -1.25 B22 =  -1.70 B33 =   2.96 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1550
Free R factor                        =     0.2257
Average Fourier shell correlation    =     0.9410
AverageFree Fourier shell correlation=     0.9214
Average correlation coefficient      =     0.9375
Overall figure of merit              =     0.8325
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03
 fvalues    266000.22       26003.668       3433647.8       3467341.8    


     CGMAT cycle number =      6

 Weight matrix   4.80000004E-02
 Actual weight    12.808375      is applied to the X-ray term


 function value    3430760.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7916     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0053, B  =    0.1926
Partial structure    1: scale =     0.3797, B  =   49.3696
Overall anisotropic scale factors
   B11 =  -1.25 B22 =  -1.72 B33 =   2.96 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1542
Free R factor                        =     0.2259
Average Fourier shell correlation    =     0.9410
AverageFree Fourier shell correlation=     0.9213
Average correlation coefficient      =     0.9380
Overall figure of merit              =     0.8322
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Gamma decreased to   2.19674082E-03
 fvalues    265828.81       25924.852       3430760.0       3433647.8    


     CGMAT cycle number =      7

 Weight matrix   4.79999967E-02
 Actual weight    12.834871      is applied to the X-ray term


 function value    3436468.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7916     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0053, B  =    0.0954
Partial structure    1: scale =     0.3799, B  =   50.0723
Overall anisotropic scale factors
   B11 =  -1.24 B22 =  -1.73 B33 =   2.97 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1535
Free R factor                        =     0.2263
Average Fourier shell correlation    =     0.9410
AverageFree Fourier shell correlation=     0.9209
Average correlation coefficient      =     0.9384
Overall figure of merit              =     0.8317
-----------------------------------------------------------------------------
 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    265725.56       25869.234       3435690.0       3430760.0    
 fvalues    265725.56       25869.234       3435690.0       3436422.8    


     CGMAT cycle number =      8

 Weight matrix   4.80000004E-02
 Actual weight    12.834884      is applied to the X-ray term


 function value    3436076.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7916     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0053, B  =    0.0290
Partial structure    1: scale =     0.3799, B  =   50.4592
Overall anisotropic scale factors
   B11 =  -1.24 B22 =  -1.73 B33 =   2.97 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1533
Free R factor                        =     0.2268
Average Fourier shell correlation    =     0.9409
AverageFree Fourier shell correlation=     0.9208
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8315
-----------------------------------------------------------------------------
 Trying gamma equal   2.70900354E-02
 Gamma decreased to   2.14324687E-02
 fvalues    265697.38       25881.027       3436076.0       3436422.8    


     CGMAT cycle number =      9

 Weight matrix   4.80000004E-02
 Actual weight    12.874236      is applied to the X-ray term


 function value    3446960.3    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7916     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0053, B  =    0.0006
Partial structure    1: scale =     0.3796, B  =   50.9069
Overall anisotropic scale factors
   B11 =  -1.24 B22 =  -1.74 B33 =   2.98 B12 =   0.00 B13 =  -0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.1534
Free R factor                        =     0.2275
Average Fourier shell correlation    =     0.9408
AverageFree Fourier shell correlation=     0.9205
Average correlation coefficient      =     0.9385
Overall figure of merit              =     0.8311
-----------------------------------------------------------------------------
 Trying gamma equal   2.14324687E-02
 Gamma decreased to   1.62892267E-02


 fvalues    265729.13       25903.328       3446688.8       3436076.0    
 fvalues    265729.13       25903.328       3446688.8       3446962.8    


     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.= 0.835 id.= 2.750 dev= -1.91 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.782 id.= 2.750 dev= -1.97 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   196  300  336
 Maximuum H,K,L                 :    49   74   82
 Minimum acceptable grid spacing:   131  199  221
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   196  300  336
 Maximuum H,K,L                 :    49   74   82
 Minimum acceptable grid spacing:   131  199  221
 Weight matrix   4.79999967E-02
 Actual weight    12.886829      is applied to the X-ray term
Norm of X_ray positional gradient                17.5
Norm of Geom. positional gradient                17.5
Norm of X_ray B-factor gradient                  24.0
Norm of Geom. B-factor gradient                  23.8
Product of X_ray and Geom posit. gradients     -0.158E+08
 Cosine of angle between them                      -0.992
Product of X_ray and Geom B-fact gradients     -0.993E+07
 Cosine of angle between them                      -0.997


Residuals: XRAY=     0.3424E+07 GEOM=     0.2593E+05 TOTAL=     0.3450E+07
 function value    3449948.8    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7916     0.001     0.017
Bond angles  : refined atoms                  12685     1.657     1.702
Bond angles  : others                         18396     1.223     1.594
Torsion angles, period  1. refined             1092     7.934     5.000
Torsion angles, period  2. refined              517    31.702    21.915
Torsion angles, period  3. refined             1292    15.095    15.000
Torsion angles, period  4. refined               63    19.959    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                  1804     0.210     0.200
VDW repulsions.others                          7922     0.188     0.200
VDW; torsion: refined_atoms                    4227     0.169     0.200
VDW; torsion.others                            4012     0.076     0.200
HBOND: refined_atoms                            515     0.154     0.200
HBOND.others                                      1     0.092     0.200
Metal-ion: refined_atoms                         14     0.117     0.200
VDW repulsions: symmetry: refined_atoms          21     0.203     0.200
VDW repulsions: symmetry: others                 42     0.161     0.200
HBOND: symmetry: refined_atoms                    5     0.187     0.200
M. chain bond B values: refined atoms          4328     2.695     4.229
M. chain bond B values: others                 4327     2.694     4.228
M. chain angle B values: refined atoms         5426     4.101     6.338
M. chain angle B values: others                5427     4.101     6.340
S. chain bond B values: refined atoms          4896     3.377     4.624
S. chain bond B values: others                 4897     3.377     4.625
S. chain angle B values: refined atoms         7255     4.891     6.887
S. chain angle B values: others                7256     4.891     6.887
Long range B values: refined atoms            10046     6.524    49.652
Long range B values: others                    9963     6.511    49.642
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0053, B  =    0.0223
Partial structure    1: scale =     0.3797, B  =   51.2663
Overall anisotropic scale factors
   B11 =  -1.24 B22 =  -1.74 B33 =   2.98 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.008    1507  99.56  3206.8  2898.9  0.20  0.20      66  3371.1  2889.3  0.25  0.23
 0.022    2541 100.00  2312.8  2375.4  0.14  0.13     140  2321.6  2399.0  0.22  0.20
 0.036    3220 100.00  2496.9  2596.5  0.12  0.11     184  2470.8  2540.6  0.19  0.18
 0.050    3807 100.00  2658.4  2672.2  0.12  0.10     193  2636.4  2750.2  0.20  0.18
 0.064    4297 100.00  2388.5  2273.7  0.13  0.11     226  2502.4  2348.5  0.18  0.16
 0.078    4708  99.98  1889.3  1753.3  0.14  0.13     266  1779.5  1637.2  0.24  0.21
 0.092    5135 100.00  1484.8  1374.4  0.17  0.15     252  1514.6  1393.2  0.23  0.21
 0.106    5479 100.00  1123.3  1128.4  0.19  0.16     307  1164.9  1177.5  0.28  0.23
 0.120    5824 100.00   817.2   910.5  0.26  0.22     304   846.7   971.4  0.36  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0075   1236   0.846    271   0.742   1507   0.827  1.021  0.9045  0.9356  0.7336  0.8957
  0.0216   2272   0.890    269   0.807   2541   0.881  0.938  0.9501  0.9639  0.8927  0.9530
  0.0358   2948   0.902    272   0.871   3220   0.899  0.939  0.9602  0.9730  0.9214  0.9669
  0.0499   3536   0.901    271   0.835   3807   0.897  0.966  0.9593  0.9713  0.9227  0.9674
  0.0640   4025   0.894    272   0.817   4297   0.889  1.011  0.9578  0.9682  0.9199  0.9642
  0.0781   4433   0.882    275   0.790   4708   0.877  1.032  0.9323  0.9601  0.8674  0.9556
  0.0922   4852   0.833    283   0.733   5135   0.828  1.016  0.9201  0.9427  0.8517  0.9407
  0.1064   5201   0.784    278   0.672   5479   0.778  0.925  0.8892  0.9184  0.8048  0.9187
  0.1205   5565   0.709    272   0.562   5837   0.702  0.797  0.8547  0.8777  0.7731  0.8933
 $$
Resolution limits                    =     47.354     2.800
Number of used reflections           =      36531
Percentage observed                  =    99.9454
Percentage of free reflections       =     5.0378
Overall R factor                     =     0.1532
Free R factor                        =     0.2278
Average Fourier shell correlation    =     0.9407
AverageFree Fourier shell correlation=     0.9203
Overall weighted R factor            =     0.1327
Free weighted R factor               =     0.1963
Overall weighted R2 factor           =     0.1551
Free weighted R2 factor              =     0.2130
Average correlation coefficient      =     0.9386
Overall correlation coefficient      =     0.9585
Free correlation coefficient         =     0.9088
DPI based on free R factor           =     0.3311
Overall figure of merit              =     0.8309
ML based su of positional parameters =     0.2358
ML based su of thermal parameters    =    12.3920
-----------------------------------------------------------------------------
 Trying gamma equal   1.62892267E-02
 Gamma decreased to   1.16135515E-02


 fvalues    265696.91       25927.033       3449749.8       3446962.8    
 fvalues    265696.91       25927.033       3449749.8       3449917.8    

    ****                              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.= 0.840 id.= 2.750 dev= -1.91 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1
B    396 TRP HD1 . - B    398 HIS NE2 . mod.= 0.785 id.= 2.750 dev= -1.97 sig.= 0.20 sym.=  1  0  0  0 ncs   1 type =  1

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

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: BO_from2-80A_R00_2-80A.mtz 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  9225     0.008     0.013
Bond distances: others                         7916     0.001     0.017
Bond angles  : refined atoms                  12685     1.659     1.702
Bond angles  : others                         18396     1.222     1.594
Torsion angles, period  1. refined             1092     7.951     5.000
Torsion angles, period  2. refined              517    31.705    21.915
Torsion angles, period  3. refined             1292    15.120    15.000
Torsion angles, period  4. refined               63    19.966    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                  1809     0.210     0.200
VDW repulsions.others                          7936     0.188     0.200
VDW; torsion: refined_atoms                    4234     0.169     0.200
VDW; torsion.others                            4031     0.076     0.200
HBOND: refined_atoms                            514     0.154     0.200
HBOND.others                                      1     0.097     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                 43     0.160     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     3.394     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            10055     6.560    49.761
Long range B values: others                    9973     6.548    49.753
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     0.0053, B  =    0.0219
Partial structure    1: scale =     0.3793, B  =   51.4771
Overall anisotropic scale factors
   B11 =  -1.24 B22 =  -1.75 B33 =   2.98 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.008    1507  99.56  3205.3  2896.0  0.21  0.20      66  3369.6  2884.7  0.26  0.23
 0.022    2541 100.00  2311.7  2373.6  0.14  0.13     140  2320.6  2397.9  0.22  0.20
 0.036    3220 100.00  2495.7  2594.5  0.12  0.11     184  2469.7  2540.0  0.19  0.18
 0.050    3807 100.00  2657.1  2670.6  0.11  0.10     193  2635.2  2748.5  0.20  0.18
 0.064    4297 100.00  2387.4  2272.4  0.13  0.11     226  2501.2  2348.6  0.18  0.16
 0.078    4708  99.98  1888.4  1753.1  0.14  0.13     266  1778.7  1636.3  0.24  0.21
 0.092    5135 100.00  1484.2  1373.4  0.17  0.15     252  1513.9  1391.1  0.23  0.21
 0.106    5479 100.00  1122.7  1127.5  0.19  0.16     307  1164.4  1177.0  0.28  0.24
 0.120    5824 100.00   816.8   909.7  0.26  0.22     304   846.3   970.4  0.36  0.30
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0075   1236   0.845    271   0.739   1507   0.826  1.021  0.9042  0.9351  0.7326  0.8946
  0.0216   2272   0.888    269   0.806   2541   0.880  0.938  0.9495  0.9635  0.8916  0.9530
  0.0358   2948   0.902    272   0.872   3220   0.899  0.939  0.9604  0.9730  0.9218  0.9668
  0.0499   3536   0.901    271   0.835   3807   0.896  0.966  0.9588  0.9711  0.9219  0.9675
  0.0640   4025   0.893    272   0.817   4297   0.889  1.011  0.9578  0.9682  0.9198  0.9642
  0.0781   4433   0.882    275   0.791   4708   0.877  1.032  0.9321  0.9601  0.8666  0.9556
  0.0922   4852   0.833    283   0.733   5135   0.827  1.016  0.9199  0.9425  0.8516  0.9406
  0.1064   5201   0.783    278   0.671   5479   0.777  0.925  0.8889  0.9182  0.8045  0.9187
  0.1205   5565   0.708    272   0.561   5837   0.701  0.797  0.8541  0.8773  0.7721  0.8931
 $$
Resolution limits                    =     47.354     2.800
Number of used reflections           =      36531
Percentage observed                  =    99.9454
Percentage of free reflections       =     5.0378
Overall R factor                     =     0.1533
Free R factor                        =     0.2282
Average Fourier shell correlation    =     0.9406
AverageFree Fourier shell correlation=     0.9201
Overall weighted R factor            =     0.1328
Free weighted R factor               =     0.1969
Overall weighted R2 factor           =     0.1554
Free weighted R2 factor              =     0.2139
Average correlation coefficient      =     0.9385
Overall correlation coefficient      =     0.9584
Free correlation coefficient         =     0.9085
DPI based on free R factor           =     0.3318
Overall figure of merit              =     0.8303
ML based su of positional parameters =     0.2358
ML based su of thermal parameters    =    12.3920
-----------------------------------------------------------------------------
  Time in seconds: CPU =       125.55
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2002   0.2438   0.814      273601.   14797.5   0.0213  1.798   1.889  1.127   0.101
       1   0.1676   0.2313   0.827      268330.   14690.9   0.0137  0.894   1.655  0.935   0.073
       2   0.1599   0.2281   0.831      267064.   14653.5   0.0103  0.688   1.640  0.922   0.066
       3   0.1568   0.2264   0.832      266366.   14626.6   0.0093  0.627   1.643  0.923   0.065
       4   0.1550   0.2257   0.832      266000.   14614.3   0.0086  0.591   1.646  0.924   0.065
       5   0.1542   0.2259   0.832      265829.   14609.0   0.0083  0.571   1.649  0.925   0.065
       6   0.1535   0.2263   0.832      265729.   14608.5   0.0081  0.559   1.651  0.925   0.065
       7   0.1533   0.2268   0.831      265697.   14608.7   0.0080  0.553   1.653  0.926   0.065
       8   0.1534   0.2275   0.831      265729.   14611.9   0.0079  0.549   1.655  0.926   0.064
       9   0.1532   0.2278   0.831      265699.   14611.8   0.0079  0.546   1.657  0.927   0.064
      10   0.1533   0.2282   0.830      265726.   14614.4   0.0078  0.544   1.659  0.928   0.064
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2002   0.1533
             R free    0.2438   0.2282
     Rms BondLength    0.0213   0.0078
      Rms BondAngle    1.8895   1.6589
     Rms ChirVolume    0.1007   0.0644
 $$

 Refmac:  End of Refmac_5.8.0258   
Times: User:     200.3s System:    0.9s Elapsed:     3:21