PDB file name : pdb2hbh.ent

Chains and HETATMs selected: 
  ATOM        A
  ATOM        B

The following atoms are removed from PDB data on concern that they may have 
abnormally large fluctuations, because they interact with few atoms.
  ATOM   1034  CG  LYS A 343      -2.366  25.879  52.037  1.00 75.42           C  
  ATOM   1035  CD  LYS A 343      -2.318  24.369  52.260  1.00 81.89           C  
  ATOM   1036  CE  LYS A 343      -2.508  24.008  53.737  1.00 98.99           C  
  ATOM   1037  NZ  LYS A 343      -3.810  24.473  54.310  1.00 95.00           N  
  ATOM   1108  CG  LYS A 352      -3.414  41.554  56.951  1.00 60.61           C  
  ATOM   1109  CD  LYS A 352      -4.536  42.508  57.388  1.00 65.21           C  
  ATOM   1110  CE  LYS A 352      -4.409  42.941  58.846  1.00 79.09           C  
  ATOM   1111  NZ  LYS A 352      -5.494  43.882  59.270  1.00 73.35           N  
  ATOM   1977  CG  ARG B 692      21.961  42.056  25.750  1.00 50.68           C  
  ATOM   1978  CD  ARG B 692      21.519  43.487  25.577  1.00 64.45           C  
  ATOM   1979  NE  ARG B 692      22.253  44.137  24.498  1.00 78.52           N  
  ATOM   1980  CZ  ARG B 692      22.043  45.386  24.101  1.00 82.33           C  
  ATOM   1981  NH1 ARG B 692      21.113  46.126  24.696  1.00 89.13           N  
  ATOM   1982  NH2 ARG B 692      22.766  45.895  23.112  1.00 77.09           N  

= Normal mode analysis calculation =

No. of modes used in the calculation : All modes.

Parameters of potential energies:
  1-4 and 1-5 non-bonded interactions: E(d) = A*exp(-d(PDB)**2/B**2)(d-d(PDB))**2.
  Loop-closing potential:              E(d) = A*(d-d(PDB))**2.
    for a disulfide bond and one of the bonds in the DNA and RNA sugar ring.
  where d and d(PDB) are distances between atoms in calculation and in PDB data, 
  respectively.

  Interaction type   A       B      Cutoff distance (A)
    1-4             1.00    5.00      100.00
    1-5             1.00    5.00      100.00
    Loop-closing  100.00

Temperature adjustment by magnitude of fluctuation:
  Set to mean displacements of atoms       0.500 A

Animation
  No. of frames: 11
  Mean displacements (A):    0.50

Displacement vector
  Mean length of vectors (A):    3.00
