PDB file name : pdb1rka.ent

Chains and HETATMs selected: 
  ATOM        A

The following atoms are removed from PDB data on concern that they may have 
abnormally large fluctuations, because they interact with few atoms.
  ATOM    623  CG  LYS A  91      34.553  53.417  16.845  1.00 34.60           C  
  ATOM    624  CD  LYS A  91      35.502  54.150  17.790  1.00 35.99           C  
  ATOM    625  CE  LYS A  91      36.952  53.803  17.498  0.00 35.44           C  
  ATOM    626  NZ  LYS A  91      37.885  54.496  18.428  0.00 35.56           N  
  ATOM   1116  CG  LYS A 160       0.069  63.818  29.031  1.00 37.78           C  
  ATOM   1117  CD  LYS A 160      -0.472  65.238  29.163  1.00 39.13           C  
  ATOM   1118  CE  LYS A 160      -1.257  65.426  30.457  1.00 41.00           C  
  ATOM   1119  NZ  LYS A 160      -0.434  65.170  31.672  1.00 42.39           N  
  ATOM   1748  CG  ARG A 244      -8.425  45.826  -7.183  1.00 34.27           C  
  ATOM   1749  CD  ARG A 244      -9.702  45.469  -7.943  1.00 36.51           C  
  ATOM   1750  NE  ARG A 244      -9.865  46.310  -9.121  1.00 39.72           N  
  ATOM   1751  CZ  ARG A 244      -9.263  46.082 -10.285  1.00 39.58           C  
  ATOM   1752  NH1 ARG A 244      -8.463  45.032 -10.427  1.00 37.92           N  
  ATOM   1753  NH2 ARG A 244      -9.434  46.925 -11.294  1.00 40.69           N  
  ATOM   2077  CG  LYS A 289      10.513  47.139  -8.569  0.00 29.28           C  
  ATOM   2078  CD  LYS A 289      11.434  46.712  -9.700  0.00 29.07           C  
  ATOM   2079  CE  LYS A 289      10.658  46.039 -10.820  0.00 28.99           C  
  ATOM   2080  NZ  LYS A 289       9.632  46.946 -11.404  0.00 28.88           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
