PDB file name : pdb2xru.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    377  CG  LYS A 171      12.441   7.042   2.922  1.00113.17           C  
  ATOM    378  CD  LYS A 171      11.672   6.927   1.611  1.00113.17           C  
  ATOM    379  CE  LYS A 171      11.527   5.471   1.162  1.00113.17           C  
  ATOM    380  NZ  LYS A 171      12.824   4.847   0.745  1.00113.17           N  
  ATOM    791  CG  ARG A 220       6.208  35.487  -2.093  1.00138.48           C  
  ATOM    792  CD  ARG A 220       5.097  35.810  -3.107  1.00138.48           C  
  ATOM    793  NE  ARG A 220       3.771  35.398  -2.633  1.00138.48           N  
  ATOM    794  CZ  ARG A 220       2.659  35.423  -3.367  1.00138.48           C  
  ATOM    795  NH1 ARG A 220       2.694  35.839  -4.627  1.00138.48           N  
  ATOM    796  NH2 ARG A 220       1.504  35.038  -2.836  1.00138.48           N  
  ATOM   1046  CG  ARG A 251      25.806  27.884  23.767  1.00202.90           C  
  ATOM   1047  CD  ARG A 251      25.699  27.120  25.096  1.00202.90           C  
  ATOM   1048  NE  ARG A 251      25.319  25.715  24.925  1.00202.90           N  
  ATOM   1049  CZ  ARG A 251      24.884  24.928  25.907  1.00202.90           C  
  ATOM   1050  NH1 ARG A 251      24.766  25.401  27.140  1.00202.90           N  
  ATOM   1051  NH2 ARG A 251      24.569  23.663  25.658  1.00202.90           N  
  ATOM   1390  CG  MET A 305      34.852  22.980  13.916  1.00113.79           C  
  ATOM   1391  SD  MET A 305      35.836  22.486  15.353  1.00113.79           S  
  ATOM   1392  CE  MET A 305      37.503  23.096  14.877  1.00113.79           C  

= 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
