PDB file name : pdb1vee.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    299  CG  LYS A  42       3.110  -5.844 -12.527  1.00  0.00           C  
  ATOM    300  CD  LYS A  42       4.046  -4.968 -13.374  1.00  0.00           C  
  ATOM    301  CE  LYS A  42       4.097  -5.378 -14.848  1.00  0.00           C  
  ATOM    302  NZ  LYS A  42       2.826  -5.094 -15.550  1.00  0.00           N  
  ATOM    333  CG  LYS A  47      -2.744  -1.980 -11.965  1.00  0.00           C  
  ATOM    334  CD  LYS A  47      -3.153  -1.135 -13.182  1.00  0.00           C  
  ATOM    335  CE  LYS A  47      -3.542  -1.918 -14.441  1.00  0.00           C  
  ATOM    336  NZ  LYS A  47      -2.428  -2.682 -15.027  1.00  0.00           N  
  ATOM    949  CG  LYS A 126      18.133   4.357 -12.623  1.00  0.00           C  
  ATOM    950  CD  LYS A 126      18.579   5.202 -13.815  1.00  0.00           C  
  ATOM    951  CE  LYS A 126      17.847   6.545 -13.811  1.00  0.00           C  
  ATOM    952  NZ  LYS A 126      18.584   7.559 -14.578  1.00  0.00           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
