PDB file name : pdb2zxq.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     57  CG  LYS A 348      94.016 -79.978 -11.611  1.00 35.80           C  
  ATOM     58  CD  LYS A 348      95.222 -79.103 -11.998  1.00 37.33           C  
  ATOM     59  CE  LYS A 348      94.886 -77.583 -11.960  1.00 46.97           C  
  ATOM     60  NZ  LYS A 348      93.842 -77.144 -12.983  1.00 49.00           N  
  ATOM   5794  CG  LYS A1092     116.762 -36.439  -6.770  1.00 49.95           C  
  ATOM   5795  CD  LYS A1092     117.127 -35.894  -8.152  1.00 53.78           C  
  ATOM   5796  CE  LYS A1092     118.351 -36.609  -8.728  1.00 54.18           C  
  ATOM   5797  NZ  LYS A1092     119.005 -35.779  -9.794  1.00 57.24           N  
  ATOM   6455  CG  LYS A1182      99.553   2.295 -20.973  1.00 49.82           C  
  ATOM   6456  CD  LYS A1182      99.694   3.138 -22.253  1.00 56.12           C  
  ATOM   6457  CE  LYS A1182     100.823   4.184 -22.111  1.00 58.76           C  
  ATOM   6458  NZ  LYS A1182     101.487   4.516 -23.414  1.00 61.12           N  
  ATOM   7097  CG  LYS A1264      89.339  12.987 -18.568  1.00 58.00           C  
  ATOM   7098  CD  LYS A1264      88.078  12.810 -19.407  1.00 61.20           C  
  ATOM   7099  CE  LYS A1264      87.329  14.119 -19.600  1.00 62.23           C  
  ATOM   7100  NZ  LYS A1264      87.990  14.960 -20.642  1.00 63.22           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
