/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 806.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 810.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 812.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 814.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 816.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 818.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 820.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 822.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CA defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4512.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CB defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4516.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CG defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4518.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CD defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4520.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NE defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4522.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom CZ defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4524.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH1 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4526.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom NH2 defined twice in residue <Residue ARG het=  resseq=1119 icode= > at line 4528.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom P defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7863.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7864.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O5' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7865.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7866.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7867.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7868.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O3' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7869.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7870.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7871.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C1' defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7872.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7873.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7874.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7875.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom N3 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7876.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7877.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom O4 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7878.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C5 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7879.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom C6 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7880.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP1 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7881.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py:284: PDBConstructionWarning: PDBConstructionException: Atom OP2 defined twice in residue <Residue   U het=  resseq=20 icode= > at line 7882.
Exception ignored.
Some atoms or residues may be missing in the data structure.
  % message, PDBConstructionWarning)
Traceback (most recent call last):
  File "/home/rpdock/mc/MC.py", line 709, in <module>
    s, datas = write_all_atoms (datas, step_real, cal.split()[0], plik, pars, historyT, historyR, rna)
  File "/home/rpdock/mc/MC.py", line 360, in write_all_atoms
    all_at_ch_rna, all_at_ch_prot = all_atom (plik, pars, transl, rotation, rna)
  File "/home/rpdock/mc/MC.py", line 297, in all_atom
    pro_ch, rna_ch = check_chains(plik, pars)
  File "/home/rpdock/mc/MC.py", line 106, in check_chains
    struc = pars.get_structure('native', plik)
  File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 83, in get_structure
    self._parse(handle.readlines())
  File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 109, in _parse
    self.trailer = self._parse_coordinates(coords_trailer)
  File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/PDBParser.py", line 225, in _parse_coordinates
    fullname, serial_number, element)
  File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/StructureBuilder.py", line 197, in init_atom
    fullname, serial_number, element)
  File "/usr/local/lib/python2.7/dist-packages/Bio/PDB/Atom.py", line 58, in __init__
    self.bfactor=bfactor
MemoryError