Hello,
Thank you for your message.
The issue is that your PDB file seems to contain residues with double occupancy, that HADDOCK cannot handle in its current version. Except if the residues concerned are really important, you can easily clean your PDB for any double occupancy by running the pdb_delocc.py present in our PDB-tools repository. Another script, pdb_format.py will help you detecting any other formatting issue your PDB might have.
I hope this will help you,
Best,
Mikael