The problem was in the charm-like naming of the Histidine residues in
the input.pdb ( so its produce mismatch). Does it possible to make some
aliases for HIS HSP HSE HSD (to His in sequence entry) as well as other
titrable residues ?
You can add aliases for residue types by editing modlib/restyp.lib and
adding them to the PDB-3 column. For example, both PRO and PRZ are
currently interpreted as "proline".