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If occupancy refinement for C-terminal amino-acid residues is configured (e.g. via "pdb2occ") and the C-terminal residue contains an OXT atom, this OXT atom will most likely have its occupancy fixed at the starting value (since it is internally assigned to a follow-up residue to maintain the internal notion what a peptide linkage should look like). You might therefore have to edit the output files (PDB and mmCIF) by hand to adjust the occupancy value accordingly.
