Somewhat confusingly, there’s several different numbering schemes in Rosetta. There’s the pose numbering scheme, which simply numbers residues sequentially starting from 1. There’s also the PDB numbering scheme, which matches the numbering scheme in the input PDB. (There’s also a renumbered PDB numbering scheme, which can be used for poses which don’t have PDB information (e.g. silent files) or when Rosetta has done something that invalidates the PDB numbering.) Typically, if there isn’t a chain mentioned, it’s the pose numbering scheme, but if there *is* a chain mentioned, then it’s whatever PDB numbering scheme is currently in effect.
My guess is that you’re doing design on a 166 residue protein with a ligand. By pose numbering the ligand may be residue 167, but by PDB numbering, it isn’t. If you’ve done things the typical way, it’s probably chain X residue 1. Check all your input files to see that all the residue numberings match. Pay particular attention to the enzdes constraint headers in the PDB and any resfiles you might be using.
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