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    I think it may be because as you are deleting and adding residues, the residue numbers begin to change internally to rosetta to keep them from 1 to X. So, if you delete 323, 322 actually becomes the new 323; so loop around and keep deleting 323 to delete 323 – 320. Also, after you fix this, if you can’t get append_polymer_residue_after_seqpos, try pose.prepend_polymer_residue_before_seqpos(res, res#, bool).