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I’m not sure I fully understand what’s going on – you have more residues in your input through -s than in your input through -native? Why? Which is the original PDB file and which (if either) has been changed?
The error is probably due to all the residues being “present” in the PDB, but with some residues malformed – typically either missing backbone atoms or having 0 occupancy for some backbone atoms.
I doubt there is a flag to magically fix this. We patch up the PDB reader when we can identify the causes of bugs like these, but by and large we just edit PDBs as necessary to get Rosetta to read them in correctly. The PDB standards are not well adhered to (or they’re just vague), so the PDB reader is not robust against all PDBs, even straight from the database.
If you can find the RMSD call in the code, you would be able to pass that function call an AtomIDMap which would let you tell it to ignore certain residues – it’s likely attempting to do this already and is just failing on this particular case.