What is the sequence of your protein? Do you have any odd residue types in the template structure? You should only get that error if you have a residue which doesn’t have a CB atom nor a 1HA atom. All standard protein residues should have one or the other of these atom, but you might run into a situation with other, non-standard residues.
Pay attention to the tracer information, and see if any unexpected chemotypes are being loaded. You may be able to solve this with the options `-load_PDB_components false -ignore_unrecognized_res`, which should cause Rosetta to ignore some of the odder chemotypes.
If that doesn’t help, the other thing you might want to try the `-restore_talaris_behavior` or `-restore_pre_talaris_2013_behavior` flags (but not both). These cause Rosetta to use an older set of residue definitions, which may result in slightly better behavior.
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