[BUG] Residue and/or chain IDs not matching when using select_fixed_atoms constraint

[rclune]

At the start of a new batch - so some designs are created successfully - an assertion error is raised with this message:

File "/path/to/miniforge3/envs/foundry/lib/python3.12/site-packages/rfd3/trainer/trainer_utils.py", line 406, in process_unindexed_outputs
    assert (res_id_ == res_id) & (chain_id_ == chain_id)

This also only seems to occur when specific atoms are chosen in the select_fixed_atoms constraint.
See full conversation in the Protein Design Slack.

In the chat linked above the user supplied files for an example that produces this error and error logs from his attempts.