ERROR Report: Assertion `res2.is_bonded(res1)` failed causing crash

Hi,I ran RFdiffusion and ProteinMPNN according to the parameters in Article "Accurate de novo design of high-affinity protein-binding macrocycles using deep learning", and all these results worked well. However, when executing a protein relaxation (FastRelax) and cyclization (PeptideCyclizeMover) workflow using PyRosetta with RosettaScripts, an assertion error Assertion res2.is_bonded(res1) failed occurs, leading to program crash. The error happens during the energy calculation phase and may be related to abnormal residue connection relationships. I don't know if this is a normal phenomenon.The error report is as follows:

core.conformation.Residue: [ WARNING ] While updating residue 16's connections to residue 17, a connection to residue 1 was overwritten!
core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 18. Returning BOGUS ID instead.
core.conformation.Residue: [ WARNING ] missing an atom: 18 H that depends on a nonexistent polymer connection!
core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.
ERROR: Assertion res2.is_bonded(res1) failed.
ERROR:: Exit from: /home/wzs/wzs/rosetta/source/src/core/scoring/etable/count_pair/CountPairFactory.cc line: 220

Start by reproducing the PyRosetta/RosettaScripts workflow using FastRelax and PeptideCyclizeMover, then inspect the residue-connection warnings for residues 16–18 and CountPairFactory.cc line 220. Done means the assertion is explained and the workflow no longer crashes, with reproducible input details or a confirmed cause.