Hi, We are using the Phenix protocol "Comprehensive Validation (CryoEM)" (version 2.0.5936). The input structure file is provided in mmCIF format. We have observed that the protocol fails when chain IDs contain three characters, whereas it completes successfully when chain IDs contain two characters. Based on this behavior, we suspect that the protocol may internally convert the input mmCIF file to the legacy PDB format. Could you please confirm whether this assumption is correct? If such a conversion is performed internally, we would also like to understand how the protocol handles structures that exceed the limitations of the PDB format, for example files containing more than 99,999 atoms or chain identifiers that are not supported by the traditional PDB specification. When the protocol fails the following warnings are reported: Bad HELIX record, was skipped: HELIX 1 1 MET0Ah 7 HIS0Ah 14 1 8 Bad HELIX record, was skipped: HELIX 2 2 SER0Ah 25 GLU0Ah 36 1 12 ... Bad sense in SHEET record: '9' Thank you for your help. Best regards, Roberto