I’ve recently had some similar issue but I think it was due to a specific problem concerning a modified residue. In that case, the generated cif file presented the protein as splited chains (Chain A for N-ter, the modified residue as chain B and then the C-terminus as chain C) I solved this by defining the ligand itself with bonds and angles and keep the original residue. First of all you should inspect the cif file from your refinement

Le 14 mai 2022 à 16:44, princeadam@163.com a écrit :

Dear all, Sorry, I made a mistake in the former email.

I used the "real space refinement"to refine my protein-ligand complex. The cif file got from "real space refinement" was put into "Prepare model for PDB depositon" and then I used "Get PDB validation report" to see the validation report. It's a pity I got the following error message from "Get PDB validation report": The PDB server reports a failure with you data. Please check that your input files following the CIF specifications. However, if I use the cif file from phenix.refine with the same procedure, I got the validation reports normally. Does anyone has similar problem? I am using Phenix 1.20.1-4487.

Thanks a lot for the help.

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