[phenixbb] problem in cif file from Real-space refinement

Xavier Brazzolotto xbrazzolotto at gmail.com
Sat May 14 07:54:47 PDT 2022

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 at 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.
> Best
> Liu
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