<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I’ve recently had some similar issue but I think it was due to a specific problem concerning a modified residue.<div class="">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)</div><div class="">I solved this by defining the ligand itself with bonds and angles and keep the original residue.</div><div class="">First of all you should inspect the cif file from your refinement<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">Le 14 mai 2022 à 16:44, <a href="mailto:princeadam@163.com" class="">princeadam@163.com</a> a écrit :</div><br class="Apple-interchange-newline"><div class=""><div style="line-height: 1.7; font-size: 14px; font-family: Arial;" class=""><div style="margin:0;" class=""><span style="font-size: 18px;" class="">Dear all,</span></div><div style="margin:0;" class=""><span style="font-size: 18px;" class="">Sorry, I made a mistake in the former email.</span></div><div style="margin:0;" class=""><br class=""></div><div style="margin:0;" class=""><span style="font-size: 18px;" class="">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.</span></div><div style="margin:0;" class=""><span style="font-size: 18px;" class="">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.</span></div><div style="margin:0;" class=""><span style="font-size: 18px;" class="">However, if I use the cif file from phenix.refine with the same procedure, I got the validation reports normally.</span></div><div style="margin:0;" class=""><span style="font-size: 18px;" class="">Does anyone has similar problem?</span></div><div style="margin:0;" class=""><span style="font-size: 18px;" class="">I am using Phenix 1.20.1-4487.</span></div><div style="margin:0;" class=""><br class=""></div><div style="margin:0;" class=""><span style="font-size: 18px;" class="">Thanks a lot for the help.</span></div><div style="margin:0;" class=""><br class=""></div><div style="margin:0;" class=""><span style="font-size: 18px;" class="">Best</span></div><div style="margin:0;" class=""><span style="font-size: 18px;" class="">Liu</span></div></div>_______________________________________________<br class="">phenixbb mailing list<br class=""><a href="mailto:phenixbb@phenix-online.org" class="">phenixbb@phenix-online.org</a><br class="">http://phenix-online.org/mailman/listinfo/phenixbb<br class="">Unsubscribe: phenixbb-leave@phenix-online.org</div></blockquote></div><br class=""></div></body></html>