Dear all, I am running phenix.ensemble_refinement on a covalent protein-ligand complex providing the same parameter-files used for phenix.refine. I also included the .def and .cif files generated by phenix.ligand_linking. However, in quite a few of the ensemble structures, the covalent link exceeds 5Å, which is obviously wrong. How can I obtain ensemble structures with reasonable covalent bond length? Best, Eike ———————————————————————————— Dr. Eike C. Schulz Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 | 22761 Hamburg | Germany Building 99 (CFEL) | Office O2.101 Phone +49 (0)40 8998-6264tel:%2B49%20%280%2940%208998-6264 | Fax +49 (0)40 8994-6264tel:%2B49%20%280%2940%208994-6264 | Website www.mpsd.mpg.dehttp://www.mpsd.mpg.de/