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

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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 8998-6264 | Fax +49 (0)40 8994-6264 | Website www.mpsd.mpg.de