Hi Jiemin, I recently had a few errors of such, and while I can't remember which Phenix program spitted it out (Phaser or phenix.refine), the issue was my models from MODELLER. Simply deleting hydrogens by running phenix.reduce -Trim insertpdbname.pdb >newpdbname.pdb on the coordinate file fixes it for me. I might be way off with your issue, but this is easy enough to try. Engin On 9/18/17 10:57 AM, Jiemin Zhao wrote:

Hi,

I got an error message when I try to refine a molecular replacement result. It says Fatal problems interpreting model file: Number of atoms with unknown nonbonding energy type symbols: 18 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply-cif-modification and apply-cif-link parameter definitions if necessary.

Could you help me with this problem?

Thanks!

Best regards,

Jiemin

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The error message says that PDB file contains unknown/nonstandard residues or ligands. This needs to be addressed before proceeding to refinement. If you indeed have some unknowns in the model then you need to provide a proper CIF file with restraints, or resolve the conflict otherwise. Pavel On 9/18/17 17:57, Jiemin Zhao wrote:

Hi,

I got an error message when I try to refine a molecular replacement result. It says Fatal problems interpreting model file: Number of atoms with unknown nonbonding energy type symbols: 18 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply-cif-modification and apply-cif-link parameter definitions if necessary.

Could you help me with this problem?

Thanks!