[phenixbb] refine error message

Dorothee Liebschner dcliebschner at lbl.gov
Mon Sep 18 11:20:56 PDT 2017

Hi Jiemin,

Under the error message you quote should be the list of atoms which create
problems (listing the name, residue number etc.).

Typically, this error occurs when:
- a ligand cif file was not supplied
- some atoms have non-standard names, which are not recognized

If you send the specific part in the log file, we can maybe comment more.
Or you send us the pdb file (make sure to send it off list!).

Best wishes,


On Mon, Sep 18, 2017 at 8:57 AM, Jiemin Zhao <zhao447 at purdue.edu> 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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