[phenixbb] Problem during refinement

Almudena Ponce Salvatierra maps.farma at gmail.com
Sat Jan 24 00:08:36 PST 2015

Dear all,

I have partially rebuilt my model after autosol and now I would like to
submit it for refinement to Phenix refine.

However when I do so, even though the R factors go down when I have a look
at the result, it just looks awful! All the model is placed out of the
electron density map, plus the electron density map doesn't look anymore
like a 3 A one, but just like sausages.

Why is this happening? The truth is I have no idea...

What I do is to provide Phenix refine with overall_best_refine_data.mtz
(coming from autosol) as phases, x Ray data and x Ray r free data.
Additionally, the starting model and the sequence.

Any suggestions are more than welcome.

Thanks a lot in advance.

Best wishes,


Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
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