[phenixbb] Low resolution refinement - rotamers and Ramachandran

Pavel Afonine pafonine at lbl.gov
Wed May 20 03:39:22 PDT 2015

Hi Mohamed,

> I am refining a low resolution structure (3.8 A). After I fix most of 
> the outliers (red bars) in Coot, phenix.refine is causing my structure 
> to be worse than the start with 13 % Ramachandran outlier and 13 % 
> rotamer outlier.

could you please send me data and model (before refinement) files then I 
will have a look. Refinement at low resolution is generally tricky and 
often requires using beyond the default settings such as secondary 
structure, rotamer and Ramachandran plot restraints, NCS (at 3.8A 
Cartesian NCS or even NCS constraints might be a better option).

If you send me files I will try plausible options to see what can be done.


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