[phenixbb] refinement questions

Sudharsan Sridharan sudhaarsan at gmail.com
Fri Aug 10 09:03:38 PDT 2007

Hi all,

I'm starting to refine a structure using phenix.refine. Almost all my
model residues have been built starting from a Sharp map. I've been
trying phenix.refine with and without SA and getting bond angle rmsds
of 1.0 -1.1 (2.5 A data, using mlhl targets; example below) (yet to
add water and also trying water picking in phenix.refine). I'm
wondering if this sounds low (I have read discussions on bond and
angle rmsds). More importantly I'd like to know how to work with
different parameters (weights etc) during refinement in phenix. Could
you please point to what params are safe to manipulate.


REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS *******************
REMARK Start: r_work = 0.3637 r_free = 0.4003 bonds = 0.010 angles = 1.175
REMARK Final: r_work = 0.2607 r_free = 0.3236 bonds = 0.007 angles = 1.017
REMARK ************************************************************************

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