[phenixbb] Rfree refuse to come down

Nathaniel Echols nechols at lbl.gov
Fri Mar 2 07:30:43 PST 2012

On Thu, Mar 1, 2012 at 11:36 PM, Vellieux Frederic
<Frederic.Vellieux at ibs.fr> wrote:
> And I'd certainly start refinement using the NCS present, to relax it
> (restraints) as the refinement proceeds (smoothly) and possibly not use any
> NCS in the final stages of the refinement. You may need to carry out
> annealing initially and so forth.

Fred is correct, you absolutely want to use NCS at this resolution -
if you use the torsion NCS parameterization (get a new-ish build for
this), you probably will not need or want to turn off the restraints.
The other thing to try is optimizing the X-ray/stereochemistry weight.
 This can take quite a long time (unless you have a large multi-core
system), but it almost always yields a better result.  You might also
want to turn off the real-space refinement, sometimes it behaves
weirdly.  At 2.4A with an R-free of 0.32 you can probably start
running the ordered solvent update, which will help a little bit.

A more general suggestion is to look through the log file and identify
where the R-factors begin to explode.  This will give you a better
idea where you need to change your strategy.

Final suggestion: make sure you're running at least version 1.7.3,
since there have been many improvements to refinement of more marginal


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