[phenixbb] Refinement Strategy vs. R gap

Nathaniel Echols nechols at lbl.gov
Wed Mar 16 12:02:54 PDT 2011

On Wed, Mar 16, 2011 at 11:10 AM, Yuri <yuri.pompeu at ufl.edu> wrote:
> I am refining a liganded structure at 2.1 and I am pretty far into my
> modeling. Rfree = .265 rwork= .20

Not great, but not awful.

> II- When I choose no XYZ refinement with anisotropic ADP for protein chain
> only with weight optimization Rwork plummets to 0.15 and Rfree also drops to
> 0.25. But my gap is now .10 !!

You shouldn't be refining any individual ADPs as anisotropic at this
resolution - except perhaps metal ions.  Use TLS groups instead; this
often has the effect of reducing the R-free/R-work gap.  (Note that
phenix.refine will still output ANISOU records for all atoms in TLS
groups, but they won't be individually refined.)

> I checked my log file and it looks like in default automatic individual ADP
> phenix.refine is picking all the residues to be anisotropic even though I
> would not try that at 2.1 A.

That seems unlikely - can you send the logfile to
help at phenix-online.org (*not* the list)?


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