Hi Ling,
I have no idea what the error estimate based on R means. In
phenix.refine the ML based coordinate error estimate is done as
described in formula #19 in
Acta Cryst. (2002). A58, 270-282
with the ML parameters determined as described here:
Acta Cryst. (1995). A51, 880-887.
and
J. Appl. Cryst. (1996). 29, 741-744.
This number is sensitive to many (irrelevant) thins such as
bulk-solvent model, etc.. So I wouldn't take it too literally. Model
to map fit, map quality, local and global, geometry stats and
Rfactors are all much more useful model quality characteristics than
this number.
Pavel.
On 8/12/10 10:04 AM, Ling Qin wrote:
Dear Colleagues,
I am refining a 2.15 A structure that was previously refined with
refmac by someone else. Without changing anything in the
refmac-refined model and using all the default phenix.refine
settings, I am getting pretty much the same R and Rfree (from
19.3%/21.7% to 18.9%/21.8%), with an ML estimated error of 0.22 A.
In the refmac-refined pdb file, the estimated error is much lower:
0.16 (based on R), 0.144 (based on Rfree), and 0.096 (based on
ML). I am using phenix.refine version 1.6_289, but also tried
1.5_2 with the same result. Is there an underlying reason for this
difference? Thank you very much for your insightful opinions in
advance.
Cheers,
Ling
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