I was being somewhat provocative - as Ian Tickle says, different cases
behave differently.
Multiple copies in the asymm unit, high solvent content, and excellent
data can all contribute to better Free R factors than the norm for a
given resolution.
However a lot of people struggle endlessly to reduce the Free R to an
unrealistc match to the working R factor, and there are numerous ways to
get the ratio wrong - change data set without copying FreeR values from
the one you have already refined against, etc etc..
Eleanor
Andrew Torelli wrote:
Professor Dodson (and the ccp4 community),
I apologize for dragging up old messages, but I'm interested in a
response you gave to a previous post and I needed time to research it
myself. On September 11th, in the "question about refinement" thread,
you commented that Rfree and R values of 24% and 20.5%, respectively
for a 2.4angstrom structure are "unreasonably close".
I understand that there are theoretical values for the
Rfree/Rfactor ratio that are expected for refined structures (at a
given resolution) using a least-squares target (thanks to Jack
Tanner's July 5th post with references from Ian Tickle's group).
However, for maximum likelihood (which I assume was being used to
refine the structure in question), I would expect the difference
between the Rfree and Rfactor to be the same or smaller compared to a
least-squares refinement. I reference:
Adams P.D., Pannu N.S., Read R.J. & Brunger A.T. (1997)
Cross-validated maximum likelihood enhances crystallographic simulated
annealing refinement. /Proc Natl Acad Sci U S A/, *94,* 5018.
Assuming a properly chosen test set (i.e. sufficient size, NCS is
accounted for properly, etc.), what considerations lead you to expect
(and desire)a much larger difference in the Rfree/Rfactor values?
Under what circumstances should one interpret large differences as
overfitting? I look forward to learning more about useful studies,
criteria and guidelines you and other members of the ccp4bb
community rely upon during (maximum likelihood) refinement.
Thank you in advance for your time,
Best Regards,
-Andy Torelli
Andrew Torelli, M.S.
Ph.D. Candidate, Dept. of Biochemistry & Biophysics
University of Rochester School of Medicine & Dentistry
Box 712, 601 Elmwood Ave, Rochester, NY 14642
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