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Re: [ccp4bb]: REFMAC5 maximum likelihood refinement
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Dear Wolfram:
I am new to refmac so I can hardly be considered and authority. But my
understanding is the idea behind m.l. refinement is to do no more
refinement than is justified, whereas minimizing a crystallographic
residual (in the conventional manner) tends to over-refine the data.
I've noticed both in CNS and in refmac that conventional
crystallographic residual refinement always gives me lower R-factors
than does m.l. refinement, all other things being equal. This does not
mean that the refinement is better. The maps, and therefore the
structure, will be less biased. Also I wouldn't call a 2% increase
"dramatic." Differences in the methods for calculating a solvent mask,
different libraries for scattering amplitudes, geometric parameters,
etc. could also easily account for some if not all of the 2%
difference. FWIW I am becoming convinced that refmac works better than
CNS for a final refinement, at least in my hands.
Bill Scott
On Wednesday, July 3, 2002, at 04:03 PM, Wolfram Tempel wrote:
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> Hi all,
> under which circumstances would maximum likelihood target refinement in
> REFMAC5 produce a dramatic INCREASE in R (from 0.187 to 0.208) and Rfree
> (from 0.232 to 0.257) with 1.8A data? This was not accompanied by
> improved geometry (reduced RMSs). Any idea where I should start looking
> for the underlying problem?
> Thank you.
> Wolfram Tempel
> U. of Georgia
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