Re: [ccp4bb]: REFMAC5 maximum likelihood refinement

["Zac A. Wood" <zac@odysseus.als.orst.edu>]

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Hello,
  I do not know how maximum liklihood is implemented in REFMAC, but in CNS
it is important that the Rfree test set be truly uncorrelated with the
working set.  I am not a guru, but my understanding is that (at least in
CNS) the maximum liklihood target uses the Rfree test set to assign
unbiased sigma A weights prior to refinement.  I had a case where I missed
a higher symmetry space group (used P21 instead of C2221), so the test set
contained symmetry mates. The maximum liklihood target hung up during
refinement, and only when I switched to the crystallographic redidual
target could I get refinement back on track.  I later discovered my
mistake in space group, and by calculating a posteriori Rfree and test set
after the fact and shaking up the structure, the maximum liklihood target
behaved well.  Having said this, I am concerned that your geometry did not
improve.  I would have assumed that if it was a case of model biasing the
refinement that the geometric component of the target would have at least
"idealized" your geometry.  I could be off base here in your case.   Good
luck with your refinement.  I would be interested in hearing how you
resolve it.

zac



On Wed, 3 Jul 2002, [iso-8859-1] 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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                          Zachary A. Wood 

Department of Biochemistry & Biophysics
2011 Agricultural and Life Sciences   
Oregon State University                Tel:(541)-737-3196
Corvallis, OR 97331-7305               Fax:(541) 737-0481
USA                                    E-mail: zac@odysseus.als.orst.edu        
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