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Re: [ccp4bb] phenix.refine and refmac
 

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CCP4bb <-- 2008 <-- March 2008 <-- 04 March 2008
Previous message:
Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Sophia Tsai sophiats {- at -} USC {- dot -} EDU
Date: 2008-03-04 		Next message:
Subject: Re: multiple sequence alignment from multiple pairwise structural alignments
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-03-04


Subject: Re: phenix.refine and refmac
From: Savvas Savvides savvas {- dot -} savvides {- at -} UGENT {- dot -} BE
Date: 2008-03-04
Hi Yang
how many reflections do you have in your test-set for calculating
R-free? Too few reflections, typically less than 500, may not
constitute a statistically robust cross-validation data set, and thus may
lead to fluctuations in R-free plus a tendency for R-free to increase
as a function of refinement cycle. Some of the early
publications from Axel Brunger on crystallographic cross-validation
address the need for enough reflections (>500) in the test-set. In
addition, the presence of even a handful of strong but inaccurately
measured/integrated low-resolution reflections in a limited test-set
can aggravate abnormal behavior in R-free.

Best wishes
Savvas


toQuoting yang li :

> Dear All,
> I have post a similar question about CNS and refmac before, now in
> another structure I met a similar problem. I have an almost finished
> structure, the Rfree of which
> is about 0.28 by refmac. Then I used phenix to refine it, below is the
> result:
> REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS
> *******************
> REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213
> REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374
> REMARK
> ************************************************************************
> Since the map from phenix couldnot be opened by coot directly--or I
> donnot know how to--I used refmac to get a mtz map file. But I found that at
> the first several cycle of
> refmac the Rfree decreased, then both the R and Rfree values continued
> increasing and FOM decreasing.
> The best R/Rfree/FOM during the refinement is
>
> -----------------------------------------------------------------------------
> Overall R factor = 0.1932
> Free R factor = 0.2513
> Overall figure of merit = 0.8168
> -----------------------------------------------------------------------------
> And after 40 cycles the final result is:
> -----------------------------------------------------------------------------
> Overall R factor = 0.2008
> Free R factor = 0.2772
> Overall figure of merit = 0.7902
> -----------------------------------------------------------------------------
> The values looks like keep going up if increase the cycles. Then which
> value should I take as the final result? The phenix or the best Refmac
> result or I have to take a converged
> value from refmac?
>
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