[ccp4bb] phenix.refine and refmac

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 04 March 2008

Previous message:
Subject: Re: WM DELETE WINDOW
From: Johan Turkenburg jpt {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-03-04

Next message:
Subject: Re: phenix.refine and refmac
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-03-04

Subject: phenix.refine and refmac
From: yang li robertcatrukie {- at -} GMAIL {- dot -} COM
Date: 2008-03-04

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?

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 04 March 2008

Previous message:
Subject: Re: WM DELETE WINDOW
From: Johan Turkenburg jpt {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-03-04

Next message:
Subject: Re: phenix.refine and refmac
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-03-04