Hi All, I have just completed the refinement of 2 structures by phenix, and I'm really really impressed. Particularly impressed by elbow and LigandFit, just wonderful. However, I would be very grateful if someone could point me to the topic already posted in the message below by Dr. Scott few days ago, exactly at: "a quick description for depositing phenix-refined coordinates?", though the full message contained very interesting points I would love to hear about (I also performed refinement by refmac/phenix, and observed kind of a similar trend for those numbers). Thanks in advance. EM *** Enrico Malito Ben-May Department for Cancer Research Center for Integrative Science, W423J The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637 Tel: 773-702-4608 Fax: 773-702-6260 On Jun 30, 2007, at 1:16 PM, William Scott wrote:
Hi folks:
With the helpful advice of the phenix crew, I've re-refined 2goz, an entry in the pdb in which I used refmac5 the first time around.
There was a small error in the pdb: One nucleotide (C8 in chain A) was rotated 180 degrees about the glycosylic bond from where it should have been. The net result is one oxygen atom was in the wrong place in the structure, and this was apparent within the difference Fourier. After I rotated the base and re-refined in refmac, the Rfactor and other stats remained essentially unchanged (so this fix has nothing to do with the following):
My refinement results in Refmac:
REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.241
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1503 ; 0.009 ; 0.021 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2331 ; 1.676 ; 3.000
Then I refined in phenix.
I get
REMARK Final: r_work = 0.1737 r_free = 0.2224 bonds = 0.003 angles = 0.745
So the working and free R factor are both lower, and the geometry is substantially tighter.
If I relax the weights in phenix, even to get rms bonds of around 0.006, the free-R goes up, which tells me this is not something I am justified in doing.
Phil Evans once told me that anything tighter than about 0.01 (conservatively) was science-fiction, in that this is within the error of the idealized libraries for bond lengths.
Other people have asked me about this too, and I didn't know how to reply.
Is bonds = 0.003 angles = 0.745 realistic, or have I done something wrong? Even if I do structure idealization in Refmac, I can't get the rms bonds below about 0.005 (and my understanding is that it uses the same monomer library).
Why is the weight multiplied by 0.5 by default? Since changing that to 1.0 slightly increases freeR, I assume it is the default for some reason.
All the best,
Bill
PS: Could someone point me to a quick description for depositing phenix-refined coordinates? (The latest phenix installer seems to have omitted the docs.)
William G. Scott
contact info: http://chemistry.ucsc.edu/~wgscott
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