[phenixbb] some general refine questions
William Scott
wgscott at chemistry.ucsc.edu
Sat Jun 30 11:16:08 PDT 2007
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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