[phenixbb] R/Rfree from phenix.autobuild

[Thomas C. Terwilliger]

Hi Graeme,

I agree with everything that Pavel pointed out yesterday.  I have added
below a tabulation of R/Rfree for a set of 46 structures from the PHENIX
library, solved with autosol and then built with autobuild. You will see
that your result is not unprecedented (e.g., the p9 structure), but a
slightly larger spread of 0.02 to 0.06 is more common:

R	Rfree	Resolution	structure
0.17	0.24	1.80	pen
0.17	0.22	2.80	rh-dehalogenase
0.18	0.23	2.52	flr
0.19	0.25	2.40	mev-kinase
0.20	0.21	1.75	p9
0.20	0.24	2.25	gpatase
0.20	0.23	2.50	aep
0.20	0.23	1.90	myoglobin
0.21	0.24	2.80	s-hydrolase
0.21	0.23	2.40	cyanase
0.21	0.26	2.00	tryparedoxin
0.22	0.25	1.80	mbp
0.22	0.26	2.00	cobd-sad
0.22	0.25	1.95	nsf-n
0.22	0.27	2.50	psd-95
0.22	0.25	3.00	1038B
0.22	0.30	2.60	gene-5
0.22	0.25	1.80	epsin
0.23	0.28	2.50	p32
0.23	0.26	2.40	armadillo
0.23	0.27	2.40	nsf-d2
0.23	0.26	1.80	ic-lyase
0.24	0.30	2.80	cp-synthase
0.24	0.29	2.30	vmp
0.24	0.26	1.10	calmodulin
0.24	0.36	3.00	hn-rnp
0.25	0.28	2.00	synapsin
0.26	0.27	1.70	insulin
0.26	0.28	2.80	ut-synthase
0.26	0.29	1.71	1063B
0.26	0.31	2.50	rnase-s
0.26	0.30	2.33	gran-orig
0.28	0.30	1.50	rnase-p
0.28	0.34	3.00	1071B
0.29	0.34	2.50	1102B
0.29	0.36	2.60	rab3a
0.29	0.33	2.00	1167B
0.30	0.35	2.70	gere
0.30	0.33	2.10	pdz
0.30	0.32	1.90	rop
0.34	0.40	3.30	sec17
0.35	0.43	2.50	qaprtase
0.41	0.47	3.20	synaptotagmin
0.41	0.48	3.80	groel
0.43	0.48	2.90	fusion-complex
0.43	0.47	3.50	group2-intron


All the best,
Tom T

> Hi Folks,
>
> Quick question about R/Rfree from phenix - I ran the autobuild and it
> kindly built pretty much all of the visible residues, and it gave me
> the following output:
>
> SOLUTION  CYCLE     R        RFREE     BUILT   PLACED
>  1         1      0.22        0.23      169       169
>  2         2      0.21        0.23      170       170
>  3         4      0.22        0.23      170       170
>
> Now, I'm not one to complain about good results, but I did feel that
> the Rfree looked a little close to the R factor - usually I would
> expect a difference of maybe 4-5%. Is there a reason for this that I
> am missing? The model seemed to fit very nicely, closely corresponded
> to the PDB entry and the waters were pretty good. There is no NCS (one
> copy in the ASU) and the phases are from SeMet mad data from Autosol.
>
> Resolution is ~1.6A, if that is any help.
>
> Just noticed this and thought it was interesting. I am used to
> Arp/wArp for automated tracing, which typically gives a bigger
> difference...
>
> Many thanks,
>
> Graeme
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