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Re: [ccp4bb] an over refined structure |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008Subject: Re: an over refined structure From: Dean Madden drm0001 {- at -} DARTMOUTH {- dot -} EDU Date: 2008-02-07 I disagree with your final sentence. Even if you don't apply NCS restraints/constraints during refinement, there is a serious risk of NCS "contaminating" your Rfree. Consider the limiting case in which the "NCS" is produced simply by working in an artificially low symmetry space-group (e.g. P1, when the true symmetry is P2): in this case, putting one symmetry mate in the Rfree set, and one in the Rwork set will guarantee that Rfree tracks Rwork. The same effect applies to a large extent even if the NCS is not crystallographic. Bottom line: thin shells are not a perfect solution, but if NCS is present, choosing the free set randomly is *never* a better choice, and almost always significantly worse. Together with multicopy refinement, randomly chosen test sets were almost certainly a major contributor to the spuriously good Rfree values associated with the retracted MsbA and EmrE structures. Best wishes, Dean Dirk Kostrewa wrote: > Dear CCP4ers, > > I'm not convinced, that thin shells are sufficient: I think, in > principle, one should omit thick shells (greater than the diameter of > the G-function of the molecule/assembly that is used to describe > NCS-interactions in reciprocal space), and use the inner thin layer of > these thick shells, because only those should be completely independent > of any working set reflections. But this would be too "expensive" given > the low number of observed reflections that one usually has ... > However, if you don't apply NCS restraints/constraints, there is no need > for any such precautions. > > Best regards, > > Dirk. > > Am 07.02.2008 um 16:35 schrieb Doug Ohlendorf: > >> It is important when using NCS that the Rfree reflections be selected is >> distributed thin resolution shells. That way application of NCS should not >> mix Rwork and Rfree sets. Normal random selection or Rfree + NCS >> (especially 4x or higher) will drive Rfree down unfairly. >> >> Doug Ohlendorf >> >> -----Original Message----- >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> Eleanor Dodson >> Sent: Tuesday, February 05, 2008 3:38 AM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] an over refined structure >> >> I agree that the difference in Rwork to Rfree is quite acceptable at >> your resolution. You cannot/ should not use Rfactors as a criteria for >> structure correctness. >> As Ian points out - choosing a different Rfree set of reflections can >> change Rfree a good deal. >> certain NCS operators can relate reflections exactly making it hard to >> get a truly independent Free R set, and there are other reasons to make >> it a blunt edged tool. >> >> The map is the best validator - are there blobs still not fitted? (maybe >> side chains you have placed wrongly..) Are there many positive or >> negative peaks in the difference map? How well does the NCS match the 2 >> molecules? >> >> etc etc. >> Eleanor >> >> George M. Sheldrick wrote: >>> Dear Sun, >>> >>> If we take Ian's formula for the ratio of R(free) to R(work) from his >>> paper Acta D56 (2000) 442-450 and make some reasonable approximations, >>> we can reformulate it as: >>> >>> R(free)/R(work) = sqrt[(1+Q)/(1-Q)] with Q = 0.025pd^3(1-s) >>> >>> where s is the fractional solvent content, d is the resolution, p is >>> the effective number of parameters refined per atom after allowing for >>> the restraints applied, d^3 means d cubed and sqrt means square root. >>> >>> The difficult number to estimate is p. It would be 4 for an isotropic >>> refinement without any restraints. I guess that p=1.5 might be an >>> appropriate value for a typical protein refinement (giving an R-factor >>> ratio of about 1.4 for s=0.6 and d=2.8). In that case, your R-factor >>> ratio of 0.277/0.215 = 1.29 is well within the allowed range! >>> >>> However it should be added that this formula is almost a >>> self-fulfilling prophesy. If we relax the geometric restraints we >>> increase p, which then leads to a larger 'allowed' R-factor ratio! >>> >>> Best wishes, George >>> >>> >>> Prof. George M. Sheldrick FRS >>> Dept. Structural Chemistry, >>> University of Goettingen, >>> Tammannstr. 4, >>> D37077 Goettingen, Germany >>> Tel. +49-551-39-3021 or -3068 >>> Fax. +49-551-39-2582 >>> >>> >>> > > > ******************************************************* > Dirk Kostrewa > Gene Center, A 5.07 > Ludwig-Maximilians-University > Feodor-Lynen-Str. 25 > 81377 Munich > Germany > Phone: +49-89-2180-76845 > Fax: +49-89-2180-76999 > E-mail: kostrewa@lmb.uni-muenchen.de > ******************************************************* > > -- Dean R. Madden, Ph.D. Department of Biochemistry Dartmouth Medical School 7200 Vail Building Hanover, NH 03755-3844 USA tel: +1 (603) 650-1164 fax: +1 (603) 650-1128 e-mail: dean.madden@dartmouth.edu CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008 |
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