Dear Rohit, Look at what percentage of the reflections are in the Rfree set, if its less say 5 %; and you have a good redundancy you can use 10 %. You might like to use the other Rfree set[1 if you have already used the 0 set] or consider using the whole set of reflections as a free set if need be if you suspect a bias in your Rfree set.
As suggested earlier I would also look at how the Fobs and Fcalc correlate as a function of resolution from the sigma A plot or CC* values. Sometimes overestimating the resolution would add up more noise and it would give you bad R values. and If the molecule is elongated you might have diffraction anisotropy and in that case The R values don't come down. I would also like to use Refmac along with Phenix; that helped in my case. So you would like to take them one by one and figure out carefully. Best Wishes Ashok Nayak Post-Doctoral Fellow, Department of Physiology and Biophysics VCU Medical Centre,1101 E Marshall ST, Richmond,VA USA On Wed, Dec 14, 2016 at 11:12 AM, Morais, Marc C. <[email protected]> wrote: > In addition to what others have mentioned, you might want to consider the > unpleasant possibility that part of your structure is simply built > incorrectly. Sometimes rebuilding a short loop or even a few residues in > that loop can do the trick. Look carefully for regions of your map with > poor density and/or regions of your model with poor geometry, and see if > there might be an alternate way to build that region. There is often a > psychological barrier to attempting these rebuilds, because they are > difficult (if they weren't we would have built correctly the first time). > However, once begun, it is often less painful than expected. SA/composite > omit maps can help. > ------------------------------ > *From:* CCP4 bulletin board [[email protected]] on behalf of Eleanor > Dodson [[email protected]] > *Sent:* Wednesday, December 14, 2016 9:49 AM > *To:* [email protected] > *Subject:* Re: [ccp4bb] R/Rfree values > > es - look carefully at your data quality indicators - batch scales, Wilson > plot - moments etc.. tHese can show up if there is a problem with ice rings > or crystal decay or whatever. > Then I always look at the REFMAC plot of <Fobs> v <Fcalc> > If they overlap well - good - but problems with scaling will show up there. > > Eleanor > > On 14 December 2016 at 15:21, Mark J van Raaij <[email protected]> > wrote: > >> Dear Rohit, >> >> I wouldn’t judge a structure just by the Rwork and Rfree values, but also >> by the validation and other statistics (bond lengths, angles, Ramachandran >> plot, map quality, fit to map, average B values). If these are all ok, you >> should be able to “get away with” an Rfree of 33%. >> In your email you state that you have already made a significant effort >> in different refinement strategies, so perhaps there is no improvement to >> be made there. >> The reason for the high-ish Rfree could be that the data is not so good, >> and reprocessing might help. Although the most likely outcome is that you >> can’t significantly improve it, but at least trying will put your mind more >> at ease. >> In the end, the only way to improve the structure, and R-factors, may be >> to grow a better crystal, cryo-protect better and/or collect better data - >> this particular crystal may just have some kind of disorder. >> >> Greetings, >> >> Mark J van Raaij >> Dpto de Estructura de Macromoleculas >> Centro Nacional de Biotecnologia - CSIC >> calle Darwin 3 >> E-28049 Madrid, Spain >> tel. (+34) 91 585 4616 >> http://wwwuser.cnb.csic.es/~mjvanraaij >> >> >> >> >> >> >> >> > On 14 Dec 2016, at 16:02, rohit kumar <[email protected]> wrote: >> > >> > Dear All, >> > >> > I am solving a data of 2.5 A (C121 space group). Right now the R/Rfree >> values are 26/33, after many cycles of refinements (With or With out water) >> the R/Rfree values still same. Zanuda suggests that the space group seems >> to be correct and the model is looking fine in coot. >> > Some one suggest what is the main problem. >> > Should I again process my data? And what is the best way to fine right >> space group (If problem with space group). >> > Please tell me if you need any information regarding may data. >> > >> > -- >> > WITH REGARDS >> > Rohit Kumar Singh >> > Lab. no. 430, >> > P.I. Dr. S. Gourinath, >> > School of Life Sciences, >> > Jawaharlal Nehru University >> > New Delhi -110067 >> > > --
