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One point which I don't understand is how can someone compare the two different programs when they don't use the same numbers for xray:geometry terms? Taking the default settings for a given resolution might not be enough.. ! On Tue, Mar 4, 2008 at 7:58 PM, Savvas Savvides <[log in to unmask]> wrote: > Hi Yang > how many reflections do you have in your test-set for calculating > R-free? Too few reflections, typically less than 500, may not > constitute a statistically robust cross-validation data set, and thus may > lead to fluctuations in R-free plus a tendency for R-free to increase > as a function of refinement cycle. Some of the early > publications from Axel Brunger on crystallographic cross-validation > address the need for enough reflections (>500) in the test-set. In > addition, the presence of even a handful of strong but inaccurately > measured/integrated low-resolution reflections in a limited test-set > can aggravate abnormal behavior in R-free. > > Best wishes > Savvas > > > toQuoting yang li <[log in to unmask]>: > > > Dear All, > > I have post a similar question about CNS and refmac before, now in > > another structure I met a similar problem. I have an almost finished > > structure, the Rfree of which > > is about 0.28 by refmac. Then I used phenix to refine it, below is the > > result: > > REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS > > ******************* > > REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213 > > REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374 > > REMARK > > ************************************************************************ > > Since the map from phenix couldnot be opened by coot directly--or I > > donnot know how to--I used refmac to get a mtz map file. But I found that at > > the first several cycle of > > refmac the Rfree decreased, then both the R and Rfree values continued > > increasing and FOM decreasing. > > The best R/Rfree/FOM during the refinement is > > > > ----------------------------------------------------------------------------- > > Overall R factor = 0.1932 > > Free R factor = 0.2513 > > Overall figure of merit = 0.8168 > > ----------------------------------------------------------------------------- > > And after 40 cycles the final result is: > > ----------------------------------------------------------------------------- > > Overall R factor = 0.2008 > > Free R factor = 0.2772 > > Overall figure of merit = 0.7902 > > ----------------------------------------------------------------------------- > > The values looks like keep going up if increase the cycles. Then which > > value should I take as the final result? The phenix or the best Refmac > > result or I have to take a converged > > value from refmac? > > > -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [log in to unmask] Phone: + 44 208 816 2515