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 <[EMAIL PROTECTED]>:
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?
