Dear Yang,
it would be better if you could provide more details about your
refinement strategies.
As I can see from your results you might have used the default values in
phenix giving you finally very low rmsd values. Refmac by default is not
using so tight restraints and even if you used tight restraints in
refmac the difference between R and Rfree might be much lower than the
7% in Phenix. I am guessing that the values that you are reporting have
to do also with the weight values each program uses and how you are
define them. Also have you used TLS in any of the two programs?
regards
Nikos
---------------------------------
Dr. Nikos Pinotsis
Section of Structural Biology
Institute of Cancer Research
Chester Beatty Laboratories
237 Fulham Road
London SW3 6JB, UK
Tel: +44 20 7153 5453 / 5447
---------------------------------
yang li wrote:
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?
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