There might be a few reasons for these R-values which seem to contradict
experience:
1) The starting phases result from MR where the model is very close and
from a data set at higher resolution. If your 3.1A data are of
respectable quality, the model would still correspond well to the data,
hence both R and Rfree are low (-er than the "10% rule": Expect the
Rwork to be around 10% of your data set resolution).
2) Your data are not complete, maybe due to the twinning
3) You messed up with your test set and entangled it to the model somehow,
e.g., because you collected a second data set and did not import
Rfree from the original one. If the model was already overrefined
against the initial model your Rfree would come too close to the
R-value, even though your model is wrong.
4) You might just be a very good modeller and your data, even though only
low resolution, are rather accurate.
I am sure there are more reasons. Yet, I would be very suspicious with
such a low Rvalue at this resolution.
John, you could try
- calculate an omit map
- remove a major part of you model, run a quick refinement and see if the
density of the removed part comes back - this should indicate that you
did not overrefine against your data
- try simulated annealing
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Tue, 23 Oct 2007, Anastassis Perrakis wrote:
Dear J.Kryst -
I am basically very puzzled to see that a 3.1 A structure has R and Rfree of
15.3 and 23.8 % respectively !
Is that the diffraction limit of the crystal or is it a home dataset
collected with rather short exposures?
Is the Wilson B very low by any chance ?
As for the gab, I am too puzzled by the absolute values to even think of it.
I would had never expected a 3.1 A twin dataset
to give Rfrees anywhere else than the high 20's- let alone R below 20 !
Tassos
PS How do you pronounce J.Kryst really?
On 23 Oct 2007, at 6:54, john kryst wrote:
Hi ccp4bb !!
I am refining a 3.1 A resolution structure which has partial twinning
with twinning fraction 0.27 (space group P61).
When i refined in CNS with twin_lsq target i got 0.1529 and 0.2384 as R and
Rfree.
There is almost 8-9% gap in R and Rfree. Map quality is good enough to
trace all
the atoms and ligands.
There is nothing much to build in the map too. Any suggestions to reduce
the gap in R and Rfree. I couldn't use shelxl because of the resolution. Is
it OK to stop refinement and submit the structure.
with warm regards
John
