What is the resolution? Are you using ncs restraints (you probably
should, on the coordinates but not on the Bs)? How does your
Ramachandran plot look?
You might tighten the geometry even more. Aside from all theoretical
arguments about how big the rmsd's should be, if they're rather
loose, things that are built incorrectly may be shoved back into
density, making mistakes harder to spot.
Have you made sure that all your side chains are not just in the
density, but in nice, non-strained rotamers?
The backbone and side chains are rather couple in refinement,
especially if you don't have very high resolution data - this means
that if you originally had the backbone slightly wrong, you may have
built the side chains in the wrong rotamers. They'll look like they
fit the density, but everything will be a bit strained until you fix
them. Particularly if your Ramachandran plot is a bit scruffy, try
optimizing the backbone geometry (by something such as lego in O),
then refitting the side chains.
Phoebe Rice
At 11:33 AM 2/4/2008, you wrote:
Hi Tim,
Thank you for your and information and suggestions. There are two
indepdent molecules in the asymmetric unit and one molecule does not
have very good density, especially in the N-terminus.
Do you think that I should remove the region in the refinement?
Best,
Sun
Tim Gruene <[EMAIL PROTECTED]> wrote:
I would agree that the difference is suspiciously high. I. Tickle and
others have published analytical expressions for how to estimate the ratio
between R and Rfree, just google for "tickle rfree" to find the
references.
You easily achieve a large difference by adding too many waters which just
model noise. There may be other reasons for which more knowledge about the
structure is required. Do you have large unmodelled regions, like loops
that do not show in the density map?
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Mon, 4 Feb 2008, Sun Tang wrote:
> Hello All,
>
> I refined a structure with Refmac in CCP4i and the R/Rfree is
0.215/0.277. The difference between R and Rfree is too much even
though I used 0.01 for weighting term in the refinement (the
default value is 0.3). The RMSD for bond length and bond angle is
0.016 A and 1.7 degree.
>
> What may be wrong with the over-refined structure? What is the
reason for leading to an over-refined structure? How to avoid it?
>
> Best wishes,
>
> Sun Tang
>
>
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Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
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