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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