Hi all,
I looked again careful in the respective files and it turns out that all
B-Factors of the protein chains which are treated with TLS are refined
to the lowest possible value of 2.00 for all atoms!
A workaround is to use the option to set the initial B-factor to 20.0 in
the GUI and than the refinement finally works. I haven't yet figured out
what goes wrong in Refmac, but it seems in the B-Factor refinement step
something gets not treated quite right.
Cheers
Christian
Am 18.06.2015 um 21:58 schrieb Shane Caldwell:
> Hi Christian, I've seen this behaviour as well. I'm not an expert but I
> rationalized the situation as the TLS parameters for an incomplete model
> getting overfit as the missing/wrong parts of the model pull on the TLS
> parameters. REFMAC doesn't alternate between TLS and coordinate
> refinement, so you can get stuck in a local minimum that moving atoms
> and refining individual B-factors won't get you out of. As more of the
> model is built correctly, the drift of this refinement gets less and less.
>
> I've found that refining comparatively few TLS cycles (I usually do 3)
> before the restrained refinement tends to avoid this problem most of the
> time - don't let the TLS refinement converge. Sometimes I'll let the
> coordinate step converge, then run another TLS refinement to bootstrap
> things along, but usually the stats only marginally improve at that
> point. In cases where I've made substantial rebuilds, it's sometimes
> been necessary to turn off TLS and refine without it like you do, then
> re-introduce the same TLS groups, setting the B-factors to fixed values.
> Not really ideal, but it gets there. Hopefully others have some more
> theoretically-sound advice.
>
> A good thing to look at doing, especially if TLS is behaving weirdly, is
> to check with the PARVATI server
> (http://skuld.bmsc.washington.edu/parvati/). If your TLS group
> boundaries set off flags, you have some more work to do on the refinement.
>
>
> Shane Caldwell
> McGill University
>
> On Thu, Jun 18, 2015 at 4:30 PM, Christian Roth
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi all,
>
> I refine a structure with TLS and restrained refinement in Refmac.
> After the run finished, I fixed a few outliers manually in Coot,
> saved that file and used that with the original TLS file from TLSMD
> for the next round of refinement. As soon as the restrained
> refinement starts the R-factors are going up and stabilise than at a
> higher values compared to the previous run.
> If I switch of the TLS refinement and just do restrained refinement
> with the same input files the R-values start initially at a higher
> values and than decrease till they stabilise. Unfortunately the
> final values are about 1.5 % higher, compared to the run with TLS
> before manual rebuilding. So TLS seems to me beneficial and I would
> like to use it, but somehow a strange combination of wrong files?,
> wrong parametrization? or whatever prevent me of doing that.
> Has anyone an idea what might be the cause of that strange behaviour.
>
> Thank you very much in advance.
>
> Cheers
>
> Christian
>
>
--
Christian Roth
Strukturanalytik von Biopolymeren
Fakultät für Chemie und Mineralogie
Universität Leipzig
Deutscher Platz 5
04103 Leipzig
Email [log in to unmask]
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