On Friday, 02 March 2012, Regina Kettering wrote:
> Rajesh;
>
> I am not sure that you have a high enough data:refinement parameters ratio to
> refine TLS.
> It just adds more parameters to refine that can lead to over-refinement of
> your model,
> especially at the 3.3 A.
I'm afraid you've got this completely backwards.
TLS uses very few parameters, and is especially useful at low resolution.
At 3.3A I would recommend trying a TLS model _instead_ of refining
individual B factors.
NCS restraints also help a lot at low resolution.
So the drop is believable, but...
You should first worry about "lots of waters were placed".
It's there that many extra parameters have been added, perhaps leading
to over-fitting. I would not expect 3.3A data to justify placement of
more than a handful of waters at most.
If you're parameter counting, you might note that 5 water molecules add
more parameters than 1 TLS model. But the TLS model may improve the model
everywhere, whereas the waters will only suppress a few local difference
density peaks.
cheers,
Ethan
>
> HTH,
>
> Regina
>
>
>
> ________________________________
> From: Rajesh kumar <ccp4...@hotmail.com>
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Friday, March 2, 2012 10:54 AM
> Subject: [ccp4bb] sudden drop in R/Rfree
>
>
>
>
> Dear All,
>
> I have a 3.3 A data for a protein whose SG is P6522. Model used was wild type
> structure of same protein at 2.3 A.
>
> After molecular replacement, first three rounds of refinement the R/Rf was
> 26/32.8, 27.1/31.72 % and 7.35/30.88 % respectively.
> In the fourth round I refined with TLS and NCS abd added water and the R/Rf
> dropped to 19.34/26.46. It has almost 7% difference. I also see lot of
> unanswerable density in the map where lot of waters were placed. Model fits
> to the map like a low resolution data with most of side chains don't have
> best density.
>
> I was not expecting such a sudden drop in the R/Rfree and a difference is
> 7.2%.
> I am wondering if I am in right direction. I am not sure if this usual for
> 3.3A data or in general any data if we consider the difference.
> I appreciate your valuable suggestions.
>
> Thanks
> Raj
