[phenixbb] Rfree and a low resolution data set

Andreas Forster docandreas at gmail.com
Wed Apr 4 03:21:40 PDT 2018

Dear Toon,

this does't answer your question, but cutting your data at 3.6 Å is
probably not the best way of continuing.  Try processing with autoPROC or
submit the full data to the staranio server (staraniso.globalphasing.com)
to get a better representation of the extent of reciprocal space that your
experiment covers.  You will end up with more reflections for refinement

All best.


On Wed, Apr 4, 2018 at 11:47 AM, Toon Van Thillo <
toon.vanthillo at student.kuleuven.be> wrote:

> Hi all,
> Currently I am refining a data set which showed anisotropic diffraction.
> Aimless suggested cutoffs at 2.3, 2.6 and 3.6 angstrom for the h,k and l
> axis.
> I chose a general 3.6 cutoff to obtain satisfactory statistics for Rmeas,
> I/sd(I) and CC1/2. At this resolution the data set consists of
> approximately 2800 reflections.
> Generally 5% of the set is set aside as the Rfree test set and I found
> that a minimum of 500 reflections in total is used to produce a reliable
> Rfree. However, 5% only amounts to 140 reflections in this case. I am
> hesitant to include more reflections as I would have to go up to 20% of the
> reflections to obtain more than 500 reflections for the test set. In a
> discussion on the CCP4 message boards some time ago it was suggested to do
> multiple refinements with different test sets:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1411&L=
> ccp4bb&F=&S=&P=125570
> In the thread it was also discussed that a least squares approach is
> prefered when using a small test set. However, when using a LS target, the
> resulting Rfree is very high (10% higher than when using the automatic
> option) and *phenix.refine*​ produces awful geometry (24% ramachandran
> outliers, 105 clashcore...). It seems that the refinement is performed
> without restraints? Optimize X-ray/stereochemistry weight does not result
> in improved stereochemistry. My question is if the LS approach is still
> relevant and if so, is there an explanation (and solution) for the bad
> statistics?
> Kind regards,
> Toon Van Thillo
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