Dean Madden wrote:
Hi Dirk,
I disagree with your final sentence. Even if you don't apply NCS
restraints/constraints during refinement, there is a serious risk of NCS
"contaminating" your Rfree. Consider the limiting case in which the
"NCS" is produced simply by working in an artificially low symmetry
space-group (e.g. P1, when the true symmetry is P2): in this case,
putting one symmetry mate in the Rfree set, and one in the Rwork set
will guarantee that Rfree tracks Rwork.
I don't think this is right- remember Rfree is not just based on Fc
but Fo-Fc. Working in your lower symmetry space group you will have
separate values for the Fo at the two "ncs-related" reflections.
Each observation will have its own random error, and like as not
the error will be in the opposite direction for the two reflections.
Hence a structural modification that improves Fo-Fc at one reflection
is equally likely to improve or worsen the fit at the related reflection.
The only way they are coupled is through the basic tenet of R-free:
If it makes the structure better, it is likely to improve the fit
at all reflections.
For sure R-free will go down when you apply NCS- but this is because
you drastically improve your data/parameters ratio.
Best,
Ed
