Dear all,
I am blessed/tormented with a 0.8 A data set for a small protein. I
first refined it using COOT/REFMAC5 until I deemed it done, which meant
manually adding quite a few water molecules that were weak and a little
more distant to the protein. R is 10.2%, R-free is 10.8%.
I realize that referees will probably ask for a SHELXL refinement, so I
spent the last few days learning about FVAR and SUMP instructions and
the like and finally got it running in a way I thought should be
correct. Using my final REFMAC5 model, I get R=10.8% and R-free=11.1% -
I can certainly live with this, but:
When I now look at the electron density, a large number of my tenderly
curated water molecules have lost their 2FO-FC electron density (50 out
of 200; I usually use a 1 sigma cutoff), or they have shifted to lie
beside a density blob. It may have to do with the fact that I assigned
0.5 occupancy to some of them and now they have been BUMPed away, others
may simply be too weak to stay in place.
I wonder what to do now. Do I have to rebuild the water structure again
and refine everything in SHELXL exclusively? Or are there any flags I
could use to keep the old waters intact (risking higher R-factors)?
Any help is highly appreciated!
Thank you in advance,
Wulf
