Dear CCP4ers,
I refined a 3.4 A SAD data in refmac ( using the 'SAD data directly' option
) and reached a plateau with an Rfree of 36%. Then I tried to extend phases
with the 2.95 A dataset which has no anomalous data (I maintain the same
Rfree flag). The maps look like a moderately good fit, but the Rfree doesn't
go below 39%.
With Autobuild in phenix, map looks good and Rfree went down to 36% but
doesn't change further. Deletion of a 10 residue loop for which no density
is visible increases Rfree.
Model bias is still persistent as sidechains deleted earlier don't come
back. Finally, even with the good density-model fit, there are huge areas of
negative difference density and few areas of positive density.
I also tried a round of simulated annealing in CNS, but it didn't change the
Rfree. Playing with the weights hasn't made much difference either. TLS
refinement also doesn't make any difference. Any ideas how to go about?
Thank you.
Kumar
