[phenixbb] TLS and ligand question
PAfonine at lbl.gov
Wed Nov 25 10:30:02 PST 2009
> I've been experimenting with using TLS to refine my 2.4 angstrom
> resolution structure. There are 2 protomers in the ASU, and each has a
> metal cluster and a small-molecule ligand. The model has a relatively
> high average B-factor for protein (~65) atoms and I also suspect that
> both the cluster and the ligand have partial occupancy. At this
> resolution however, I've modeled both groups with 100% occupancy and the
> average B-factors for the atoms of these groups are expectedly higher,
> ~100 after individual_sites and individual_adp refinement (i.e. no TLS).
Still, I would try refining group occupancy factor for ligands (one
refinable occupancy per whole ligand), and before doing so I would
re-set ligand's B-factors to an average value.
> My problem arises when I try to use TLS. I determined the boundaries
> for the TLS groups using the TLSMD server, which identified 3 groups per
> protomer (roughly coincide with domain boundaries). After including TLS
> refinement, the R and R-free both improve by 1-2%, but the B-factors for
> the clusters and ligands end up very high.
As far as I know there is still no consensus about if one needs to
include water, ions or small ligands into TLS groups. I did a few
experiments in the past and at that point I found that not including
them into TLS groups worked better. But I was using really a few test
structures so this is not conclusive.
I would not include them into TLS groups, and try refining group occupancy.
> Metal atoms in the cluster
> have B-factors >350 and the ligand atoms have B-factors >120. The
> average B-factor for protein atoms is slightly higher too (~70). Also,
> the gap between R and Rfree is larger than I'd expect (19% R and 26%
> Rfree), although this isn't unheard of and more importantly, the values
> have fully converged yet.
Try optimizing weights: "optimize_wxc=true optimize_wxu=true", it may help.
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