Hi Andy,
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. Pavel.