[phenixbb] TLS and ligand question

[Pavel Afonine]

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.