[phenixbb] TLS and ligand question

Andy Torelli att29 at cornell.edu
Wed Nov 25 10:19:33 PST 2009

To the Phenixbb community:

	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).

	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.  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.

	So, should I be treating the ligands differently if I intend to use 
TLS?  I tried including them with one of the TLS groups, but that didn't 
help.  Any other ideas are welcome.

Best Regards,
-Andy Torelli

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