Dear all,
I'm refining a structure (with TLS, Hs in riding positions) to 2.9A -
Rfree ~29.9%/Rfac 26.5% in Refmac5 v5.2.0019. Rmsd bonds 0.008A/1.1deg
angles.
In COOT (0.31) many of the residues whose side chains are (fully or
partially) set to 0.00 occupancy have really bad geometry...for want of
a better description, the side-chains literally look like they have
exploded...a few are intact but have distorted planarity. This occurs in
25 residues out of 480 in the ASU.
I have tried:
1. refining without TLS - no change
2. no hydrogens - no change
3. refining OVERall B-factors instead of ISOtropic - overall geometry
much worse (rmsd 0.088 bonds)
4. DAMP 0.5 0.5 - no change
5. BABINET scaling instead of SIMPLE - no change in geometry, Rfree and
Rfac increase ~3%
6. relaxing geometry (rmsd 0.019A bonds/1.8deg angles)
This occurs with two other structures at higher resolution (~2.5A),
although only a few violations..it seems to be much worse at low resolution.
Any ideas ?
Thanks,
Iain
