Hi Ethan,
> > I also reset the temperature factors to 20 at
> > the beginning of each refinement round. The refinement resolution is 75
> > to 1.8 A, and the space group is C2, if it matters.
>
> I am virtually certain that refinement of individual anisotropic
> U^ij terms cannot be justified at 1.8A. Too many parameters,
> too few observations.
In some cases (high solvent) there may be enough reflections to give your atoms
anisotropic B-factors. Look for instance at PDB entry 1tv4, it has 19.5
reflections per atom, 1rzh has even more. When in doubt, I use a Hamilton test
to see if anisotropic Bs are acceptable.
That said, of course your residual B-factors after TLS can be anisotropic, but
TLS + anisotropic Bs don't seem right to me either. You might as well use
anisotropic B-factors and then extract TLS tensors from them. That was the
original point of TLS anyway.
Cheers,
Robbie
>
>
>
>
> >
> > The problem comes when I take the output from such a run, model build in
> > Coot, and feed it back in for the next round of refinement. As you can
> > see from the summary table below (trimmed for brevity), the refinement
> > blows up rather badly, making the R factors and the geometry
> > substantially worse.
> >
> > Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND
> > rmsANGL zANGL rmsCHIRAL $$
> > $$
> > 0 0.3376 0.3576 0.556 115671. 6318.1 0.0
> > 0.0 0.0 0.0 0.0
> > 5 0.2676 0.2921 0.680 109411. 6009.2 0.0
> > 0.0 0.0 0.0 0.0
> > 9 0.2529 0.2785 0.703 108589. 5978.4 0.0
> > 0.0 0.0 0.0 0.0
> > 10 0.2516 0.2787 0.710 108459. 5975.2 0.0170
> > 0.829 1.534 0.731 0.097
> > 15 0.2503 0.2876 0.711 108711. 6042.1 0.0241
> > 0.998 1.729 0.833 0.111
> > 20 0.2739 0.3152 0.672 110787. 6147.3 0.0268
> > 1.103 1.837 0.885 0.119
> > 25 0.2949 0.3388 0.638 112219. 6215.4 0.0255
> > 1.049 1.808 0.866 0.116
> > 30 0.3114 0.3575 0.609 113094. 6257.7 0.0243
> > 1.006 1.794 0.854 0.114
> >
> > This refinement also throws out an enormous number of warnings about
> > adjacent atoms' B factors being substantially different. Most of these
> > warnings appear to involve the autobuilt riding hydrogens and their
> > adjacent heavy atoms.
> >
> > If I use pdbcur to strip out the ANISOU lines, but otherwise keep the
> > file and refinement protocol unchanged, it goes along nicely:
> >
> > Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND
> > rmsANGL zANGL rmsCHIRAL $$
> > $$
> > 0 0.2912 0.3233 0.667 112220. 6151.2 0.0
> > 0.0 0.0 0.0 0.0
> > 5 0.2476 0.2787 0.751 107853. 5934.7 0.0
> > 0.0 0.0 0.0 0.0
> > 9 0.2468 0.2764 0.754 107501. 5915.6 0.0
> > 0.0 0.0 0.0 0.0
> > 10 0.2469 0.2763 0.754 107480. 5914.2 0.0170
> > 0.829 1.534 0.731 0.097
> > 15 0.1933 0.2387 0.810 101501. 5723.3 0.0238
> > 0.994 1.791 0.868 0.118
> > 20 0.1849 0.2327 0.817 100446. 5694.7 0.0239
> > 0.992 1.826 0.884 0.120
> > 25 0.1818 0.2316 0.821 100034. 5681.0 0.0223
> > 0.925 1.775 0.855 0.114
> > 30 0.1804 0.2296 0.824 99820. 5669.4 0.0221
> > 0.913 1.763 0.848 0.113
> >
> > (Without TLS refinement, the final R and Rfree would be 0.1896 and 0.2503.)
> >
> > So, what's happening here? Does Refmac not like ANISOU lines in the
> > input PDB file? I don't usually work with structures at a resolution
> > high enough to warrant aniso B refinement, so I haven't encountered this
> > before.
> >
> > Thanks for any advice,
> >
> > Matt
> >
> >
> >
>
> --
> Ethan A Merritt
> Biomolecular Structure Center, K-428 Health Sciences Bldg
> University of Washington, Seattle 98195-7742
