[phenixbb] Failed ADP refinement with active TLS and weight optimization
Pavel Afonine
pafonine at lbl.gov
Mon Aug 10 11:12:02 PDT 2015
Hi Carsten,
please send me files off-line so that I can investigate.
Thanks,
Pavel
On 8/10/15 11:08, Schubert, Carsten [JRDUS] wrote:
>
> Hi,
>
> I am running into some strange issues with regards to ADP refinement
> especially when I am putting final touches on a structure for PDB
> submission. The problem manifests itself most prominent in the
> B-factor refinement of solvent, but also maps are affected and are
> becoming noisier, so I assume this problem affects the protein as
> well. I checked this against the current release 1.9 and the latest
> pre1.10 dev version, both versions show the issue. Refinement protocol
> includes individual_xyz, individual_adp, TLS and weight optimization.
>
> The problem I am running into is that the ADP of waters only changes
> by a global offset. The problem is tricky to spot but more evident
> when looking at solvent placed in coot with the default ADP (30). The
> ADP changes only by a global offset, no individual refinement takes
> place. Since the protein is refined by TLS the problem is not as
> evident, but as mentioned the fofc maps get noisier from cycle to
> cycle even though no manual change to the geometry was performed. To
> me an indicator that the B-factors are not refined properly.
>
> The problem can be circumvented by reverting back to isotropic
> B-factors and then refine with weight refinement for 5-10 cycles.
> After that TLS can be switched back on for a final polishing cycle. In
> stubborn cases I had to randomly assign B-factors close to Wilson-B
> and refine for more cycles to get out of the hole I refined myself into.
>
> Another indicator that something went awry is the weight refinement
> for the B-factors:
>
> ----------Individual ADP refinement----------
>
> R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS
>
> work free delta data restr
>
> 20.66 26.39 5.73 5.712 67.871 2.160 5.225
>
> 20.66 26.38 5.73 5.712 67.871 0.030 5.225
>
> 20.66 26.38 5.73 5.712 67.871 0.125 5.225
>
> 20.66 26.38 5.73 5.712 67.871 0.500 5.225
>
> 20.66 26.38 5.73 5.712 67.871 1.000 5.225
>
> 20.66 26.38 5.73 5.712 67.871 1.500 5.225
>
> 20.66 26.38 5.73 5.712 67.871 2.000 5.225
>
> 20.66 26.38 5.73 5.712 67.871 2.500 5.225
>
> 20.66 26.38 5.73 5.712 67.871 3.000 5.225
>
> 20.66 26.38 5.73 5.712 67.871 3.500 5.225
>
> 20.66 26.38 5.73 5.712 67.871 4.000 5.225
>
> 20.66 26.38 5.73 5.712 67.871 4.500 5.225
>
> 20.66 26.38 5.73 5.712 67.871 5.000 5.225
>
> Essentially there is no change in R/Rfree with regards to different
> weights.
>
> I have not figured out the exact time point when this happens during
> the course of the refinement but it seems to be coupled to using TLS
> in combination with ADP refinement and during the final stages of the
> refinement.
>
> I can provide data offline to reproduce the issue
>
> Cheers,
>
> Carsten
>
>
>
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