[phenixbb] Failed ADP refinement with active TLS and weight optimization

[Pavel Afonine]

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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