[phenixbb] Group ADP refinement restraints

[Taylor Stevens]

Hello,

I am currently refining a low-ish resolution structure (through the phenix.refine GUI) with phenix version 1.14 and had some questions about the use of restraints in group ADP refinement. In the phenix.refine documentation (https://www.phenix-online.org/documentation/reference/refinement.html#refinement-of-atomic-displacement-parameters-adp-or-b-factors <https://www.phenix-online.org/documentation/reference/refinement.html#refinement-of-atomic-displacement-parameters-adp-or-b-factors>) it is stated that “Group isotropic ADP or TLS refinement do not use any restraints”, however, this does not seem to be the case. If I look in the log file I can see the following lines of text which I believe indicate that the restraints are being applied:

|-group b-factor refinement (macro cycle = 0; iterations = 0)————————|
| r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = None  |
|——————————————————————————————————————|
|-group b-factor refinement (macro cycle = 1; iterations = 22)————————|
| r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871|
|——————————————————————————————————————|
|-group b-factor refinement (macro cycle = 2; iterations = 22)————————|
| r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871|
|——————————————————————————————————————|
|-group b-factor refinement (macro cycle = 3; iterations = 22)————————|
| r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871|
|——————————————————————————————————————|

If I manually set the wu parameter to 0 under “Refinement target weights" nothing changes, however, if I navigate to "All parameters > ADP settings > Group B-Factors" in the GUI there is a “Use restraints” box that is checked by default. If I uncheck this box, there are no longer any restraints being applied according to the log file, and in the case of the structure I am refining, there is a substantial drop in the rfree/rwork. Is this an issue with the program or documentation? Or am I misunderstanding how the program is supposed to work? Is it generally a good idea to use group ADP refinement without restraints?

Thanks,

Taylor
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