Hi, I’m assuming you’re running a real-space refinement when you observe zero B values after refinement. This is likely because you’re using a sharpened map. Map sharpening is essentially subtracting a common B factor from the map. If you project this onto your model, it means subtracting the mean B from all atoms. Naturally, some fraction of atoms in your model will have B values smaller than the mean, which pushes them toward negative values — but since B values are capped at zero, those atoms end up with zero. As for why your refinement hangs… To find out, we’d usually need to reproduce the problem. That means we’d ask for all input files as well as any refinement parameters you changed. Before we get to that, could you please check if the refinement still hangs using the latest version: https://phenix-online.org/download/nightly_builds.cgi?show_all=1 Pavel On 3/17/25 07:28, [email protected] wrote:

Dear all,

I am encountering issues related to B-factors and ADP refinement in Phenix and would appreciate any insights or suggestions. I am currently working on my first PDB file, but I've noticed that many atoms in the PDB file have a B-factor of 0. As far as I understand, B-factor values are calculated by ADP refinement in Phenix real-space refinement, but even after running real-space refinement (with ADP on in refinement settings), the B-factor remains 0 for many atoms. I am currently using Phenix 1.20 on Windows (Newest version available on window). I also attempted to run Phenix 1.21 on a Linux in other computer, but when ADP refinement is enabled, the process starts normally but halts during the ADP refinement step. So I couldn't test whether the issue is fixed in the newest version.

Aside from the B-factor issue, I am also experiencing an inssue related to ADP refinement:

When I run real-space refinement with ADP refinement enabled, the process starts normally but halts during the ADP refinement step. According to the log file, other refinement steps proceed without issues, but it fails to progress at the ADP refinement stage.​ Additionally, when I try to pause the process, I receive a "NoSuchProcess" error, so ADP refinement process may have unexpectedly terminated.

At first, I thought it's the issue related to system performance or hardware differences, because adp refinement with this pdb file and identical parameters works on some computer but fails on others (the same version of Phenix). Still it's weird because this issue has occurred unexpectedly, as ADP refinement previously worked in my computer under the same conditions without any problems and also other PDB files run without any problems in my computer.

I would appreciate any insights or suggestions on how to resolve this. Thanks _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s