Hi Kendall,

I am resetting the B factors in both cases. TLS definitely helps (does it every not help?).

The goal of using TLS model is not to reduce R-factor, but is to use more physically correct model (this is primary), and eventually reduced R-factor (this is secondary) is the reward for doing so; while increased R-factor will indicate the incorrect ADP model.

If poor fit is the problem, why do I not see the variance with individual ADPs?

Because the ADP restraints are used in case of individual ADP refinement, and no restrains are used in case of group B refinement. Did you try refining individual ADPs with two scenarios:
- using "wxu_scale=true" to optimize weights;
- manually setting very string ADP restraints ?
I would definitely try both options.

I still don’t think it makes physical sense to have one residue in a helix with an ADP of 100 and the next one with 200,

I did not say it is correct or makes physical sense. I just tried to explain why it happens (the most likely reason).

which is what I’m seeing with the one per residue setting. With respect thermal motion, the adjacent residues are attached, so it makes sense to me to have their values restrained.

Copy-paste from my previous email:
"""Imagine one residue that fits density well and its group B-factor refines to a good value and the adjacent residue is out of density and, no surprises, its refined group B is very high. In this case if we apply restrains, we will spoil the group B-factor of the good residue by the high B-factor of the bad one, and we will force the high B of the bad residue to be unrealistically smaller than supported by the density."""

which is saying differently : If both residues fit density well, then applying restraints will not do any harm, and this is not the case otherwise.

If in your particular case both residues fit density very good and the difference between their refined group B-factors is very large, then the problem is somewhere else, and this needs more investigation (which may take a day or more). Also, I will need to be able to reproduce it myself (I need the data and model for this). I will see what it takes to add restrains for group B refinement, at least for experimenting.

Pavel.