Hello Juan
First, there's a phenix.refine bulletin board, on which you might
attract the attention of the developers, which might help.
http://www.phenix-online.org/mailman/listinfo/phenixbb
I've been using 1.17-3644 without issues after transitioning from
something older. Consider downgrading to something new-ish.
At first glance this looks like a change in the weighting between the
X-ray term and the (sum of) the geometric terms - if you are using a
wxc_scale command or explicit weighting value I'd turn that off and see
what happens. But you say that you've been using weight optimization,
which seems to suggest otherwise.
What are your Rwork, Rfree, RMSD bonds, RMSD angles, Rama stats for the
same model in the two refinement program versions ? If the weight
changes the Rwork vs geometry should be a pretty easy indicator. If you
get worse geometry with the same Rwork that's a lot more troubling.
And, try REFMAC. REFMAC is usually faster, and on a couple of high
resolution projects gave a significant drop in Rfree. Usually they are
comparable but it's worth running both to see what happens.
Things that traditionally give me issues in phenix.refine are: real
space refine subprocess sometimes "unrefines" my structure (try turning
it off); there appears to be enough of a difference between first and
subsequent passes of the weight estimation that the weight-refinement
scheme gets thrown off.
Phil Jeffrey
Princeton
On 7/21/20 10:40 AM, JUAN ESTEVEZ GALLEGO wrote:
Dear all,
I have been working on the refinement of a crystal structure using
phenix.refine from the 1.12-2828-Intel-Linux-2.6 version of Phenix. I
have recently replaced my computer by a MacBook and I have upgraded
Phenix to the 1.18.2-3874-MacOs version. However, I found that the
refinement introduced an amazing huge amount of outliers, specially
C-beta and ramachandran.
The structure is at 2.5A resolution and I used the following refinement
strategy: XYZ coordinates, Real-space, Individual B-factors,
occupancies, X-ray/stereochemistry weight optimization, no experimental
phase restrain, automatic metal and ligand linking and automatic correct
N/H/Q errors. I also tried using TLS instead of Indivudal B-factors, but
the problems persist.
Does anybody know why this could be happening? Thanks a lot for your help!
Best,
Juan
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