I usually send the pdb back to the tlsmd server after any manipulation of the model just to be on the safe side. I'm not sure whether that'll make any difference in your case but it's perhaps worth trying.
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
E-mail: [log in to unmask]
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [[log in to unmask]] on behalf of Christian Roth [[log in to unmask]]
Sent: Thursday, June 18, 2015 11:30 PM
To: [log in to unmask]
Subject: [ccp4bb] Refmac refinement R factors going up..... TLS issue?
I refine a structure with TLS and restrained refinement in Refmac. After
the run finished, I fixed a few outliers manually in Coot, saved that
file and used that with the original TLS file from TLSMD for the next
round of refinement. As soon as the restrained refinement starts the
R-factors are going up and stabilise than at a higher values compared to
the previous run.
If I switch of the TLS refinement and just do restrained refinement with
the same input files the R-values start initially at a higher values and
than decrease till they stabilise. Unfortunately the final values are
about 1.5 % higher, compared to the run with TLS before manual
rebuilding. So TLS seems to me beneficial and I would like to use it,
but somehow a strange combination of wrong files?, wrong
parametrization? or whatever prevent me of doing that.
Has anyone an idea what might be the cause of that strange behaviour.
Thank you very much in advance.