[phenixbb] Refinement

mohamed noor mohamed.noor34 at gmail.com
Tue Mar 24 02:43:29 PDT 2015

Dear all

I have a structure at 1.4 A currently with an Rfactor of 21/26 %. I notice
from the plot by cycle that everytime the RMS bonds/angles reduce, the
Rfactor increases a few percent. Is there any way of telling phenix.refine
to not 'restrain' the model too much?

I have already used automatic weighting. Also, RINGER identified a few
alternate conformations, so I'm thinking that modeling this might account
for a better model. However, as I have an NCS of 4, this can be tedious to
do by hand, and AFAIK, phenix.refine does not create new conformations. Is
there an alternative?

Final question, some residues were flagged as having high B factors but not
in all the copies. How do I deal with this?

Some background: I initially had problems with refinement being stuck at
30-35 % in SG P 3 2 1 (as suggested by Pointless and Xtriage). However, the
beamline scientist suggested that there could've been lattice translocation
and that it is actually P 3. Reintegrating seems to have solved the
problem. With integrated data up to 1.2 A, I tried cut-off at 1.4, 1.3 and
1.2 A. Together with CC1/2 and refinement results, I chose 1.4 A, but
should I cut it a bit lower?

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