Hi Appu,
you start already with a fixed spacegroup (scaled merged data) according
to your pointless log. So you can't get another possible solution from
pointless.
Cheers
Am 22.04.2015 um 22:28 schrieb Appu kumar:
Dear CCP4 Member,
I seek your advice on the refinement issues at the low resolution 4A. I
am trying to refine a membrane protein structure after getting the
phases from MR using the PHASER. The soluble domain structure which
comprises of 40% of protein has been used as template (sequence identity
80%) in MR search . The PHASER gave a good solution having TFZ value of
about 14.3. I have then created the polyA model for the transmembrane
domain from distant homolog which share 30% sequence identity for TM
region and try to find the phases for whole TM domain keeping the
soluble domain fixed. I got lucky in getting the phases for the whole
protein using the PHASER (TFZ=17.6) but the during the refinement, Rwork
and Rfree got stalled at the 41 and 44 respectively after several cycle
of the refinement in both refmac and phenix. I checked the spacegroup
with pointless and it suggests C2221. I have attached the pointless and
phenix.xtriage run file with this mail for your evaluation.
Phenix.xtriage suggests no major pathologies with the data except the
mild psuedomerohedral twining. There are two molecules of protein in
ASU. Evaluation of the density maps, suggest reasonable map for the most
of protein part. I am wondering why Rwork and Rfree are not coming down
despite of the good MR solution and what i am doing wrong with
refinement and if there is some pathologies associated with the data
which needs to be answered before heading to refinement.
Thanks for your help in advance.
Appu
