Hard to comment on PHEIX refne but check these things: such results must either mean your molecular replacement solution is wrong or there is something wrong with the data. Refinement packages will always try to match the Mean B factor to the Wilson plot B so I think the problem must be before refinement..
Look at the Wilson plot. Is it as a protein should show? ( There is CCP4 documemtation with a picture I think.. What is the etimated B from that? (You can run your data through the aimless pipeline and it will report all these things. and I am sure Xtriage does too.) Then look at a plot of <Fobs> v <Fcalc> v resolution. (again provided by REMAC and prob. PHENIX) Does it look sensible? Are the two curves overlapping? Good luck Eleanor On Sun, 11 Nov 2018 at 04:11, Daniel M. Himmel, Ph. D. < danielmhim...@gmail.com> wrote: > By the way, I would recommend running simulated annealing with each > composite omit map you generate to help in overcoming model bias. > > -Daniel > > > On Sat, Nov 10, 2018 at 9:31 PM Daniel M. Himmel, Ph. D. < > danielmhim...@gmail.com> wrote: > >> Anandhi, >> >> Assuming the data reduction went well, and you're in the right space goup, >> there could be a lot of model bias in your structure stemming from the >> starting model. >> >> There are a lot of things to try. I would >> set all the B-factors to an artificially low B-factor to help de-mask >> errors. Then, >> you can generate a composite omit map and FEM maps to see if any obvious >> model errors show up in the electron density. After correcting these, >> you can try running >> Autobuild and PhaseAndBuild in Phenix. Compare all the models you get >> from >> each of these, especially in regions where your original model had high >> b-factors. >> Use Coot to identify areas of poor agreement with electron density and >> areas >> of poor geometry. Once you spent a while correcting the model, put it >> through >> one or more cycles of simulated annealing at different temperatures in >> parallel. >> Select several sets of coordinates that give the best Rfree convergence, >> and then >> subject those models to individual B-factor refinement. After that, >> check again in Coot >> for areas of high B-factors and areas of poor geometry (try especially to >> improve >> your Ramachandran Plot). Use MolProbity to help in identifying errors >> and clashes. >> If a few rounds of simulated annealing and model building don't improve >> things, try some >> refinement in CCP4 Refmac. PDB_REDO, which uses Refmac, can also help >> give you alternative models. While doing all these, don't be afraid to >> "cut-and-paste" >> regions from one model into another model and then correct the geometry >> in Coot. >> If B-factors don't come down no matter what you do, you could be in the >> wrong space >> group or have problems with the original data that need to be addressed. >> >> I hope this helps. >> >> Daniel >> >> ___________ >> >> Daniel M. Himmel, Ph. D. >> >> URL: http://www.DanielMHimmel.com/index_Xtal.html >> <http://www.danielmhimmel.com/> >> >> >> >> >> On Thu, Nov 8, 2018 at 7:41 PM Anandhi Anandan < >> anandhi.anan...@uwa.edu.au> wrote: >> >>> Hello everyone, >>> >>> >>> I am trying to solve the structure of a protein with a bound ligand at >>> 2.65 A resolution. XDS was used for data reduction, phaser-MR for molecular >>> replacement and Phenix for refinement. The refinement was done with the >>> default settings ( individual B factors, occupancy and TLS parameters). The >>> resultant atomic B factors are quite high. The overall B factor is 82 with >>> a minimum value of 34.57 and maximum of 225.13. I would like to know if any >>> of the data reduction parameters can affect the B factors and how best to >>> deal with this issue. >>> >>> >>> Anandhi >>> >>> >>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >>> >> > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
