Thank you for the tips Brent. I will try what you suggest. There are actually multiple lattices. And I actually only processed the dominant one in XDS. On May 8, 2014 2:26 PM, "Segelke, Brent W." <segel...@llnl.gov> wrote:
> Completeness looks pretty good and you have a good enough resolution > that you should be able to get this eventually. > > > > A couple of things to look at to start. First, suspect your data > processing. As others have already said, double check your space group. You > could even do an initial sanity check by expanding your MR solution into P1 > and refining with strong NCS in P1 reduced data. You will automatically get > a lower R because you are introducing more parameters, but if you use > strong NCS and both R and Rfree are better behaved, then something is going > on with the merging (e.g., wrong space group). > > > > Look in your log and see if there are an unusual number of reflection or > frames thrown out, it should be only a few percentage. If you have more > than 10-15% rejected, something probably went awry. Tweak your error model > and/or summing box, etc. > > > > You could also try refining to a less ambitious resolution to start, > assuming anisotropy will affect the higher resolution to a greater degree. > > > > Hope this helps. > > > > Brent > > > > *From:* yarrowmadr...@gmail.com [mailto:yarrowmadr...@gmail.com] *On > Behalf Of *Yarrow Madrona > *Sent:* Thursday, May 08, 2014 1:50 PM > *To:* Segelke, Brent W.; CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] stalled refinement after MR solution > > > > Hi Brent, > > > > I forgot to mention the resolution and other statistics. Here they are > (XDS -unmerged data P2 below). Overall completeness is 93.4(85.2)% for 2.2A. > > I do have some anisotropy in the b-direction. I have tried running phaser > with data scaled by the UCLA anisotropy server and obtained the same > results. > > > > -Yarrow > > > > SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF > RESOLUTION > > RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR > COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT > OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr > > > > 6.40 4788 1487 1718 86.6% 2.7% 2.9% > 4675 33.78 3.2% 99.8* 20* 0.895 873 > > 4.60 8644 2667 2852 93.5% 3.0% 3.1% > 8511 30.77 3.6% 99.8* 9 0.856 1461 > > 3.78 10659 3301 3598 91.7% 3.0% 3.1% > 10559 31.05 3.6% 99.8* 0 0.789 1747 > > 3.28 12398 3874 4261 90.9% 3.7% 3.7% > 12319 25.46 4.4% 99.7* -4 0.779 1981 > > 2.94 14970 4587 4766 96.2% 4.8% 4.9% > 14886 20.15 5.8% 99.7* -2 0.779 2476 > > 2.69 16718 5129 5292 96.9% 6.7% 6.9% > 16638 15.44 8.1% 99.4* -2 0.767 2681 > > 2.49 17842 5536 5722 96.7% 9.3% 9.4% > 17734 11.89 11.1% 98.9* -2 0.755 2779 > > 2.33 19743 6017 6133 98.1% 12.0% 12.6% > 19623 9.27 14.3% 98.4* -4 0.737 3132 > > 2.20 16777 5566 6533 85.2% 17.4% 16.9% > 16420 6.77 21.2% 96.8* -8 0.749 2334 > > total 122539 38164 40875 93.4% 5.3% 5.4% > 121365 17.41 6.4% 99.7* -2 0.776 19464 > > > > > > NUMBER OF REFLECTIONS IN SELECTED SUBSET OF IMAGES 134095 > > NUMBER OF REJECTED MISFITS 11536 > > NUMBER OF SYSTEMATIC ABSENT REFLECTIONS 0 > > NUMBER OF ACCEPTED OBSERVATIONS 122559 > > NUMBER OF UNIQUE ACCEPTED REFLECTIONS 38170 > > > > > > On Thu, May 8, 2014 at 10:48 AM, Segelke, Brent W. <segel...@llnl.gov> > wrote: > > You didn’t report your resolution and completeness. Also, is there > anisotropy in your data? > > > > Brent > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Yarrow > Madrona > *Sent:* Thursday, May 08, 2014 10:12 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] stalled refinement after MR solution > > > > Hello CCP4 community, > > > > I am stumped and would love some help. I have a molecular replacement > solution that has Rfree stuck around 40% while Rwork is aorund 30%. The > model is actually the same enzyme with a similar inhibitor bound. Relevant > information is below. > > > > -Yarrow > > > > I have solved a structure in a P21 spacegroup: > > > > 51.53 88.91 89.65, beta = 97.1. > > > > Processing stats (XDS) are very good with low Rmerge (~5% overall) and > good completeness. > > > > I don't think twinning is an option with these unit cell dimensions. My > data was highly aniosotropic. I ran the data through the UCLA anisotropic > server to scale in the B- direction ( > http://services.mbi.ucla.edu/anisoscale/) > > > > I get a small (a little over 5) patterson peak suggesting there is not > much t-NCS to worry about. However, the output structure does have 2 fold > symmetry (see below) and as Dale Tronrud pointed out, there is always tNCS > in a P21 space group with two monomers related by a 2-fold axis. > > I calculated the translation to be unit cell fractions of 0.36 0.35, 0.32. > > > > rota_matrix -0.9860 -0.1636 -0.0309 > > rota_matrix -0.1659 0.9511 0.2605 > > rota_matrix -0.0132 0.2620 -0.9650 > > tran_orth 34.3310 -24.0033 107.0457 > > > > center_orth 15.7607 7.2426 77.7512 > > > > *Phaser stats:* > > * SOLU SET RFZ=20.3 TFZ=19.5 PAK=0 LLG=1314 RF++ TFZ=63.8 PAK=0 LLG=4745 > LLG=4947* > > > > > > >
