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Hi Paul This sounds like there might be a recently-introduced bug which should be reported to the author. I have several structures in I2 & I haven't noticed anything like this. Can you tell which program is introducing this error, e.g. by looking at the mtzdump outputs? Cheers -- Ian On 4 November 2016 at 12:00, Paul Paukstelis <[log in to unmask]> wrote: > Thanks to all that responded. I sorted this out. > > It all appears to stem from the C2->I2 conversion. Forcing everything in > processing to stick with C2 fixes all the issues! > > > Thanks again, > > --paul > > > > On 11/03/2016 12:39 PM, Paul Paukstelis wrote: > >> CCP4BB, >> >> I posted some time back about a DNA oligonucleotide structure we were >> working on. I had difficulty phasing it despite strong signal from >> bromines, but finally managed to get reasonable enough maps from a few >> datasets to build, only to find that despite the density looking quite >> good, it simply wouldn't refine past R/Rfree of around 28/32. With help >> from ccp4bb it began to become clear that this might be a candidate for a >> lattice with translocation defects. >> >> I had my student make a variant in which two 3' nucleotides that weren't >> involved in base pairing contacts were removed. This crystallized under the >> same conditions in a different space group and was now diffracting to ~1.0 >> A (from about 2.2 in the previous space group). Images overall looked good, >> though we collected on some crystals that clearly had more than one lattice >> that made indexing more difficult. The best looking data still had some >> tails on spots, but was easily indexed in C2, which Pointless quite happily >> changed to I2 to minimize the beta angle. There are no clear alternating >> strong/weak intensities. Phaser finds a strong solution using the >> previously built dimer, but notes a 25% over origin peak in native >> Patterson. Maps look very good, though after the first round of refinement >> it is apparent that there is another dimer in the ASU, but it is clearly >> overlapping the first. If I'm not mistaken, all these clues suggest lattice >> translocation defects. Question 1: any thoughts on how likely it would be >> for a molecule to intrinsically pack in such a way that it results in >> lattice translocation defects? >> >> I thought it would be worthwhile pressing on given the high resolution it >> would be possible to do grouped occupancy refinement of the dimers without >> taking too huge a hit in observation/parameters. Refinement with refmac >> using occupancy groups leads to a best R/Rfree of 18/24, though geometry >> could be better in some spots. Curiously, refmac (or phenix.refine) in the >> PDB header reports only 50% completeness in the resolution range, though >> all the data reduction and analysis (aimless, xtriage) report 99% >> completeness. Question 2: Why is this? Phenix logfile says something about >> removing about half the reflections as systematic absences. I have been >> working with everything in I2 after Pointless switched it over. >> >> Question 3: Any other suggestions on how to proceed with refinement in a >> case like this? My gut instinct tells me that it would be better to not do >> intensity correction due to the high resolution, but perhaps that's >> something to pursue? >> >> Thank you in advance. >> >> --paul >> >