On Tue, Jun 14, 2011 at 2:54 PM, Ms Chiung-Wen Chang
i have some issues with the refinement of my twinning dataset the dataset has 2.1 A resolution the twin fraction is around 0.43 i did not detwin and ran the refinement directly (with twinning refinement)
The attached is the polygon
so far the R: 0.1905 Rfree: 0.21 RMSD angles: 0.91 bonds: 0.006 clashscore: 28.176 average B: 45.8
are the clashscore and Average B in the reasonable range ? because the pattern of the polygon is looked wired
Average B is on the high side, but it's within the observed distribution. I wouldn't worry about it unless there are other problems with the structure. The clashscore is definitely higher than it should be, but not so high that it will be terribly difficult to fix. The polygon looks particularly weird because your bonds and angles are unusually tight - which probably isn't a bad thing, but you could get away with a slightly higher X-ray/stereochemistry weight if you wanted. (I'd leave it alone, though - based on the statistics alone, it sounds like you're nearly done.)
what can I do more to get them better ?
Load the output in Coot, and make sure the Probe dots are displayed by clicking "Re-load Probe dots" in the "Protein" sub-tab of the "Molprobity" tab in either the phenix.refine or validation GUIs. You can also run Probe directly from Coot - it's in the "Validation" menu, and if you launch Coot from Phenix it will have the correct program paths set. Once you have the dots displayed, hopefully it will be more or less obvious what to fix. (Keep in mind that they are calculated with explicit hydrogens, so if you're not usually looking at these when you build, it may not be obvious why atoms are clashing.) -Nat