On Tue, Apr 5, 2011 at 1:32 PM, Jason <span dir="ltr"><<a href="mailto:phenix.upitt@gmail.com">phenix.upitt@gmail.com</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>I have a refined structure with phenix.</div><div><br></div><div>The resolution=3.8 angstrom. Molprobity analysis shows following. Can anyone tell me if the structure is acceptable or I need to do something to improve it before going to publication? Thanks.</div>
<div><br></div><div><span style="font-family:Optima, Palatino, Times, serif;font-size:medium"><table border="1" width="100%" style="color:rgb(0, 0, 0);background-color:rgb(255, 255, 255);font-family:Optima, Palatino, Times, serif">
<tbody><tr><td>Poor rotamers</td><td bgcolor="#ff9999">20.95%</td><td>Goal: <1%</td></tr><tr><td>Ramachandran outliers</td><td bgcolor="#ff9999">6.15%</td><td>Goal: <0.2%</td></tr><tr><td>Ramachandran favored</td><td bgcolor="#ff9999">
80.13%</td><td>Goal: >98%</td></tr><tr><td>Cβ deviations >0.25Å</td><td bgcolor="#ffff99">23</td><td>Goal: 0</td></tr><tr><td>Residues with bad bonds:</td><td bgcolor="#99ff99">0.00%</td><td>Goal: 0%</td></tr><tr><td>
Residues with bad angles:</td><td bgcolor="#ff9999">0.75%</td></tr></tbody></table></span></div></blockquote><div><br></div><div>What's the clashscore? RMS(bonds), RMS(angles), R-work, R-free?</div><div><br></div><div>
The Ramachandran statistics are poor; I've seen worse published, but it would be wise to fix these. I'm assuming you don't have a high-resolution structure that you can use as a reference model - this is usually the best option. Otherwise, adding Ramachandran restraints will probably help a lot, but you should first fix all outliers manually in Coot (also applying real-space refinement with Coot's Ramachandran restraints turned on), as the default potential is very tight and can pull residues the wrong way if they're starting from a very bad position.</div>
<div><br></div><div>The rotamer outliers are difficult to avoid without a reference model, unfortunately; I'd like to fix this, but it's going to take time. The c-beta deviations and bad angles should be fixed; this may require optimizing the X-ray/stereochemistry weight during refinement. However, they may result from sidechains sticking out of the density, which often results in local distortions.</div>
<div><br></div><div>-Nat</div></div>