<div dir="ltr">Hello Pavel and Robert<div><br></div><div>Thanks for your replies. After re-investigating the model we didn't find any major issues and the electron densities are fitted pretty well. Even the ligand shows strong density on a SA-omit map. So I think we will stop at this stage and take this model for further analysis.</div><div><br></div><div>Thanks again!</div><div><br></div><div>Sam<br><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, 6 Apr 2019 at 03:30, Pavel Afonine <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Sam,<br>
<br>
> I am refining a structure with Phenix.refine and encounter an issue <br>
> which I appreciate your comments. The structure is in P1 and refined <br>
> to 36A-3A. Rw/Rf = 23.9%/29.1%, RMS bonds 0.002, RMS angles 0.544, <br>
> Ramachandran favoured 97.5%. The statistics is acceptable to me<br>
<br>
This look fine to me too!<br>
<br>
> but two numbers raised my concern. First is the clashscore of 7.7, <br>
> which is below minimum of other structures shown by Polygon.<br>
<br>
The lower, the better. So this is good! If it's lower than the others <br>
(as shown by Polygon) then you are doing better on this one!<br>
<br>
> Second is an average B of 37, with a minimum of 9.2. When I checked <br>
> again in Coot (Average Temp fact. analysis), none of the residues or <br>
> water look abnormal. I refined both individual and group B-factors and <br>
> applied 'Optimize X-ray/adp weight'.<br>
<br>
This looks fine too.<br>
<br>
> So my questions are:<br>
> (1) if a clashscore too high means a lot of bad contacts, how do you <br>
> comprehend a clashscore too low? How can I modify my strategy to get <br>
> around?<br>
<br>
It can't be "too low". Zero means you don't have any single steric <br>
clash, which is good.<br>
<br>
> (2) is there an acceptable low value of B? (I sort of went through a <br>
> similar thread in phenixbb appeared 9 years ago but seems the <br>
> discussion did not come to a conclusion). Any advice I should reliax <br>
> or tighten the adp restraints?<br>
<br>
Check out recent thread on ccp4bb: "acceptable difference between <br>
Average B-factor and Wilson B".<br>
Bottom line, I think what you have is just fine, unless you meaningfully <br>
and clearly define "low".<br>
<br>
Pavel<br>
<br>
</blockquote></div>