Yeah, the protein is huge, around 450KD. Changing the ASU content did help a little bit. By searching two copies in ASU, I got a solution with better LLG<br><br>#+ #* Initial LLG Initial R Refined LLG Refined R Unique Tmplt<br>
1 1 4885.54 61.38 4885.54 61.38 YES <br>But the Rfactor are still high and stuck during refinement. <br><br>Regarding the possible effect of space group, I reindexed the dataset from P2 to P21. AutoMR also gave similar solutions with high R values.<br>
<br><h3 class="gD" style="color: rgb(204, 0, 96);"><span><br></span></h3><br><div class="gmail_quote">2011/3/15 Ed Pozharski <span dir="ltr"><<a href="mailto:epozh001@umaryland.edu">epozh001@umaryland.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">On Tue, 2011-03-15 at 11:45 -0400, Zhang yu wrote:<br>
> Fast Rotation Function Table: 1<br>
> -------------------------------<br>
> #SET Top (Z) Second (Z) Third (Z)<br>
> 1 -1129.09 32.53 --- --- --- ---<br>
> ---- ---------- ----- ---------- ----- ---------- -----<br>
><br>
<br>
</div>Well, your Z-score is very promising. What size protein/DNA you have?<br>
The likely asu content is over a megadalton, so unless the protein is<br>
huge, you probably have more than one copy - this would explain bad<br>
initial R-values. Patterson suggests that too. You probably need to<br>
play with the estimate of asu content a bit to get rid of negative LLG.<br>
What happens if you run a search looking for the second copy with the<br>
first one in place?<br>
<font color="#888888"><br>
--<br>
</font><div><div></div><div class="h5">"I'd jump in myself, if I weren't so good at whistling."<br>
Julian, King of Lemurs<br>
<br>
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