<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hey,<div><br></div><div>I played around with the RMSD value that helped at least for me. Try to make it higher.</div><div><br></div><div>Best,</div><div><br></div><div>Daniel</div><div><br><div><div>On 15.03.2011, at 16:45, Zhang yu wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><font size="4"><br>Hi, Pozharski<br><br>I attached part of log file.</font><br><br><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>FINAL SELECTION<br>---------------<br><br> Mean used for final selection = -5302.48<br>
Cutoff used for final selection = -2172.44<br> Number of sets stored before final selection = 1<br> Number of solutions stored before final selection = 1<br> Number of sets stored (deleted) after final selection = 1 (0)<br>
Number of solutions stored (deleted) after final selection = 1 (0)<br><br><br> Select by Percentage of Top value: 75<br> Top TF = -5085.32<br> Mean TF used for final selection = -7813.43<br> LLG Cutoff used for final selection = -5767.35<br>
Number of solutions stored before final selection = 1<br> Number of solutions stored (deleted) after final selection = 1 (0)<br> Top TFZ = 21.3024<br><br>-----------------<br>TABLES OF RESULTS<br>-----------------<br>
<br><br> Fast Translation Function Table: Space Group P 1 2 1<br> ----------------------------------------------------<br> #SET #TRIAL Top (Z) Second (Z) Third (Z) Ensemble<br> 1 1 -5085.32 (21.30) - - - - 1<br>
---- ------ <br><br><br><br>Solutions:<br>=====================<br>Solution #1: Likelihood Gain -4625.06<br>ENSE 1 - EULER 326.300, 61.849, 83.068 - FRAC 0.529, -0.001, 0.102<br><br><br><br>Unit cell: (186.376, 103.164, 295.884, 90, 98.789, 90)<br>
Space group: P 1 2 1 (No. 3)<br><br>SPACE GROUP OF SOLUTION: 'P 1 2 1'<br><font size="4"><br>By the way, the Xtrige in Phenix tells that translational pseudo-symmetry is very likely present. I also attached the log file.<br>
<br></font>
Twinning and intensity statistics summary (acentric data):<br><br>Statistics independent of twin laws<br> <I^2>/<I>^2 : 2.148<br> <F>^2/<F^2> : 0.803<br> <|E^2-1|> : 0.729<br> <|L|>, <L^2>: 0.391, 0.215<br>
Multivariate Z score L-test: 9.366<br><br> The multivariate Z score is a quality measure of the given<br> spread in intensities. Good to reasonable data are expected<br> to have a Z score lower than 3.5.<br> Large values can indicate twinning, but small values do not<br>
necessarily exclude it.<br><br><br><br>No (pseudo)merohedral twin laws were found.<br><br><br>Patterson analyses<br> - Largest peak height : 56.002<br> (corresponding p value : 2.915e-05)<br><br><br>The analyses of the Patterson function reveals a significant off-origin<br>
peak that is 56.00 % of the origin peak, indicating pseudo translational symmetry.<br>The chance of finding a peak of this or larger height by random in a <br>structure without pseudo translational symmetry is equal to the 2.9153e-05.<br>
The detected tranlational NCS is most likely also responsible for the elevated intensity ratio.<br>See the relevant section of the logfile for more details.<br>The results of the L-test indicate that the intensity statistics<br>
are significantly different than is expected from good to reasonable,<br>untwinned data.<br>As there are no twin laws possible given the crystal symmetry, there could be<br>a number of reasons for the departure of the intensity statistics from normality.<br>
Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems<br> as well as bad data quality might be possible reasons.<br>It could be worthwhile considering reprocessing the data.<br><br><br>Yu Zhang<br>
<br><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><div></div><div class="h5">On Mon, 2011-03-14 at 18:32 -0400, Zhang yu wrote:<br>
> I am working on a DNA-protein complex, the protein apo structure is<br>
> already known. Recently I got a dataset of the DNA-protein complex, I<br>
> tried to find a solution by autoMR in Phenix with the known protein<br>
> coordinate as template. I got only one solution with very negative LLG<br>
> (around -4000), and after rigid body refinement, the both Rwork and<br>
> Rfree is around 0.55. Was there anyone in the same situation as me?<br>
> What does that mean if there is just one solution while with very high<br>
> negative LLG?<br>
<br>
</div></div>Could mean several things, but one thing is for sure - R~55% suggests<br>
that molecular replacement did not work. One possibility is that your<br>
protein undergoes conformational change when it binds to DNA. If it has<br>
distinct domains, you may be able to get a solution if running them as<br>
separate models.<br>
<br>
Negative LLG could mean that you did not correctly guess the unit cell<br>
content. Or maybe the space group is wrong. You may want to post the<br>
phaser log-file, since it's not obvious to me what you mean by only one<br>
solution. What were the Z-scores at rotation/translation steps?<br>
<font color="#888888"><br>
--<br>
"I'd jump in myself, if I weren't so good at whistling."<br>
Julian, King of Lemurs<br>
</font><div><div></div><div class="h5"><br>
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