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Hi Geoffrey,<br>
<br>
thanks for sending me the data and model - this helped me to find
out what happens in your and other similar repeatedly reported
cases.<br>
<br>
Have a quick look at the total model structure factor formula that
is used in all phenix.refine, phenix.model_vs_data, phenix.maps and
many other similar tools:<br>
<br>
see page 6 here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf">http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf</a><br>
<br>
and glance through the page 29, PHENIX Newsletter:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/newsletter/CCN_2010_07.pdf">http://www.phenix-online.org/newsletter/CCN_2010_07.pdf</a><br>
<br>
As you see there is overall anisotropic scale matrix Ucryst (see
<meta charset="utf-8">
<span class="Apple-style-span" style="border-collapse: separate;
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font-variant: normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: 2; text-indent: 0px; text-transform:
none; white-space: normal; widows: 2; word-spacing: 0px;
font-size: medium;"><i>Acta Cryst.</i><span
class="Apple-converted-space"> </span>(2005). D<b>61</b>,
850-855</span> and references therein for deeper level of
details). In refinement, the trace of this matrix is subtracted from
it and added to individual ADPs and Bsol, making Fmodel invariant
under this manipulation. Most of the time, this is a small value,
but sometimes it is relatively large.<br>
<br>
Now, let's see what happens in your particular case.<br>
The Wilson B-factor is 27.<br>
If we reset all B-factors to 27 and repeat the refinement until
convergence using two scenarios:<br>
<br>
1) we add the trace of Ucryst to individual ADPs,<br>
2) we do not add the trace of Ucryst to individual ADPs,<br>
<br>
we will get the following:<br>
<br>
1) R-work = 0.1728, R-free = 0.2177<br>
Bcryst (Ucryst reported as B) =
(-10.42,-11.48,21.90,-0.00,0.00,0.00); trace/3= 0.00<br>
ksol= 0.33 Bsol= 54.75<br>
Average ADP = 43.56<br>
<br>
2) R-work = 0.1744, R-free = 0.2171<br>
Bcryst (Ucryst reported as B) = (4.42,3.35,36.58,0.00,0.00,0.00);
trace/3= 14.78<br>
ksol= 0.32 Bsol= 40.00<br>
Average ADP = 29.03<br>
<br>
Clearly, in case "2)" you get almost exact match of Wilson B and
Average ADP (27 and 29), while in case "1)" the B-factors are
higher. Note, the R-factors in both cases are "identical"
(negligibly different given the resolution and the R-factor value).<br>
<br>
So I guess everything is more or less consistent and clear. It
depends where and how you keep different contributions to the total
ADP, and which values you use to compute mean ADP.<br>
<br>
Answering your very original question "Should I be concerned about
this?": the answer is no. But I had a quick look at your maps: and
this is what I would spend some more time: you have a lot of
positive and negative peaks, some of them are very strong: larger
than 6sigma! I guess you are missing some ions, and alternative
conformations may need some more attention. This is normal, it just
needs some care and time to be spent before your structure is ready
to go (to PDB). <br>
<br>
Pavel.<br>
<br>
PS> I'm sending you the results of these two runs off list.<br>
<br>
<br>
On 8/3/10 10:20 PM, Geoffrey Feld wrote:
<blockquote
cite="mid:AANLkTimd9FKpAQ9e0PCZSXWM77OEPSnASNFCNrkJ-MK7@mail.gmail.com"
type="cite">Dear PhenixBBers,<br>
<br>
I'm working on a 1.45 A structure I solved using MR (phaser) and
I'm pretty close to finishing, just plopping in waters and fixing
rotamers. Rw = 19.8 Rfree= 22.8. I am a little concerned because
my Wilson B is 27.00 while my average B for macromolecule is more
like 43, and for solvent is 48. I have enough data to use
anisotropic ADP refinement, which was a big help in bringing down
the Rfree, but the average B hasn't really moved much. Should I be
concerned about this? Should I try adjusting the wxu, or some
other parameter? <br>
<br>
Thanks!<br>
</blockquote>
<br>
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