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<div class="moz-cite-prefix">Hi Florian,<br>
<br>
Wilson B is just an estimate, and your refined B reflect your
data.. Assumptions made to derive Wilson B include uniformly
distributed atoms in the unit cell, same atom type and B-factor
(what else?). This is not quite true for protein crystals, which
typically consist of atoms of different kind, have different
degree of disorder (B-factors), and they kind of form some
structure (definitely not randomly distributed in the unit cell).
So to me it's a miracle that oftentimes Wilson B closely matches
refined average B. We should acknowledge that when it doesn't
that's a valid possibility.<br>
<br>
Regarding papers.. Exactly that plot I sent you before was not
published (I guess it did not go to the phenixbb for the reason
Nat explained yesterday), but the tools and methods are described
here:<br>
<br>
<meta charset="utf-8">
<span style="color: rgb(0, 0, 0); font-family: verdana, helvetica,
arial, sans-serif; font-size: 14.44444465637207px; font-style:
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word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); display: inline !important; float: none;">Afonine, P.V.,
Grosse-</span><span class="SpellE" style="color: rgb(0, 0, 0);
font-family: verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">Kunstleve</span><span
style="color: rgb(0, 0, 0); font-family: verdana, helvetica,
arial, sans-serif; font-size: 14.44444465637207px; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); display: inline !important; float: none;">, R.W., Chen,
V.B.,<span class="Apple-converted-space"> </span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family: verdana,
helvetica, arial, sans-serif; font-size: 14.44444465637207px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">Headd</span><span style="color: rgb(0, 0, 0);
font-family: verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); display: inline
!important; float: none;">, J.J., Moriarty, N.W., Richardson,
J.S., Richardson, D.C.,<span class="Apple-converted-space"> </span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family: verdana,
helvetica, arial, sans-serif; font-size: 14.44444465637207px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">Urzhumtsev</span><span style="color: rgb(0, 0, 0);
font-family: verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); display: inline
!important; float: none;">, A.,<span
class="Apple-converted-space"> </span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family: verdana,
helvetica, arial, sans-serif; font-size: 14.44444465637207px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">Zwart</span><span style="color: rgb(0, 0, 0);
font-family: verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); display: inline
!important; float: none;">, P.H. & Adams, P.D. (2010).<span
class="Apple-converted-space"> </span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family: verdana,
helvetica, arial, sans-serif; font-size: 14.44444465637207px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);"><span class="GramE"><b>phenix.model</b></span><b>_vs_data</b></span><b
style="color: rgb(0, 0, 0); font-family: verdana, helvetica,
arial, sans-serif; font-size: 14.44444465637207px; font-style:
normal; font-variant: normal; letter-spacing: normal;
line-height: normal; orphans: auto; text-align: justify;
text-indent: -23.999998092651367px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">: a high-level tool for
the calculation of crystallographic model and data statistics</b><span
style="color: rgb(0, 0, 0); font-family: verdana, helvetica,
arial, sans-serif; font-size: 14.44444465637207px; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); display: inline !important; float: none;">. J. Appl.<span
class="Apple-converted-space"> </span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family: verdana,
helvetica, arial, sans-serif; font-size: 14.44444465637207px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">Crystallogr</span><span style="color: rgb(0, 0, 0);
font-family: verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); display: inline
!important; float: none;">. 43, 669-676.<br>
</span><br>
<span style="color: rgb(0, 0, 0); font-family: verdana, helvetica,
arial, sans-serif; font-size: 14.44444465637207px; font-style:
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text-transform: none; white-space: normal; widows: auto;
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255); display: inline !important; float: none;">
<meta charset="utf-8">
<span style="color: rgb(0, 0, 0); font-family: verdana,
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letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255,
255, 255);"><span style="font-style: normal; font-variant:
normal; font-weight: normal; font-size: 7pt; line-height:
normal; font-family: 'Times New Roman';"><span
class="Apple-converted-space"> </span></span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family:
verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0px; background-color: rgb(255, 255, 255);"><span>Urzhumtsev</span></span><span
style="color: rgb(0, 0, 0); font-family: verdana, helvetica,
arial, sans-serif; font-size: 14.44444465637207px; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255,
255, 255);">, A., Afonine, P.V. & Adams P.D. (2009).<span
class="Apple-converted-space"> </span><b>On the use of
logarithmic scales for analysis of diffraction data</b>.<span
class="Apple-converted-space"> </span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family:
verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0px; background-color: rgb(255, 255, 255);">Acta</span><span
style="color: rgb(0, 0, 0); font-family: verdana, helvetica,
arial, sans-serif; font-size: 14.44444465637207px; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255,
255, 255); display: inline !important; float: none;"><span
class="Apple-converted-space"> </span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family:
verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0px; background-color: rgb(255, 255, 255);">Cryst</span><span
style="color: rgb(0, 0, 0); font-family: verdana, helvetica,
arial, sans-serif; font-size: 14.44444465637207px; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255,
255, 255); display: inline !important; float: none;">. D65,
1283-1291.</span><br>
</span><br>
<meta charset="utf-8">
<span class="SpellE" style="color: rgb(0, 0, 0); font-family:
verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">Urzhumtseva</span><span
style="color: rgb(0, 0, 0); font-family: verdana, helvetica,
arial, sans-serif; font-size: 14.44444465637207px; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255); display: inline !important; float: none;">, L., Afonine,
P.V., Adams, P.D. &<span class="Apple-converted-space"> </span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family: verdana,
helvetica, arial, sans-serif; font-size: 14.44444465637207px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">Urzhumtsev</span><span style="color: rgb(0, 0, 0);
font-family: verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); display: inline
!important; float: none;">, A. (2009).<span
class="Apple-converted-space"> </span></span><b style="color:
rgb(0, 0, 0); font-family: verdana, helvetica, arial,
sans-serif; font-size: 14.44444465637207px; font-style: normal;
font-variant: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255);">Crystallographic model
quality at a glance</b><span style="color: rgb(0, 0, 0);
font-family: verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); display: inline
!important; float: none;">.<span class="Apple-converted-space"> </span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family: verdana,
helvetica, arial, sans-serif; font-size: 14.44444465637207px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">Acta</span><span style="color: rgb(0, 0, 0); font-family:
verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); display: inline
!important; float: none;"><span class="Apple-converted-space"> </span></span><span
class="SpellE" style="color: rgb(0, 0, 0); font-family: verdana,
helvetica, arial, sans-serif; font-size: 14.44444465637207px;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: auto;
text-align: justify; text-indent: -23.999998092651367px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color: rgb(255, 255,
255);">Cryst</span><span style="color: rgb(0, 0, 0);
font-family: verdana, helvetica, arial, sans-serif; font-size:
14.44444465637207px; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: justify; text-indent:
-23.999998092651367px; text-transform: none; white-space:
normal; widows: auto; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); display: inline
!important; float: none;">. D65, 297-300.</span><br>
<br>
and the source of information used for all the analysis described
in above papers is PDB. Also, I guess, you can obtain that plot
from PHENIX GUI.<br>
<br>
Pavel<br>
<br>
On 3/23/13 6:53 AM, Florian Brückner wrote:<br>
</div>
<blockquote cite="mid:E9554617-5125-4DC7-AD2D-A68ECA2417EB@psi.ch"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
Thanks, Pavel.
<div><br>
</div>
<div>So you don't think that the difference between Wilson B
(66.45 according to phenix) and average B (52 after refinement)
is still too large? Where did you take the statistics from? Is
that published anywhere?</div>
<div><br>
</div>
<div>Best regards</div>
<div><br>
</div>
<div>Florian</div>
<div><br>
<div>
<div>Am 22.03.2013 um 07:09 schrieb Pavel Afonine <<a
moz-do-not-send="true" href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>>:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<div bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi Florian,<br>
<br>
I think it is pretty convincing that refinement went all
right and the mean B you get is what it actually is.
Also I just looked at the files that you sent me the
other day and I did not notice anything suspicious.<br>
<br>
Pavel<br>
<br>
P.S.: Sorry if you received multiple copies of this
email: I was trying to attach a tiny image with some PDB
statistics but our server did not let me do it.<br>
<br>
On 3/21/13 1:00 AM, Florian Brückner wrote:<br>
</div>
<blockquote
cite="mid:0887C157-EEDF-41FD-B48A-AB256083EC51@psi.ch"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
Dear Pavel
<div><br>
</div>
<div>yes, the refinement did converge. I did 6
macrocycles and in separate runs started from
different average atomic B-factors of 32, 66 and 97
keeping the distribution as in the original high
resolution molecular replacement model from the same
crystal form (i.e. adding 0, 34 and 65 to all atomic
B-factors in the starting pdb). In all cases after 6
macrocycles I get an almost identical distribution of
B-factors and also average B-factor of about 52. Also
setting all B-factors to the same value of 66 gave a
similar distribution after refinement with an average
of 52. However, in the latter case the R-free was
about 2% higher compared to starting from the original
distribution, but it dropped by about 1% during
refinement.</div>
<div><br>
</div>
<div>Best regards</div>
<div><br>
</div>
<div>Florian</div>
<div><br>
</div>
<div><br>
<div>
<div>Am 21.03.2013 um 06:40 schrieb Pavel Afonine
<<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>>:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<div bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">Hi Florian,<br>
<br>
I'm glad it works now. Regarding difference
between Wilson B and mean refined B: well,
it's hard to quantify what's "too low" or "too
different". Average refined B may deviate from
Wilson B and the difference in your case does
not seem to be terribly large. <br>
Did the refinement converge? What if you do
say 10 or 20 macro-cycles instead of default
3? Will B-factors further change between
macro-cycles?<br>
<br>
Pavel<br>
<br>
On 3/19/13 7:37 AM, Florian Brückner wrote:<br>
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Dear Keitaro and Pavel,
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<div>thank you for your suggestions. I have
now used the latest nightly build (1326).
With this version, the average B-factor
converges at about 52 A**2 and also the
distribution is very similar, regardless
with what B-factors I start the refinement
(I tried average B-factors between 32 and
97). So clearly the behavior of this newest
version is different from the version I have
been using before (1.8.1 stable release
1168) and also from the latest stable
release (1.8.2 stable release 1309), which
behaves the same as 1168. To me the
B-factors still look a bit too low, since
the Wilson B-factor calculated by phenix is
66.45, the Wilson B-factor I determined
manually from the linear part of the Wilson
plot is 97.</div>
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<div>Best regards</div>
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<div>Florian</div>
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<div>Am 19.03.2013 um 00:06 schrieb
Keitaro Yamashita <<a
moz-do-not-send="true"
href="mailto:yamashita@castor.sci.hokudai.ac.jp">yamashita@castor.sci.hokudai.ac.jp</a>>:</div>
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<blockquote type="cite">Dear Florian,<br>
<br>
Maybe you are using phenix-dev-1311 or
earlier?<br>
I am afraid that you have experienced
the bug that overall B-factor is<br>
not applied to individual atomic
B-factors in certain cases, which I<br>
have also experienced recently. That bug
was fixed in dev-1312 if I<br>
recall correctly.<br>
<br>
Hope it helps,<br>
Keitaro<br>
<br>
2013/3/19 Florian Brückner <<a
moz-do-not-send="true"
href="mailto:florian.brueckner@psi.ch">florian.brueckner@psi.ch</a>>:<br>
<blockquote type="cite">Dear all<br>
<br>
I am refining a structure at 3.2 A
with phenix.refine using automatic<br>
optimization of target weights, solved
by molecular replacement with a 2.1A<br>
structure of the same crystal form.
Rwork=26%, Rfree=28%. I use individual<br>
atomic B-factor refinement. The
obtained distribution of B-factors
after<br>
refinement looks reasonable and quite
similar to the distribution in the<br>
higher resolution model, which I
suppose would be expected, since it is
the<br>
same crystal form. However, the
average B-factor does not change<br>
substantially, i.e. if I start with
the B-factors from the high resolution<br>
model (average B-factor around 32
A**2) after 6 macrocycles the average<br>
B-factor is still around 32 A**2. If I
set all B-factors to the Wilson<br>
B-factor determined by phenix.refine
(66 A**2), after 6 macrocycles the<br>
distribution of B-factors looks again
very similar to the high resolution MR<br>
model, but the average B-factor is
still around 65 A**2. What should I
make<br>
of this? Is this an expected behavior
at this resolution, i.e. the fact that<br>
the absolute values of B-factors
cannot be determined during
refinement,<br>
although a reasonable distribution can
be obtained as judged by plotting<br>
average B-factors vs. residue#? Since
the average B-factor does not change<br>
much during refinement, which average
B-factor should I start refinement<br>
with to end up with reasonable
absolute values? I have manually
determined<br>
the Wilson B-factor from the linear
part of the Wilson plot (4.5-3.2 A) to<br>
be 97 A**2. This seems high to me.
Would that be expected for the given<br>
resolution, given that the 2.1A
structure of the same crystal form has
32<br>
A**2? I should add, that there is not
a substantial effect of the average<br>
refined B-factor on Rfree.<br>
<br>
Thanks for any comments or
suggestions.<br>
<br>
Best regards<br>
<br>
Florian<br>
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