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Hi,<br>
<br>
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<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black">I am trying to do the real space
refinement for my model against a 5.0 angstrom cryoEM map.
All parameters look pretty good except the B factor. The
mean of the B factor is close to 400. I am just wondering
whether the low resolution makes the B factor this high.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Courier
New";color:black">Does anyone have any idea or
suggestion on the high B factor during real space
refinement? Is it possible to reduce it? What is the actual
meaning of this B factor?</span><br>
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<br>
given how much cryo-EM maps are 'massaged' along the way, B factors
are not necessarily very meaningful. They are refined though to
provide the best match between model and cryo-EM maps to give you
realistic map-model correlations. <br>
Apart from this, refining Bs at this resolution may result in large
numbers to compensate for the lack of density for side chains, for
example.<br>
<br>
Bottom line, I don't think this is something to worry about.<br>
<br>
Pavel<br>
<br>
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