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Hi Reza,<br>
<br>
this may mean several things. Perhaps TLS group selection isn't
optimal or incorrect? phenix.find_tls_groups relies on B factors to
annotate TLS groups. Were B factors meaningful (refined before
running phenix.find_tls_groups)?<br>
<br>
You can try weight optimization.<br>
<br>
Values of TLS matrices cannot be interpreted directly, they can be
positive or negative. This is discussed in great details here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://journals.iucr.org/d/issues/2015/08/00/rr5096/rr5096.pdf">http://journals.iucr.org/d/issues/2015/08/00/rr5096/rr5096.pdf</a><br>
<br>
You can check if TLS matrices are physically meaningful by running<br>
<br>
phenix.tls_analysis model.pdb<br>
<br>
If it runs all the way till completion - all is good. Otherwise, in
case of nonsensical TLS it will stop and tell what's wrong.<br>
<br>
Perhaps you enabled TLS refinement too early (model isn't good yet)?<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 4/30/17 05:30, Reza Khayat wrote:<br>
</div>
<blockquote type="cite" cite="mid:1493555417111.4078@ccny.cuny.edu">
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<p>Hi,<br>
</p>
<p><br>
</p>
<p>I'm having difficulty with performing TLS refinement on
a highly symmetric system. The difference between the R_work and
R_free increases with TLS refinement (16.5/21.4 changes to
14.4/22.2). The TLS tensors for some of the group are not
sensible (if I understand the literature correctly) -there are
some negative numbers for the T and L tensors (see below). The
TLS groups were identified with phenix.find_tls_groups. Any
suggestions would be appreciated. <br>
</p>
<p><br>
</p>
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<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> SELECTION: chain
</span><span class="s2">'A'</span><span class="s1"> and (resid
</span><span class="s2">38</span><span class="s1"> through
</span><span class="s2">68</span><span class="s1"> )</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> ORIGIN FOR THE GROUP (A):
</span><span class="s2">56</span><span class="s1">.</span><span
class="s2">6459</span><span class="s1"> -</span><span
class="s2">23</span><span class="s1">.</span><span class="s2">5648</span><span
class="s1"> -</span><span class="s2">59</span><span class="s1">.</span><span
class="s2">0695</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> T TENSOR</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> T11:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">2105</span><span class="s1"> T22:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">2895</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> T33:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0962</span><span class="s1"> T12:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0829</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> T13:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0473</span><span class="s1"> T23:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0007</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> L TENSOR</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> L11:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0446</span><span class="s1"> L22:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0120</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> L33:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0096</span><span class="s1"> L12:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0246</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> L13:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0209</span><span class="s1"> L23:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0106</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> S TENSOR</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> S11:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0228</span><span class="s1"> S12: -</span><span
class="s2">0</span><span class="s1">.</span><span class="s2">0268</span><span
class="s1"> S13: -</span><span class="s2">0</span><span
class="s1">.</span><span class="s2">0023</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> S21: -</span><span class="s2">0</span><span
class="s1">.</span><span class="s2">0507</span><span
class="s1"> S22:
</span><span class="s2">0</span><span class="s1">.</span><span
class="s2">0526</span><span class="s1"> S23: -</span><span
class="s2">0</span><span class="s1">.</span><span class="s2">0287</span></p>
<p class="p1"><span class="s1">REMARK </span><span class="s2">3</span><span
class="s1"> S31: -</span><span class="s2">0</span><span
class="s1">.</span><span class="s2">0296</span><span
class="s1"> S32: -</span><span class="s2">0</span><span
class="s1">.</span><span class="s2">0137</span><span
class="s1"> S33: </span><span class="s2">0</span><span
class="s1">.</span><span class="s2">0534</span></p>
<p><br>
</p>
<p>The data set is complete at 2.3Å resolution and there are no
strange crystal phenotypes. <br>
</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
</p>
<p><br>
</p>
<div id="Signature">
<div name="divtagdefaultwrapper"
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:; margin:0">
Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
<br>
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