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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Dear Toon,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I think some of your questions are addressed by the work<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt">Praznikar, J. & Turk, D. (2014) Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures. Acta Cryst. D70, 3124-3134<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">(that does not say how to validate the result without the R-free but shows how to get this result).
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Please look it.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Note that the authors talk about ML and not about LS refinement; I wonder why you need to use LS.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Sacha Urzhumtsev<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="FR" style="font-size:11.0pt;font-family:"Calibri",sans-serif">De :</span></b><span lang="FR" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org]
<b>De la part de</b> Toon Van Thillo<br>
<b>Envoyé :</b> mercredi 4 avril 2018 11:48<br>
<b>À :</b> phenixbb@phenix-online.org<br>
<b>Objet :</b> [phenixbb] Rfree and a low resolution data set<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Hi all,<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Currently I am refining a data set which showed anisotropic diffraction. Aimless suggested cutoffs at 2.3, 2.6 and 3.6 angstrom for the h,k and l axis.<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">I chose a general 3.6 cutoff to obtain satisfactory statistics for Rmeas, I/sd(I) and CC1/2. At this resolution the data set consists of approximately 2800 reflections.<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Generally 5% of the set is set aside as the Rfree test set and I found that a minimum of 500 reflections in total is used to produce a reliable Rfree. However, 5% only amounts to 140 reflections
in this case. I am hesitant to include more reflections as I would have to go up to 20% of the reflections to obtain more than 500 reflections for the test set. In a discussion on the CCP4 message boards some time ago it was suggested to do multiple refinements
with different test sets:<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><a href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1411&L=ccp4bb&F=&S=&P=125570">https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1411&L=ccp4bb&F=&S=&P=125570</a><o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">In the thread it was also discussed that a least squares approach is prefered when using a small test set. However, when using a LS target, the resulting Rfree is very high (10% higher than when
using the automatic option) and <em><span style="font-family:"Calibri",sans-serif">phenix.refine</span></em> produces awful geometry (24% ramachandran outliers, 105 clashcore...). It seems that the refinement is performed without restraints? Optimize X-ray/stereochemistry
weight does not result in improved stereochemistry. My question is if the LS approach is still relevant and if so, is there an explanation (and solution) for the bad statistics?<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Kind regards,<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black">Toon Van Thillo<o:p></o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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