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Dear <span style="font-family: Calibri, sans-serif; font-size: 14.6667px; background-color: rgb(255, 255, 255); display: inline !important">
Pavel</span>,</div>
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Thanks for your reply.</div>
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The output file is attached. Please check.</div>
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Look forward to the reply.</div>
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Best regards</div>
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<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Yong Zhou</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Pavel Afonine <pafonine@lbl.gov><br>
<b>Sent:</b> Tuesday, March 12, 2019 6:47 PM<br>
<b>To:</b> yong zhou; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] completeness issue</font>
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<div style="background-color:#FFFFFF">Can you send the file to me off-list? I'll have a closer look once I have the file.<br>
Pavel<br>
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<div class="x_moz-cite-prefix">On 3/11/19 16:10, yong zhou wrote:<br>
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Hi,</p>
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<p style="margin-top: 0px; margin-bottom: 0px;margin-top:0px; margin-bottom:0px; font-size:14px; font-family:SimSun">
Recently I deposited a structure to PDB. However, I was told t<span>here is a large difference between reported (77.89%) and calculated (88.36%) values for data completeness.</span></p>
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In order to confirm the information, I used the command phenix.reflection_statistics and the result is as following.</p>
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<span style="font-variant-ligatures:no-common-ligatures">Resolution range: 31.6787 1.91132</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">Completeness in resolution range: 0.783333</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">Completeness with d_max=infinity: 0.783193</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">Anomalous completeness in resolution range: 0.599544</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">Bijvoet pairs: 15786</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">Lone Bijvoet mates: 9291</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">Mean anomalous difference: 0.0671</span></p>
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<span style="font-variant-ligatures:no-common-ligatures"></span></p>
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<span style="font-variant-ligatures:no-common-ligatures">Space group of the intensities: P 2 2 2</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">Space group of the metric:<span> <span> </span></span>P m m m</span></p>
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<span style="font-variant-ligatures:no-common-ligatures"><span> <span> </span></span>Tolerance used in the determination of the</span></p>
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<span style="font-variant-ligatures:no-common-ligatures"><span> <span> </span></span>lattice symmetry: 3 degrees</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">Possible twin laws: None</span></p>
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<span style="font-variant-ligatures:no-common-ligatures"></span></p>
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<span style="font-variant-ligatures:no-common-ligatures">Completeness of 4-8-(GlcNAc)5/output4-8.sca:I(+),SIGI(+),I(-),SIGI(-):</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">unused:<span> </span><span> <span> </span></span>- 31.6830 [<span> <span> </span></span>0/9<span> <span> </span></span>] 0.000</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">bin<span> <span> </span></span>1: 31.6830 -<span> <span> </span></span>1.9113 [28083/29673] 0.946</span></p>
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<span style="font-variant-ligatures:no-common-ligatures">unused:<span> <span> </span></span>1.9113 -<span> </span><span> <span> </span></span>[<span> <span> </span></span>0/0<span> <span> </span></span>]</span></p>
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There are two completeness values 0.783 and 0.946.</p>
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So which is the correct one?</p>
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Look forward to the reply.</p>
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Yong Zhou</p>
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<pre class="x_moz-quote-pre">_______________________________________________
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