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<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Hi everyone,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>I have a P31 twin crystal, resolution 2.0, and with</span></font><span
lang=EN-US> </span><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>twin fraction 0.451. I use phenix.refine to refine the
structure and with freeR set to 8%.<o:p></o:p></span></font></p>
<pre><font size=1 face=Arial><span lang=EN-US style='font-size:9.0pt;
font-family:Arial'><o:p> </o:p></span></font></pre><pre><font size=1
face=Arial><span lang=EN-US style='font-size:9.0pt;font-family:Arial'>% phenix.refine data.sca model.pdb twin_law="h,-h-k,-l" xray_data.r_free_flags.generate=True xray_data.r_free_flags.fraction=0.08<o:p></o:p></span></font></pre>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Result:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Final: r_work = 0.1793 r_free = 0.2258 bonds = 0.011
angles = 1.557<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>REMARK 3 FREE R
VALUE
: 0.2258<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>REMARK 3 FREE R VALUE TEST SET
SIZE (%) : 3.67<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>REMARK 3 FREE R VALUE TEST SET
COUNT : 2013<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>After the refinement, it seems like my freeR set size reduced
by half (3.67%). Is it due to the twin effect, or something is wrong with my
refinement?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>And if I use ccp4 program “scalpeak2mtz “ to
convert the .sca to .mtz and with freeR fraction set to 8%. Then refine it with
phenix.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<pre><font size=1 face=Arial><span lang=EN-US style='font-size:9.0pt;
font-family:Arial'>% phenix.refine data.mtz model.pdb twin_law="h,-h-k,-l" <o:p></o:p></span></font></pre>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Final: r_work = 0.1669 r_free = 0.1970 bonds = 0.010
angles = 1.406<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>REMARK 3 FREE R
VALUE
: 0.2022<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>REMARK 3 FREE R VALUE TEST SET
SIZE (%) : 7.80<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>REMARK 3 FREE R VALUE TEST SET
COUNT : 4326<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>It turns out, my test set is still 8%, and R/Rfree looks
even better than the first one. So I am wondering which one is the correct one</span></font><span
lang=EN-US> and why</span><font size=1 face=Arial><span lang=EN-US
style='font-size:9.0pt;font-family:Arial'>?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<pre><font size=1 face=Arial><span lang=EN-US style='font-size:9.0pt;
font-family:Arial'>Thanks!<o:p></o:p></span></font></pre>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Lauren<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
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