Hi Wolfram,<div><br></div><div>a few points:</div><div><br></div><div>- R-factors in twin refinement vs non-twin refinement are not directly comparable:</div><div><br>G.N. Murshudov, Appl. Comput. Math., V.10, N.2, 2011, pp.250-261
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<br><a class="moz-txt-link-freetext" href="http://www.science.az/acm/V10,%20N2,%202011,%20pdf/250-261.pdf">http://www.science.az/acm/V10,%20N2,%202011,%20pdf/250-261.pdf</a>
<br><div class="gmail_quote"><br></div><div class="gmail_quote">- did you make sure free-R flags assigned &quot;having twinning in mind&quot; (what phenix.refine always does)? Otherwise you have a risk of having this:</div>
<div class="gmail_quote"><br></div><div class="gmail_quote">see page 14 here:</div><div class="gmail_quote"><a href="http://phenix-online.org/presentations/latest/pavel_validation.pdf">http://phenix-online.org/presentations/latest/pavel_validation.pdf</a></div>
<div class="gmail_quote"><br></div><div class="gmail_quote">Pavel</div><div class="gmail_quote"><br></div><div class="gmail_quote"><br></div><div class="gmail_quote">On Thu, Mar 1, 2012 at 6:00 PM, wtempel <span dir="ltr">&lt;<a href="mailto:[log in to unmask]"><a href="/cgi-bin/wa-jisc.exe?LOGON=A3%3Dind1203%26L%3DCCP4BB%26E%3Dquoted-printable%26P%3D152981%26B%3D--14dae93410b928b65a04ba39d7cc%26T%3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D" target="_parent" >[log in to unmask]</a></a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear CCp4ers,<div>A good morning to everyone.<br><div>Today, I have a structure that I initially refined in space group P6522, 1mol/asu.</div>
<div>Scaling stats (scalepack): 2.30-2.26A: Rsym=99.9%; &lt;I&gt;/&lt;sigma&gt; &gt; 3</div>

<div>2.61-2.55A: Rsym=39.6%, &lt;I&gt;/&lt;sigma&gt; &gt; 10</div><div>50.00-6.13: Rsym=6.4%</div><div>Some mild anisotropy in the resolution limits is apparent on the diffraction images. Say, visible spots at 2.2A in one direction, 2.6A in the other.</div>


<div>Rfree, using data to 2.3A, was stuck in mid-30%s. The map appears like 3.5A resolution, with some difference density for loops that cannot be interpreted with reasonable geometry.</div><div>Rsym is very similar for data scaled in P3, in all resolution shells. Xtriage does not suggest merohedral twinning.</div>


<div>Nevertheless, I extended my free flags in sftools from P6522 to P32 and cad&#39;d them to amplitudes merged in spacegroup P32. Correspondingly, I expanded my model to a homotetramer and ran Refmac with amplitude based twinning. (Would this be a reasonable input to twin refinement?)</div>


<div>From the output coordinates:</div><div><div>REMARK   3  TWIN DETAILS</div><div>REMARK   3   NUMBER OF TWIN DOMAINS  :    4</div><div>REMARK   3      TWIN DOMAIN   :    1</div><div>REMARK   3      TWIN OPERATOR :  H,  K,  L</div>


<div>REMARK   3      TWIN FRACTION : 0.269</div><div>REMARK   3      TWIN DOMAIN   :    2</div><div>REMARK   3      TWIN OPERATOR : -K, -H, -L</div><div>REMARK   3      TWIN FRACTION : 0.171</div><div>REMARK   3      TWIN DOMAIN   :    3</div>


<div>REMARK   3      TWIN OPERATOR :  K,  H, -L</div><div>REMARK   3      TWIN FRACTION : 0.258</div><div>REMARK   3      TWIN DOMAIN   :    4</div><div>REMARK   3      TWIN OPERATOR : -H, -K,  L</div><div>REMARK   3      TWIN FRACTION : 0.302</div>


</div><div>Does this establish twinning versus underestimated symmetry? And what do I need to know about my free-R? Did refmac assign a new flag? Whereas the output file&#39;s flags are all 1s and 0s, the input file had 0 ... 19. During the first run, Rfree dropped to &lt;28%. But on a subsequent run, Rfree was stuck &gt;30% when I used the initial job&#39;s output MTZ.</div>


<div>Many thanks in advance for your helpful comments.</div><div>Wolfram Tempel</div><div><br></div></div>
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