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This is fixed in recent versions (nightly builds):<br>
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<a class="moz-txt-link-freetext" href="http://phenix-online.org/download/nightly_builds.cgi">http://phenix-online.org/download/nightly_builds.cgi</a><br>
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Pavel<br>
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<div class="moz-cite-prefix">On 2/22/19 06:11, Edwin Pozharski
wrote:<br>
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cite="mid:CAG_VP0ievRzuAprvnO9LU_J0umL59v9TJf+=MPWFjFhM-87SdQ@mail.gmail.com">
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<div dir="ltr">Not sure whether anyone would care now that we
got our marching orders to abandon PDB format and move to
mmCIF, but the output of phenix.real_space_refine includes a
number of lines that are not legit PDB records, i.e. this
section</div>
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<div dir="ltr">...</div>
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<div dir="ltr">REMARK 3</div>
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<div dir="ltr">GEOMETRY RESTRAINTS LIBRARY: CDL v1.2</div>
<div dir="ltr">DEVIATIONS FROM IDEAL VALUES.</div>
<div dir="ltr"> BOND : 0.004 0.049 74053</div>
<div dir="ltr"> ANGLE : 0.747 12.299 100513</div>
<div dir="ltr"> CHIRALITY : 0.052 0.232 11312</div>
<div dir="ltr"> PLANARITY : 0.006 0.069 13125</div>
<div dir="ltr"> DIHEDRAL : 11.589 179.958 44947</div>
<div dir="ltr"> MIN NONBONDED DISTANCE : 2.276 </div>
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<div dir="ltr">MOLPROBITY STATISTICS.</div>
<div dir="ltr"> ALL-ATOM CLASHSCORE : 5.04</div>
<div dir="ltr"> RAMACHANDRAN PLOT:</div>
<div dir="ltr"> OUTLIERS : 0.30 %</div>
<div dir="ltr"> ALLOWED : 8.63 %</div>
<div dir="ltr"> FAVORED : 91.06 %</div>
<div dir="ltr"> ROTAMER OUTLIERS : 8.76 %</div>
<div dir="ltr"> CBETA DEVIATIONS : 0</div>
<div dir="ltr"> PEPTIDE PLANE:</div>
<div dir="ltr"> CIS-PROLINE : 3.7037037037</div>
<div dir="ltr"> CIS-GENERAL : 0.0</div>
<div dir="ltr"> TWISTED PROLINE : 1.85185185185</div>
<div dir="ltr"> TWISTED GENERAL : 0.316455696203</div>
<div dir="ltr">REMARK 3</div>
<div>...</div>
<div><br>
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<div>This does result in errors when this output PDB file is
used as input to other software that is more stringent
with format compliance. </div>
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<div>Cheers,</div>
<div><br>
</div>
<div>Ed.</div>
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