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<div>Hi Pavel,</div>
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<div>Thx for getting back to me so soon.&nbsp;</div>
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<div>I have several examples, however if you are looking for PDB files you can fetch directly from the RCSB etc. then&nbsp;I dont know if I can help.</div>
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<div>But some of the files I have piped through my pipeline, always results in the before mentioned error. Both the&nbsp;starting model and map have been fetched&nbsp;directly&nbsp;from the RCSB and the&nbsp;<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">EMDB
 respectively.</span>&nbsp;<br>
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<div>I have included dropbox download links for one such example.&nbsp;<br>
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<div>The PDB file:&nbsp;<a href="https://www.dropbox.com/s/xi2qlqczmth69bv/last_frame.pdb?dl=0">https://www.dropbox.com/s/xi2qlqczmth69bv/last_frame.pdb?dl=0</a></div>
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<div>The corresponding map:&nbsp;<a href="https://www.dropbox.com/s/igweq3avgf6o7uk/emd_3765.mrc?dl=0">https://www.dropbox.com/s/igweq3avgf6o7uk/emd_3765.mrc?dl=0</a></div>
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<div>The example PDB (and map) is a structure of the nucleosome containing both protein and DNA, and&nbsp;the stated resolution of the map is 4.8.</div>
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<div>I&nbsp;use default settings for the pehnix.real.space.refine run so my run&nbsp;command is:<br>
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<div>phenix.real_space_refine last_frame.pdb emd_3765.mrc resolution=4.8<br>
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<div>I should mention that it seems we are running&nbsp;<span style="background-color:rgb(255,255,255)">phenix version dev-2614 at our department, which&nbsp;</span><span style="background-color:rgb(255,255,255)">I am guessing&nbsp;is not the newest official release?</span></div>
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<div><span style="background-color:rgb(255,255,255)">Anyway I will try and get our sys-admin to install the newest&nbsp;version and then run the same files through phenix.RSR and see what happens.</span></div>
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<div><span style="background-color:rgb(255,255,255)">Thx again for getting back to me</span></div>
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<div><span style="background-color:rgb(255,255,255)">Cheers</span></div>
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<div><span style="background-color:rgb(255,255,255)">/Ruki</span></div>
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<blockquote type="cite">
<div>On 14 Nov 2017, at 16.20, Pavel Afonine &lt;pafonine@lbl.gov&gt; wrote:</div>
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<div><span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">Hi
 Ruki,</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
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<blockquote type="cite" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; background-color:rgb(255,255,255)">
<div class="" style="margin-top:0px; margin-bottom:0px">I have been playing around with phenix.real.space.refine as part of a small pipeline I am making for EM structures.<br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">Testing various deposited EM&nbsp;structures and their corresponding maps,&nbsp;within&nbsp;my pipeline, I sometimes run&nbsp;in to the below error:<br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">RuntimeError: Bond distance &gt; max_reasonable_bond_distance: 79.8663 &gt; 50:<br class="">
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</blockquote>
<br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">I'm
 trying to chase this down and eliminate. So if you come across a case that can be reproduced please send it to me and I will start from there.</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">For
 now simply set &quot;max_reasonable_bond_distance=999&quot; for all your refinements that will mask but not fix the problem. However, this should not affect the refinement results.</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">Make
 sure you are using the latest Phenix version.</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
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<blockquote type="cite" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; background-color:rgb(255,255,255)">
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<div class="" style="margin-top:0px; margin-bottom:0px">Followed by a list of distances between, what I am assuming is, atom numbers and the actual distance.<br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">I can get past it simply&nbsp;by changing the&nbsp;max_reasonable_bond_distance&nbsp;for the run&nbsp;to, in this case, 80.<br class="">
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<br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">This
 happens because the procedure optimizes weights by trying a large sample of possible weight values. For some values restraints may be too weak and atoms run one onto another, thus creating a huge clash and strong repulsion that stretches the bond. This leads
 to the crash.</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
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<div class="" style="margin-top:0px; margin-bottom:0px">But I tend to see, that the final&nbsp;results gets significantly&nbsp;worse when I use this bypass.<br class="">
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<div class="" style="margin-top:0px; margin-bottom:0px">This is based on very similar&nbsp;models going through the pipeline, where the ones which yields the error, scores much worse&nbsp;when using the above mentioned bypass, compared to the models that showed no max_reasonable_distance_error.<span class="Apple-converted-space">&nbsp;</span><br class="">
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<br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">Again,
 I'm very keep to investigate concrete reproducible cases. So if you have anything to share that would be most helpful!</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
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<blockquote type="cite" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; background-color:rgb(255,255,255)">
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B: Any ide what I can do, to avoid&nbsp;running&nbsp;into this bond distance&nbsp;problem?<br class="">
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<br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; background-color: rgb(255, 255, 255); float: none; display: inline;">I'd
 say help us to identify the issue so that we fix it and then you don't run into it any more.</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">All
 the best,</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<span class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">Pavel</span><br class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
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