<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Hi Esra,</p>
<p>1) running refinement with all default settings</p>
<p>phenix.refine MR.1.updated_refine_002.{pdb,mtz}</p>
<p>works just s expected. So I'm not sure how you get "Sorry: Fatal
problems interpreting PDB file" message.</p>
<p>2) The data set is overall very incomplete: 63% and per
resolution :</p>
<p> Resolution Compl<br>
52.332-12.028 97.09<br>
11.996-9.598 100.00<br>
9.540-7.569 98.58<br>
7.557-6.001 98.47<br>
6.000-4.760 99.23<br>
4.758-3.775 98.73<br>
3.774-2.994 97.20<br>
2.993-2.374 91.01<br>
2.374-1.883 68.22<br>
1.883-1.664 22.61</p>
<p>3) Looks like the model came straight after MR. Is it complete
and matches the sequence (or, asking differently, does it need
some rounds of model building before running refinement starts
making sense?)?</p>
<p>4) Lot's of atoms in the model has zero occupancy.</p>
<p>All in all, it looks line you are facing a number of typical
structure solution issues that you need to address first before
"fighting with R-factors"!</p>
<p>Good luck!<br>
Pavel<br>
</p>
<div class="moz-cite-prefix">On 8/2/23 14:05, Esra A wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CA+dV_isGLk44VXQEB9CMun4W9y00e-wmJCBhnBATqGS7T0AoUQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hello everyone,
<div><br>
</div>
<div>I am Esra Ayan.</div>
<div>I would like to ask you about getting an error in Phenix: <font
face="monospace"><b>Sorry: Fatal problems interpreting PDB
file</b></font></div>
<div><i><br>
</i></div>
<div><u>I followed the below command to resolve this issue:</u></div>
<div><br>
</div>
<div>1. just running "<span style="background-color:rgb(248,249,250);color:rgb(0,0,0);font-family:monospace,monospace;font-size:14px;white-space:pre-wrap">phenix.ready_set MR.1.pdb"</span></div>
<div><font color="#000000"><span style="font-size:14px;white-space:pre-wrap"><font face="arial, sans-serif">2. then running </font><font face="monospace, monospace">"</font></span></font><span style="color:rgb(0,0,0);font-family:monospace,monospace;font-size:14px;white-space:pre-wrap"><span style="background-color:rgb(248,249,250)">phenix.refine MR.1.updated.pdb MR.1.mtz MR.1.ligands.cif </span></span><span
style="font-size:10pt;font-family:monospace,monospace;color:rgb(0,0,0);background-color:rgb(255,255,255)">refinement.input.xray_data.r_free_flags.generate=True</span></div>
<div><font face="monospace, monospace" color="#000000"><span
style="font-size:13.3333px"><br>
</span></font></div>
<div><font color="#000000"><span style="font-size:13.3333px"><font
face="arial, sans-serif">This way, i was able to solve
the problem but still getting high Rwork and Rfree
values. </font></span></font>I still couldn't lower the
values even though I tried many ways.</div>
<div><br>
</div>
<div>What is your recommendation about this issue? <br>
i was wondering if I did a mistake by using Step 1 and Step 2
commands.</div>
<div><br>
</div>
<div>You can find the reference pdb and mtz files in
the attachment.</div>
<div><br>
</div>
<div>Any help would be appreciated.</div>
<div><br>
</div>
<div>Kind regards,</div>
<div><br>
</div>
<div>Esra Ayan</div>
</div>
</blockquote>
</body>
</html>