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SAVES v5.0_HLA-A6823_SWISS-MODEL.html
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SAVES v5.0_HLA-A6823_SWISS-MODEL.html
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<h1 id="svtop" style="color:#444;">SAVES v5.0</h1>
<br>
<b>Notice</b>: Undefined offset: 1 in <b>/var/www/hlib/work.php</b> on line <b>166</b><br>
<br>
<b>Notice</b>: Undefined offset: 2 in <b>/var/www/hlib/work.php</b> on line <b>167</b><br>
<div class="nav"><a href="http://servicesn.mbi.ucla.edu/WHATCHECK">WHATCHECK</a> • <a href="http://servicesn.mbi.ucla.edu/PROCHECK">PROCHECK</a> • <a href="http://servicesn.mbi.ucla.edu/ERRAT">ERRAT</a> • <a href="http://servicesn.mbi.ucla.edu/Verify3D">Verify3D</a> • <a href="http://servicesn.mbi.ucla.edu/PROVE">PROVE</a> • <a href="http://servicesn.mbi.ucla.edu/CRYST">CRYST</a> • <a href="http://servicesn.mbi.ucla.edu/pdbU">pdbU</a> <span class="qbtn"><a href="http://servicesn.mbi.ucla.edu/SAVES/ask?srvr=SAVES">?</a></span></div><br><script>
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<span class="btn"><a href="http://servicesn.mbi.ucla.edu/SAVES">New Job</a></span><br><br><div class="topPanel"><table class="jstatus"><tbody><tr></tr><tr><th id="verify_head">VERIFY</th><th id="errat_head">ERRAT</th><th id="prove_head">PROVE</th><th id="procheck_head">PROCHECK</th><th id="whatcheck_head">WHATCHECK</th></tr>
<tr><td><center><div class="vmsg">99.27% of the residues have<br>averaged 3D-1D score >= 0.2</div><div id="vfpass">Pass</div></center></td><td><center><div id="erratVerdict">Overall Quality Factor<br><b>A: 98.4906</b></div></center></td><td><center>Buried outlier protein atoms total<br>from 1 Model: 2.6% <span class="warning">Warning</span></center></td><td><center><p>Out of 9 evaluations</p><ul class="mli">
<li> <span class="error">Errors: 0</span></li>
<li> <span class="warning">Warning: 6 </span></li>
<li> <span class="pass">Pass: 3 </span></li>
</ul></center></td><td><center><table class="wctab"><tbody><tr><td style="background:#f99;color:black;"> <span id="wc1 " class="wcDetails" title="1 : Error: Missing unit cell information">1 </span></td><td style="background:#f99;color:black;"> <span id="wc2 " class="wcDetails" title="2 : Error: Missing symmetry information">2 </span></td><td style="background:#5f5;color:black;"> <span id="wc3 " class="wcDetails" title="3 : Note: No rounded coordinates detected">3 </span></td><td style="background:#5f5;color:black;"> <span id="wc4 " class="wcDetails" title="4 : Note: Valine nomenclature OK">4 </span></td><td style="background:#5f5;color:black;"> <span id="wc5 " class="wcDetails" title="5 : Note: Threonine nomenclature OK">5 </span></td><td style="background:#5f5;color:black;"> <span id="wc6 " class="wcDetails" title="6 : Note: Isoleucine nomenclature OK">6 </span></td><td style="background:#5f5;color:black;"> <span id="wc7 " class="wcDetails" title="7 : Note: Leucine nomenclature OK">7 </span></td><td style="background:yellow;color:black;"> <span id="wc8 " class="wcDetails" title="8 : Warning: Arginine nomenclature problem">8 </span></td></tr><tr><td style="background:#5f5;color:black;"> <span id="wc9 " class="wcDetails" title="9 : Note: Tyrosine torsion conventions OK">9 </span></td><td style="background:yellow;color:black;"> <span id="wc10 " class="wcDetails" title="10 : Warning: Phenylalanine convention problem">10 </span></td><td style="background:#5f5;color:black;"> <span id="wc11 " class="wcDetails" title="11 : Note: Aspartic acid torsion conventions OK">11 </span></td><td style="background:yellow;color:black;"> <span id="wc12 " class="wcDetails" title="12 : Warning: Glutamic acid convention problem">12 </span></td><td style="background:#5f5;color:black;"> <span id="wc13 " class="wcDetails" title="13 : Note: L or D conformation checked OK">13 </span></td><td style="background:#5f5;color:black;"> <span id="wc14 " class="wcDetails" title="14 : Note: Chain names are unique">14 </span></td><td style="background:#5f5;color:black;"> <span id="wc15 " class="wcDetails" title="15 : Note: Weights checked OK">15 </span></td><td style="background:#5f5;color:black;"> <span id="wc16 " class="wcDetails" title="16 : Note: No missing atoms detected">16 </span></td></tr><tr><td style="background:#5f5;color:black;"> <span id="wc17 " class="wcDetails" title="17 : Note: All bond lengths OK">17 </span></td><td style="background:yellow;color:black;"> <span id="wc18 " class="wcDetails" title="18 : Warning: Low bond length variability">18 </span></td><td style="background:yellow;color:black;"> <span id="wc19 " class="wcDetails" title="19 : Warning: Directionality in bond lengths">19 </span></td><td style="background:yellow;color:black;"> <span id="wc20 " class="wcDetails" title="20 : Warning: Unusual bond angles">20 </span></td><td style="background:#5f5;color:black;"> <span id="wc21 " class="wcDetails" title="21 : Note: Normal bond angle variability">21 </span></td><td style="background:#5f5;color:black;"> <span id="wc22 " class="wcDetails" title="22 : Note: Side chain planarity OK">22 </span></td><td style="background:#f99;color:black;"> <span id="wc23 " class="wcDetails" title="23 : Error: Connections to aromatic rings out of plane">23 </span></td><td style="background:yellow;color:black;"> <span id="wc24 " class="wcDetails" title="24 : Warning: Strange PRO puckering amplitudes">24 </span></td></tr><tr><td style="background:#5f5;color:black;"> <span id="wc25 " class="wcDetails" title="25 : Note: PRO puckering phases OK">25 </span></td><td style="background:yellow;color:black;"> <span id="wc26 " class="wcDetails" title="26 : Warning: Torsion angle evaluation shows unusual residues">26 </span></td><td style="background:yellow;color:black;"> <span id="wc27 " class="wcDetails" title="27 : Warning: Backbone torsion angle evaluation shows unusual conformations">27 </span></td><td style="background:#5f5;color:black;"> <span id="wc28 " class="wcDetails" title="28 : Note: Ramachandran Z-score OK">28 </span></td><td style="background:#5f5;color:black;"> <span id="wc29 " class="wcDetails" title="29 : Note: Omega angle restraint OK">29 </span></td><td style="background:#5f5;color:black;"> <span id="wc30 " class="wcDetails" title="30 : Note: chi-1/chi-2 angle correlation Z-score OK">30 </span></td><td style="background:#5f5;color:black;"> <span id="wc31 " class="wcDetails" title="31 : Note: Ramachandran plot">31 </span></td><td style="background:#5f5;color:black;"> <span id="wc32 " class="wcDetails" title="32 : Note: Secondary structure">32 </span></td></tr><tr><td style="background:#f99;color:black;"> <span id="wc33 " class="wcDetails" title="33 : Error: Abnormally short interatomic distances">33 </span></td><td style="background:yellow;color:black;"> <span id="wc34 " class="wcDetails" title="34 : Warning: Abnormal packing environment for some residues">34 </span></td><td style="background:yellow;color:black;"> <span id="wc35 " class="wcDetails" title="35 : Warning: Abnormal packing environment for sequential residues">35 </span></td><td style="background:#5f5;color:black;"> <span id="wc36 " class="wcDetails" title="36 : Note: Structural average packing environment OK">36 </span></td><td style="background:#5f5;color:black;"> <span id="wc37 " class="wcDetails" title="37 : Note: Backbone oxygen evaluation OK">37 </span></td><td style="background:#5f5;color:black;"> <span id="wc38 " class="wcDetails" title="38 : Note: Rotamers checked OK">38 </span></td><td style="background:yellow;color:black;"> <span id="wc39 " class="wcDetails" title="39 : Warning: Unusual backbone conformations">39 </span></td><td style="background:#f99;color:black;"> <span id="wc40 " class="wcDetails" title="40 : Error: Backbone conformation Z-score very low">40 </span></td></tr><tr><td style="background:#5f5;color:black;"> <span id="wc41 " class="wcDetails" title="41 : Note: Symmetry related water molecules check not performed">41 </span></td><td style="background:#f99;color:black;"> <span id="wc42 " class="wcDetails" title="42 : Error: Average B-factor error">42 </span></td><td style="background:#f99;color:black;"> <span id="wc43 " class="wcDetails" title="43 : Error: HIS, ASN, GLN side chain flips">43 </span></td><td style="background:#5f5;color:black;"> <span id="wc44 " class="wcDetails" title="44 : Note: Histidine type assignments">44 </span></td><td style="background:yellow;color:black;"> <span id="wc45 " class="wcDetails" title="45 : Warning: Buried unsatisfied hydrogen bond donors">45 </span></td><td style="background:#5f5;color:black;"> <span id="wc46 " class="wcDetails" title="46 : Note: Buried hydrogen bond acceptors OK">46 </span></td><td style="background:#5f5;color:black;"> <span id="wc47 " class="wcDetails" title="47 : Note: Overall summary report">47 </span></td></tr></tbody></table></center></td></tr></tbody></table></div><h2>Job results for:model.pdb | <a href="http://servicesn.mbi.ucla.edu/SAVES/?job=375479">Link to this job:375479</a><br> <a href="http://servicesn.mbi.ucla.edu/SAVES/Ramachandran/?job=375479">Interactive Ramachandran Plot</a> | <a href="http://servicesn.mbi.ucla.edu/viewer/?job=375479">View Structure</a></h2><i>Amino acid distributions determined from 145,098 PDB structures (2019/03/20)</i>
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<span class="btn"><a href="http://servicesn.mbi.ucla.edu/Verify3D/downloaddata?job=375479">Save data to file</a></span><br><br><br><br><br><div id="erratResults">ERRAT results <span class="btnsvtop">↑ TOP</span></div><p>Input: <a href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/9567606.pdb">model.pdb (model.pdb)</a></p><p><br></p><p>Quality Factor: A: 98.4906 | <a href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/qq_aaaa.pdb_errat.pdf">PDF</a> | <a href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/qq_aaaa.pdb_errat.ps">PostScript</a> | <a href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/qq_aaaa.pdb_errat.logf">Log</a> </p><div><div class="chartjs-size-monitor" style="position: absolute; left: 0px; top: 0px; right: 0px; bottom: 0px; overflow: hidden; pointer-events: none; visibility: hidden; z-index: -1;"><div class="chartjs-size-monitor-expand" style="position:absolute;left:0;top:0;right:0;bottom:0;overflow:hidden;pointer-events:none;visibility:hidden;z-index:-1;"><div style="position:absolute;width:1000000px;height:1000000px;left:0;top:0"></div></div><div class="chartjs-size-monitor-shrink" style="position:absolute;left:0;top:0;right:0;bottom:0;overflow:hidden;pointer-events:none;visibility:hidden;z-index:-1;"><div style="position:absolute;width:200%;height:200%;left:0; top:0"></div></div></div> <canvas id="erratPlot1" width="1834" height="450" class="chartjs-render-monitor" style="display: block; height: 300px; width: 1223px;"></canvas> </div>
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<br><br><br><br><br><br><br><div id="proveResults">PROVE results <span class="btnsvtop">↑ TOP</span></div><table><tbody><tr><td>Input file: <b>model.pdb</b><table id="provetable"><tbody><tr><td>Model : 24 buried outlier protein atoms, 2.6% <span class="warning">Warning</span></td></tr><tr><td><a href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/prove/9567606.pdb.out">Job Run Report</a> | <a href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/prove/PROVE_9567606.pdb.pdb">Labeled pdb</a></td></tr><tr><th colspan="2">• <a href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/prove/PROVE_ps.out">Job output</a></th></tr><tr><th colspan="2">• <a href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/prove/PROVE_PLOT.ps">Plot PS</a> | <a href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/prove/PROVE_PLOT.pdf">Plot PDF</a></th></tr><tr><th colspan="2">• <a href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/prove/log">Job run log</a></th></tr></tbody></table></td><td><span class="pvsi" style="display: none;">working on structure image</span></td></tr></tbody></table><div id="procheckResults">PROCHECK results <span class="btnsvtop">↑ TOP</span> </div>
<p>Out of 9 evaluations</p><ul class="mli">
<li> <span class="error">Errors: 0</span></li>
<li> <span class="warning">Warning: 6 </span></li>
<li> <span class="pass">Pass: 3 </span></li>
</ul><table><tbody><tr><td><div class="pcfiles"><ol><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/procheck_run.out">Program Output</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.sum">Results Summary</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606_01.pdf">Main Ramachandran plot</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606_02.pdf">All-residue Ramachandran plots</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606_03.pdf">All-residue chi1-chi2 plots</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606_04.pdf">Main-chain parameters</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606_05.pdf">Side-chain parameters</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606_06.pdf">Residue properties plot</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606_07.pdf">Main-chain bond lengths</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606_08.pdf">Main-chain bond angles</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606_09.pdf">RMS distances from planarity</a></b></li><li><b><a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606_10.pdf">Distorted geometry</a></b></li></ol></div><div style="font-size:0.8em;color:#a55bad;">Remaining log and data files<ol><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/anglen.log">anglen.log</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/anglen.log"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/9567606.out">9567606.out</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.out"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/9567606.pln">9567606.pln</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.pln"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/clean.log">clean.log</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/clean.log"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/bplot.log">bplot.log</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/bplot.log"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/procheck_run.out">procheck_run.out</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/procheck_run.out"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/9567606.nb">9567606.nb</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.nb"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/9567606.new">9567606.new</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.new"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/procheck.prm">procheck.prm</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/procheck.prm"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/9567606.sum">9567606.sum</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.sum"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/pplot.log">pplot.log</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/pplot.log"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/tplot.log">tplot.log</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/tplot.log"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/nb.log">nb.log</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/nb.log"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/fort.27">fort.27</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/fort.27"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/9567606.sdh">9567606.sdh</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.sdh"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/9567606.sco">9567606.sco</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.sco"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/secstr.log">secstr.log</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/secstr.log"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/9567606.lan">9567606.lan</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.lan"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/9567606.dis">9567606.dis</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.dis"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li><li><span class="fbtn" id="/SAVES/Jobs/9567606/pc/9567606.rin">9567606.rin</span> <a target="_blank" href="http://servicesn.mbi.ucla.edu/SAVES/Jobs/9567606/pc/9567606.rin"><img src="./SAVES v5.0_HLA-A6823_SWISS-MODEL_files/linkout.png" width="10"></a></li></ol></div></td><td><div id="fpanel"></div></td></tr></tbody></table><br><br><br><br><br><script>
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<div id="whatcheckResults">WHATCHECK results <span class="btnsvtop">↑ TOP</span></div><div class="wcitem" id="pwc1">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">1.</span>
<span class="wchead">Error: Missing unit cell information</span> <span class="error">Error</span> <br>
<div class="wcdata">
No SCALE matrix is given in the PDB file.
</div>
</div><div class="wcitem" id="pwc2">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">2.</span>
<span class="wchead">Error: Missing symmetry information</span> <span class="error">Error</span> <br>
<div class="wcdata">
Problem: No CRYST1 card is given in the PDB file.
</div>
</div><div class="wcitem" id="pwc3">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">3.</span>
<span class="wchead">Note: No rounded coordinates detected</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
No significant rounding of atom coordinates has been detected.
</div>
</div><div class="wcitem" id="pwc4">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">4.</span>
<span class="wchead">Note: Valine nomenclature OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
No errors were detected in valine nomenclature.
</div>
</div><div class="wcitem" id="pwc5">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">5.</span>
<span class="wchead">Note: Threonine nomenclature OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
No errors were detected in threonine nomenclature.
</div>
</div><div class="wcitem" id="pwc6">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">6.</span>
<span class="wchead">Note: Isoleucine nomenclature OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
No errors were detected in isoleucine nomenclature.
</div>
</div><div class="wcitem" id="pwc7">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">7.</span>
<span class="wchead">Note: Leucine nomenclature OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
No errors were detected in leucine nomenclature.
</div>
</div><div class="wcitem" id="pwc8">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">8.</span>
<span class="wchead">Warning: Arginine nomenclature problem</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
The arginine residues listed in the table below have their N-H-1
and N-H-2 swapped.
97 ARG (121 ) A
219 ARG (243 ) A
</div>
</div><div class="wcitem" id="pwc9">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">9.</span>
<span class="wchead">Note: Tyrosine torsion conventions OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
No errors were detected in tyrosine torsion angle conventions.
</div>
</div><div class="wcitem" id="pwc10">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">10.</span>
<span class="wchead">Warning: Phenylalanine convention problem</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
The phenylalanine residues listed in the table below have their
chi-2 not between -90.0 and 90.0.
208 PHE (232 ) A
</div>
</div><div class="wcitem" id="pwc11">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">11.</span>
<span class="wchead">Note: Aspartic acid torsion conventions OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
No errors were detected in aspartic acid torsion angle conventions.
</div>
</div><div class="wcitem" id="pwc12">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">12.</span>
<span class="wchead">Warning: Glutamic acid convention problem</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
The glutamic acid residues listed in the table below have their
chi-3 outside the -90.0 to 90.0 range.
198 GLU (222 ) A
232 GLU (256 ) A
</div>
</div><div class="wcitem" id="pwc13">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">13.</span>
<span class="wchead">Note: L or D conformation checked OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
All amino acids in the structure have the L conformation.
</div>
</div><div class="wcitem" id="pwc14">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">14.</span>
<span class="wchead">Note: Chain names are unique</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
All chain names assigned to polymer molecules are unique.
</div>
</div><div class="wcitem" id="pwc15">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">15.</span>
<span class="wchead">Note: Weights checked OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range.
</div>
</div><div class="wcitem" id="pwc16">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">16.</span>
<span class="wchead">Note: No missing atoms detected</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
All expected atoms are present.
</div>
</div><div class="wcitem" id="pwc17">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">17.</span>
<span class="wchead">Note: All bond lengths OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
All bond lengths are in agreement with standard bond lengths using
a tolerance of 4 sigma (both standard values and sigma for amino acid
residues have been taken from Engh and Huber [REF])
</div>
</div><div class="wcitem" id="pwc18">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">18.</span>
<span class="wchead">Warning: Low bond length variability</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
Bond lengths were found to deviate less than normal from the mean
Engh and Huber [REF] standard bond lengths. The RMS Z-score given
below is expected to be around 1.0 for a normally restrained data
set. The fact that it is lower than 0.667 in this structure might
indicate that too-strong constraints have been used in the
refinement.
Z-score for bond lengths: 0.660
RMS-deviation in bond distances: 0.014
</div>
</div><div class="wcitem" id="pwc19">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">19.</span>
<span class="wchead">Warning: Directionality in bond lengths</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
Comparison of bond distances with Engh and Huber [REF] standard
values shows a significant systematic deviation. The bonds in one
direction are systematically longer than in other directions.
If this is not an XRAY structure this effect is hard to explain.
Otherwise you will have seen symmetry problems earlier. Please
correct these and rerun this check to see the implications on the
cell axes.
</div>
</div><div class="wcitem" id="pwc20">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">20.</span>
<span class="wchead">Warning: Unusual bond angles</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
The bond angles listed in the table below were found to deviate
more than 4 sigma from standard bond angles (both standard values
and sigma have been taken from Engh and Huber [REF]). In the table
below for each strange angle the bond angle and the number of
standard deviations it differs from the Engh and Huber values is
given. Please note that only bond angles within protein residues
are taken into account: disulphide bridges and peptide bonds are
neglected.
29 ASP (53 ) A CA CB CG 107.112 -5.5
63 ASN (87 ) A CA CB CG 108.492 -4.1
74 ASP (98 ) A CA CB CG 117.856 5.3
129 ASP (153 ) A CA CB CG 117.525 4.9
188 HIS (212 ) A CD2 CG ND1 110.314 4.2
191 HIS (215 ) A CA CB CG 118.548 4.7
192 HIS (216 ) A CD2 CG ND1 110.159 4.1
227 ASP (251 ) A CA CB CG 108.058 -4.5
231 VAL (255 ) A N CA CB 117.657 4.2
241 PHE (265 ) A CA CB CG 109.220 -4.6
260 HIS (284 ) A CD2 CG ND1 110.237 4.1
263 HIS (287 ) A CD2 CG ND1 110.380 4.3
</div>
</div><div class="wcitem" id="pwc21">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">21.</span>
<span class="wchead">Note: Normal bond angle variability</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
Bond angles were found to deviate normally from the mean Engh and
Huber [REF] standard bond angles. The RMS Z-score given below is
expected to be around 1.0 for a normally restrained data set, and
this is indeed observed for very high resolution X-ray structures.
More common values are around 1.55
Z-score for bond angles: 1.046
RMS-deviation in bond angles: 1.872
</div>
</div><div class="wcitem" id="pwc22">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">22.</span>
<span class="wchead">Note: Side chain planarity OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
All of the side chains of residues that have a planar group are
planar within expected RMS deviations.
</div>
</div><div class="wcitem" id="pwc23">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">23.</span>
<span class="wchead">Error: Connections to aromatic rings out of plane</span> <span class="error">Error</span> <br>
<div class="wcdata">
The atoms listed in the table below are connected to a planar
aromatic group in the sidechain of a protein residue but were found
to deviate from the least squares plane.
For all atoms that are connected to an aromatic side chain in a
protein residue the distance of the atom to the least squares plane
through the aromatic system was determined. This value was divided
by the standard deviation from a distribution of similar values
from a database of small molecule structures.
192 HIS (216 ) A CB 5.060
145 HIS (169 ) A CB 4.673
159 TYR (183 ) A CB 4.248
260 HIS (284 ) A CB 4.221
</div>
</div><div class="wcitem" id="pwc24">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">24.</span>
<span class="wchead">Warning: Strange PRO puckering amplitudes</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
The proline residues listed in the table below have a puckering
amplitude that is outside of normal ranges. Puckering parameters
were calculated by the method of Cremer and Pople [REF]. Normal PRO
rings have a puckering amplitude Q between 0.20 and 0.45
Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this
could indicate disorder between the two different normal ring forms
(with C-gamma below and above the ring, respectively). If Q is
higher than 0.45 Angstrom something could have gone wrong during the
refinement.
269 PRO (293 ) A 0.10 LOW
</div>
</div><div class="wcitem" id="pwc25">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">25.</span>
<span class="wchead">Note: PRO puckering phases OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
Puckering phases for all PRO residues are normal
</div>
</div><div class="wcitem" id="pwc26">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">26.</span>
<span class="wchead">Warning: Torsion angle evaluation shows unusual residues</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
The residues listed in the table below contain bad or abnormal
torsion angles.
These scores give an impression of how ``normal'' the torsion
angles in protein residues are. All torsion angles except omega are
used for calculating a `normality' score. Average values and
standard deviations were obtained from the residues in the WHAT IF
database. These are used to calculate Z-scores. A residue with a
Z-score of below -2.0 is poor, and a score of less than -3.0 is
worrying. For such residues more than one torsion angle is in a
highly unlikely position.
207 SER (231 ) A -2.7010
52 ILE (76 ) A -2.3234
</div>
</div><div class="wcitem" id="pwc27">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">27.</span>
<span class="wchead">Warning: Backbone torsion angle evaluation shows unusual conformations</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
The residues listed in the table below have abnormal backbone torsion
angles.
Residues with ``forbidden'' phi-psi combinations are listed, as
well as residues with unusual omega angles (deviating by more than
3 sigma from the normal value). Please note that it is normal if
about 5 percent of the residues is listed here as having unusual
phi-psi combinations.
4 SER (28 ) A omega poor
20 PRO (44 ) A omega poor
27 TYR (51 ) A omega poor
29 ASP (53 ) A Poor phi/psi
33 PHE (57 ) A Poor phi/psi
43 GLN (67 ) A Poor phi/psi
44 ARG (68 ) A omega poor
86 ASN (110 ) A Poor phi/psi
123 TYR (147 ) A Poor phi/psi
130 LEU (154 ) A Poor phi/psi
131 ARG (155 ) A Poor phi/psi
147 TRP (171 ) A omega poor
151 HIS (175 ) A Poor phi/psi
207 SER (231 ) A Poor phi/psi
209 TYR (233 ) A PRO omega poor
220 ASP (244 ) A Poor phi/psi
227 ASP (251 ) A Poor phi/psi
256 ARG (280 ) A omega poor
</div>
</div><div class="wcitem" id="pwc28">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">28.</span>
<span class="wchead">Note: Ramachandran Z-score OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
The score expressing how well the backbone conformations of all residues
are corresponding to the known allowed areas in the Ramachandran plot is
within expected ranges for well-refined structures.
Ramachandran Z-score : -0.213
</div>
</div><div class="wcitem" id="pwc29">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">29.</span>
<span class="wchead">Note: Omega angle restraint OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
The omega angles for trans-peptide bonds in a structure is
expected to give a gaussian distribution with the average around
+178 degrees, and a standard deviation around 5.5. In the current
structure the standard deviation agrees with this expectation.
Standard deviation of omega values : 6.671
</div>
</div><div class="wcitem" id="pwc30">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">30.</span>
<span class="wchead">Note: chi-1/chi-2 angle correlation Z-score OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
The score expressing how well the chi-1/chi-2 angles of all residues
are corresponding to the populated areas in the database is
within expected ranges for well-refined structures.
chi-1/chi-2 correlation Z-score : 0.230
</div>
</div><div class="wcitem" id="pwc31">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">31.</span>
<span class="wchead">Note: Ramachandran plot</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
In this Ramachandran plot large crosses represent glycines and
small crosses represent the other residues. If too many small crosses
fall outside the boxed areas then the molecule is poorly refined (or
worse).
In the TeX file, a plot has been inserted here
Chain identifier: A
</div>
</div><div class="wcitem" id="pwc32">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">32.</span>
<span class="wchead">Note: Secondary structure</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
This is the secondary structure according to DSSP. Only helix (H), strand
(S), turn (T) and coil (blank) are shown. [REF]
Secondary structure assignment
The DSSP executable was not found
/software/what/whattest/dssp/DSSP.EXE
WARNING. You don`t have the DSSP program installed. Therefore
the emulator will be used. This emulator gives rather poor results,
but it prevents WHAT IF from crashing. See the writeup about this.
10 20 30 40 50 60
| | | | | |
1 - 60 GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
1 - 60 SSSSSSSSSS T TT SSSSSSST T SSST T T S T3 33 TTHHHH
70 80 90 100 110 120
| | | | | |
61 - 120 DRNTRNVKAQSQTDRVDLGTLRGYYNQSEAGSHTIQRMYGCDVGSDGRFLRGYRQDAYDG
61 - 120 HHHHHHHHHHHHHHHHHHHHHHHHHT T T SSSSS SSS3 T SSSSSSSTTT
130 140 150 160 170 180
| | | | | |
121 - 180 KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQWRAYLEGTCVEWLRRYLENGKETLQ
121 - 180 T S T T S HHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHH 3HT
190 200 210 220 230 240
| | | | | |
181 - 240 RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
181 - 240 T S SSSSSSS SSSSSSSSTSS SSSSSTTTT 3 TTS S T T
250 260 270
| | |
241 - 275 FQKWVAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE
241 - 275 SSSSSSSSST T33 3TSSSSST T SSS
</div>
</div><div class="wcitem" id="pwc33">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">33.</span>
<span class="wchead">Error: Abnormally short interatomic distances</span> <span class="error">Error</span> <br>
<div class="wcdata">
The pairs of atoms listed in the table below have an unusually
short distance.
The contact distances of all atom pairs have been checked. Two
atoms are said to `bump' if they are closer than the sum of their
Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs
a tolerance of 0.55 Angstrom is used. The first number in the
table tells you how much shorter that specific contact is than the
acceptable limit. The second distance is the distance between the
centers of the two atoms.
The last text-item on each line represents the status of the atom
pair. The text `INTRA' means that the bump is between atoms that
are explicitly listed in the PDB file. `INTER' means it is an
inter-symmetry bump. If a line contains the text 'HB', the bump
criterium was relaxed because there could be a hydrogen bond. If
the text 'BF' is present, the sum of the B-factors of the atoms is
higher than 80, which makes the appearance of the bump somewhat
less severe because the atoms probably aren't there anyway.
Bumps between atoms for which the sum of their occupancies is lower
than one are not reported. In any case, each bump is listed in only
one direction.
101 CYS (125 ) A SG -- 164 CYS (188 ) A C 0.068 3.332 INTRA
218 GLN (242 ) A CD -- 260 HIS (284 ) A NE2 0.024 3.076 INTRA
</div>
</div><div class="wcitem" id="pwc34">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">34.</span>
<span class="wchead">Warning: Abnormal packing environment for some residues</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
The residues listed in the table below have an unusual packing
environment.
The packing environment of the residues is compared with the
average packing environment for all residues of the same type in
good PDB files. A low packing score can indicate one of several
things: Poor packing, misthreading of the sequence through the
density, crystal contacts, contacts with a co-factor, or the
residue is part of the active site. It is not uncommon to see a few
of these, but in any case this requires further inspection of the
residue.
17 ARG (41 ) A -8.39
14 ARG (38 ) A -6.04
48 ARG (72 ) A -5.71
256 ARG (280 ) A -5.63
131 ARG (155 ) A -5.54
226 GLN (250 ) A -5.40
</div>
</div><div class="wcitem" id="pwc35">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">35.</span>
<span class="wchead">Warning: Abnormal packing environment for sequential residues</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
A stretch of at least three sequential residues with a questionable packing
environment was found. This could indicate that these residues are part
of a strange loop, but might also be an indication of misthreading.
The table below lists the first and last residue in each stretch found,
as well as the average residue score of the series.
16 GLY (40 ) A --- 18 GLY (42 ) A -5.54
</div>
</div><div class="wcitem" id="pwc36">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">36.</span>
<span class="wchead">Note: Structural average packing environment OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
The structural average quality control value is within normal ranges.
Average for range 1 - 275 : -0.573
</div>
</div><div class="wcitem" id="pwc37">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">37.</span>
<span class="wchead">Note: Backbone oxygen evaluation OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
All residues for which the local backbone conformation could be
found in the WHAT IF database have a normal backbone oxygen
position.
</div>
</div><div class="wcitem" id="pwc38">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">38.</span>
<span class="wchead">Note: Rotamers checked OK</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
None of the residues that have a normal backbone environment have
abnormal rotamers.
</div>
</div><div class="wcitem" id="pwc39">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">39.</span>
<span class="wchead">Warning: Unusual backbone conformations</span> <span class="warning">Warning</span> <br>
<div class="wcdata">
For the residues listed in the table below, the backbone formed by
itself and two neighboring residues on either side is in a
conformation that is not seen very often in the database of solved
protein structures. The number given in the table is the number of
similar backbone conformations in the database with the same amino
acid in the center.
For this check, backbone conformations are compared with database
structures using C-alpha superpositions with some restraints on the
backbone oxygen positions.
A residue mentioned in the table can be part of a strange loop, or
there might be something wrong with it or its directly surrounding
residues. There are a few of these in every protein, but in any
case it is worth looking at!
3 HIS (27 ) A 0
4 SER (28 ) A 0
5 MET (29 ) A 0
6 ARG (30 ) A 0
7 TYR (31 ) A 0
8 PHE (32 ) A 0
9 TYR (33 ) A 0
10 THR (34 ) A 0
11 SER (35 ) A 0
12 VAL (36 ) A 0
13 SER (37 ) A 0
14 ARG (38 ) A 0
15 PRO (39 ) A 0
16 GLY (40 ) A 0
17 ARG (41 ) A 0
18 GLY (42 ) A 0
19 GLU (43 ) A 0
20 PRO (44 ) A 0
21 ARG (45 ) A 0
22 PHE (46 ) A 0
23 ILE (47 ) A 0
24 ALA (48 ) A 0
25 VAL (49 ) A 0
26 GLY (50 ) A 0
27 TYR (51 ) A 0
And so on for a total of 271 lines
</div>
</div><div class="wcitem" id="pwc40">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">40.</span>
<span class="wchead">Error: Backbone conformation Z-score very low</span> <span class="error">Error</span> <br>
<div class="wcdata">
A comparison of the backbone conformation with database proteins
shows that the backbone fold in this structure is very unusual.
Backbone conformation Z-score : -28.122
</div>
</div><div class="wcitem" id="pwc41">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">41.</span>
<span class="wchead">Note: Symmetry related water molecules check not performed</span> <span class="pass">Pass</span> <br>
<div class="wcdata">
Since there is no symmetry, the position check for symmetry related
water molecules can not be performed
</div>
</div><div class="wcitem" id="pwc42">
<span class="btnsvtop">↑ TOP</span>
<span style="font-size:1.2em;">42.</span>
<span class="wchead">Error: Average B-factor error</span> <span class="error">Error</span> <br>
<div class="wcdata">
The average B-factor for all buried protein atoms normally lies between
10--20. Values around 3--5 are expected for X-ray studies performed
at liquid nitrogen temperature.
Because of the extreme value for the average B-factor, no further analysis
of the B-factors is performed.
Average B-factor for buried atoms : 0.883