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index e881069..d90afe2 100644
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             <a class="nav" href="z_83fe3c7e416da4d9_fix_chirality_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_83fe3c7e416da4d9_fix_chirality_py.html b/coverage/z_83fe3c7e416da4d9_fix_chirality_py.html
index a144522..c5077f7 100644
--- a/coverage/z_83fe3c7e416da4d9_fix_chirality_py.html
+++ b/coverage/z_83fe3c7e416da4d9_fix_chirality_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_83fe3c7e416da4d9_fix_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -217,7 +217,7 @@ <h2>
             <a class="nav" href="z_83fe3c7e416da4d9_fix_pdb_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_83fe3c7e416da4d9_fix_pdb_py.html b/coverage/z_83fe3c7e416da4d9_fix_pdb_py.html
index 4d93cc7..65fe0a2 100644
--- a/coverage/z_83fe3c7e416da4d9_fix_pdb_py.html
+++ b/coverage/z_83fe3c7e416da4d9_fix_pdb_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_83fe3c7e416da4d9_fix_pdb_utils_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -235,7 +235,7 @@ <h2>
             <a class="nav" href="z_83fe3c7e416da4d9_fix_pdb_utils_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_83fe3c7e416da4d9_fix_pdb_utils_py.html b/coverage/z_83fe3c7e416da4d9_fix_pdb_utils_py.html
index c3ba970..69fcf57 100644
--- a/coverage/z_83fe3c7e416da4d9_fix_pdb_utils_py.html
+++ b/coverage/z_83fe3c7e416da4d9_fix_pdb_utils_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_83fe3c7e416da4d9_fix_side_chain_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -1097,7 +1097,7 @@ <h2>
             <a class="nav" href="z_83fe3c7e416da4d9_fix_side_chain_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_83fe3c7e416da4d9_fix_side_chain_py.html b/coverage/z_83fe3c7e416da4d9_fix_side_chain_py.html
index e1fc44c..5482d4f 100644
--- a/coverage/z_83fe3c7e416da4d9_fix_side_chain_py.html
+++ b/coverage/z_83fe3c7e416da4d9_fix_side_chain_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_83fe3c7e416da4d9_fix_ssbonds_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -227,7 +227,7 @@ <h2>
             <a class="nav" href="z_83fe3c7e416da4d9_fix_ssbonds_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_83fe3c7e416da4d9_fix_ssbonds_py.html b/coverage/z_83fe3c7e416da4d9_fix_ssbonds_py.html
index 8e2039c..19c1e2e 100644
--- a/coverage/z_83fe3c7e416da4d9_fix_ssbonds_py.html
+++ b/coverage/z_83fe3c7e416da4d9_fix_ssbonds_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_83fe3c7e416da4d9_mutate_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -217,7 +217,7 @@ <h2>
             <a class="nav" href="z_83fe3c7e416da4d9_mutate_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_83fe3c7e416da4d9_mutate_py.html b/coverage/z_83fe3c7e416da4d9_mutate_py.html
index fe6ec66..4f467f4 100644
--- a/coverage/z_83fe3c7e416da4d9_mutate_py.html
+++ b/coverage/z_83fe3c7e416da4d9_mutate_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3531ae296f7407e1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -237,7 +237,7 @@ <h2>
             <a class="nav" href="z_3531ae296f7407e1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_c2a2934247a9a3e6___init___py.html b/coverage/z_c2a2934247a9a3e6___init___py.html
index 7feccba..889e2f2 100644
--- a/coverage/z_c2a2934247a9a3e6___init___py.html
+++ b/coverage/z_c2a2934247a9a3e6___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_c2a2934247a9a3e6_file_utils_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -89,7 +89,7 @@ <h2>
             <a class="nav" href="z_c2a2934247a9a3e6_file_utils_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_c2a2934247a9a3e6_file_utils_py.html b/coverage/z_c2a2934247a9a3e6_file_utils_py.html
index 319ace7..16eb061 100644
--- a/coverage/z_c2a2934247a9a3e6_file_utils_py.html
+++ b/coverage/z_c2a2934247a9a3e6_file_utils_py.html
@@ -54,9 +54,9 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">381 statements &nbsp;</span>
+            <span class="text">382 statements &nbsp;</span>
             <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">165<span class="text"> run</span></button>
-            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">216<span class="text"> missing</span></button>
+            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">217<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
         <p class="text">
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_c2a2934247a9a3e6_test_fixtures_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -105,7 +105,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">        <span class="nam">parent_dir</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">.</span><span class="nam">cwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t">    <span class="key">if</span> <span class="key">not</span> <span class="nam">extension</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t">        <span class="nam">extension</span> <span class="op">=</span> <span class="str">""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t">    <span class="key">while</span> <span class="key">True</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t">    <span class="key">while</span> <span class="key">True</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t">        <span class="nam">name</span> <span class="op">=</span> <span class="str">f"{uuid.uuid4()}{extension}"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t">        <span class="nam">file_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">parent_dir</span><span class="op">)</span><span class="op">.</span><span class="nam">resolve</span><span class="op">(</span><span class="op">)</span><span class="op">,</span> <span class="nam">name</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">file_path</span><span class="op">.</span><span class="nam">exists</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -859,7 +859,7 @@ <h2>
             <a class="nav" href="z_c2a2934247a9a3e6_test_fixtures_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_c2a2934247a9a3e6_test_fixtures_py.html b/coverage/z_c2a2934247a9a3e6_test_fixtures_py.html
index 981f0a1..7aa19ed 100644
--- a/coverage/z_c2a2934247a9a3e6_test_fixtures_py.html
+++ b/coverage/z_c2a2934247a9a3e6_test_fixtures_py.html
@@ -54,9 +54,9 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">196 statements &nbsp;</span>
+            <span class="text">197 statements &nbsp;</span>
             <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">93<span class="text"> run</span></button>
-            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">103<span class="text"> missing</span></button>
+            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">104<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
         <p class="text">
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3e55ad8bf5ba42c0___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -357,7 +357,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">        <span class="nam">print</span><span class="op">(</span><span class="str">"To compare images, please install the following packages: Pillow, imagehash"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">        <span class="key">return</span> <span class="key">False</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">    <span class="str">""" Compare two files using size """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">    <span class="str">""" Compare two files using size """</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">    <span class="nam">print</span><span class="op">(</span><span class="str">"Comparing images of both files:"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">    <span class="nam">print</span><span class="op">(</span><span class="str">f"     IMAGE_A: {file_a}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">    <span class="nam">print</span><span class="op">(</span><span class="str">f"     IMAGE_B: {file_b}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -382,7 +382,7 @@ <h2>
             <a class="nav" href="z_3e55ad8bf5ba42c0___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.3">coverage.py v7.5.3</a>,
-            created at 2024-05-30 13:02 +0000
+            created at 2024-05-31 13:33 +0000
         </p>
     </div>
 </footer>
diff --git a/flake8/index.html b/flake8/index.html
index 49bbc97..45699b6 100644
--- a/flake8/index.html
+++ b/flake8/index.html
@@ -9,7 +9,7 @@
       <div id="masthead" class="sev-2"></div>
       <div id="page">
           <h1>flake8 violations</h1>
-         <p id="versions">Generated on 2024-05-30 13:01
+         <p id="versions">Generated on 2024-05-31 13:33
             with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.11.1, pyflakes: 3.2.0
          </p>
          <ul id="index">
diff --git a/junit/junit.xml b/junit/junit.xml
index d860c56..8182a75 100644
--- a/junit/junit.xml
+++ b/junit/junit.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="8" time="29.759" timestamp="2024-05-30T13:01:53.456740" hostname="biobb-runners"><testcase classname="biobb_model.test.unitests.test_model.test_checking_log.TestCheckingLog" name="test_launch" time="17.075" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_altlocs.TestFixAltlocs" name="test_launch" time="1.181" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_amides.TestFixAmides" name="test_launch" time="1.941" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_chirality.TestFixChirality" name="test_launch" time="1.445" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_pdb.TestFixPdb" name="test_launch" time="4.244" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_side_chain.TestFixSideChain" name="test_launch" time="1.383" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_ssbonds.TestFixSSBonds" name="test_launch" time="0.678" /><testcase classname="biobb_model.test.unitests.test_model.test_mutate.TestFixSideChain" name="test_launch" time="1.219" /></testsuite></testsuites>
\ No newline at end of file
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="8" time="31.643" timestamp="2024-05-31T13:33:04.003252" hostname="biobb-runners"><testcase classname="biobb_model.test.unitests.test_model.test_checking_log.TestCheckingLog" name="test_launch" time="18.481" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_altlocs.TestFixAltlocs" name="test_launch" time="1.151" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_amides.TestFixAmides" name="test_launch" time="1.975" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_chirality.TestFixChirality" name="test_launch" time="1.418" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_pdb.TestFixPdb" name="test_launch" time="4.893" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_side_chain.TestFixSideChain" name="test_launch" time="1.408" /><testcase classname="biobb_model.test.unitests.test_model.test_fix_ssbonds.TestFixSSBonds" name="test_launch" time="0.534" /><testcase classname="biobb_model.test.unitests.test_model.test_mutate.TestFixSideChain" name="test_launch" time="1.227" /></testsuite></testsuites>
\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index 92bedef..3943cfe 100644
--- a/junit/report.html
+++ b/junit/report.html
@@ -7,7 +7,7 @@
   </head>
   <body>
     <h1 id="title">report.html</h1>
-    <p>Report generated on 30-May-2024 at 13:02:23 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 31-May-2024 at 13:33:35 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
         v4.1.1</p>
     <div id="environment-header">
       <h2>Environment</h2>
@@ -61,7 +61,7 @@ <h2>Environment</h2>
         <h2>Summary</h2>
         <div class="additional-summary prefix">
         </div>
-        <p class="run-count">8 tests took 00:00:29.</p>
+        <p class="run-count">8 tests took 00:00:31.</p>
         <p class="filter">(Un)check the boxes to filter the results.</p>
         <div class="summary__reload">
           <div class="summary__reload__button hidden" onclick="location.reload()">
@@ -108,7 +108,7 @@ <h2>Summary</h2>
     </table>
   </body>
   <footer>
-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.9.19&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.2.1&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_model/test/unitests/test_model/test_checking_log.py::TestCheckingLog::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_checking_log.py::TestCheckingLog::test_launch&#34;, &#34;duration&#34;: &#34;00:00:17&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_checking_log.py::TestCheckingLog::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:17&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-30 13:01:53,773 [MainThread  ] [INFO ]  Executing biobb_model.model.checking_log Version: 4.1.0\n2024-05-30 13:01:53,774 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/checking_log/9a7c7861-b1cd-49d6-bdaf-96a0e57e2784\n2024-05-30 13:01:53,774 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/checking_log/9a7c7861-b1cd-49d6-bdaf-96a0e57e2784/2ki5.pdb checkall &amp;gt; /tmp/biobb/unitests_107/checking_log/9a7c7861-b1cd-49d6-bdaf-96a0e57e2784/output_log_path.log\n\n2024-05-30 13:02:10,824 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-30 13:02:10,825 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/checking_log/9a7c7861-b1cd-49d6-bdaf-96a0e57e2784&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/checking_log/output_log_path.log\nComparing ignoring lines containing this words: [&amp;#x27;loaded&amp;#x27;]\n     FILE_A: /tmp/biobb/unitests_107/checking_log/output_log_path.log\n     FILE_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/checking.log\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/checking_log/checking_log_log.out:file_utils.py:391 Executing biobb_model.model.checking_log Version: 4.1.0\nINFO     /tmp/biobb/unitests_107/checking_log/checking_log_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/checking_log/9a7c7861-b1cd-49d6-bdaf-96a0e57e2784\nINFO     /tmp/biobb/unitests_107/checking_log/checking_log_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/checking_log/9a7c7861-b1cd-49d6-bdaf-96a0e57e2784/2ki5.pdb checkall &amp;gt; /tmp/biobb/unitests_107/checking_log/9a7c7861-b1cd-49d6-bdaf-96a0e57e2784/output_log_path.log\n\nINFO     /tmp/biobb/unitests_107/checking_log/checking_log_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/checking_log/checking_log_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/checking_log/9a7c7861-b1cd-49d6-bdaf-96a0e57e2784&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_altlocs.py::TestFixAltlocs::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_altlocs.py::TestFixAltlocs::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_altlocs.py::TestFixAltlocs::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-30 13:02:10,866 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_altlocs Version: 4.1.0\n2024-05-30 13:02:10,867 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/3ebp.pdb to /tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77\n2024-05-30 13:02:10,867 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77/3ebp.pdb -o /tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77/output_pdb_path.pdb --force_save --non_interactive altloc --select A339:A,A171:B,A768:A\n\n2024-05-30 13:02:11,674 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-30 13:02:11,674 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77/3ebp.pdb loaded\n PDB id: 3EBP \n Title: glycogen phosphorylase b/flavopiridol complex\n Experimental method: x-ray diffraction\n Keywords: glycogen phosphorylase, rational inhibitor design, glycogenolysis, diabetes type 2, allosteric enzyme, carbohydrate metabolism, glycogen metabolism, glycosyltransferase, nucleotide-binding, phosphoprotein, pyridoxal phosphate, transferase-transferase inhibitor complex\n Resolution (A): 2.0\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  1097\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  288\n Num. ligands or modified residues:  2\n Num. water mol.:  286\n Num. atoms:  6918\nModified residues found\nLLP A680\nSmall mol ligands found\nCPB A940\nRunning altloc. Options: --select A339:A,A171:B,A768:A\nDetected 3 residues with alternative location labels\nCYS A171\n  CB   A (0.50) B (0.50)\n  SG   A (0.50) B (0.50)\nASP A339\n  CG   A (0.50) B (0.50)\n  OD1  A (0.50) B (0.50)\n  OD2  A (0.50) B (0.50)\nHIS A768\n  CG   A (0.50) B (0.50)\n  ND1  A (0.50) B (0.50)\n  CD2  A (0.50) B (0.50)\n  CE1  A (0.50) B (0.50)\n  NE2  A (0.50) B (0.50)\nSelecting location A339:A,A171:B,A768:A\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  1097\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  288\nFinal Num. ligands or modified residues:  2\nFinal Num. water mol.:  286\nFinal Num. atoms:  6918\nModified residues found\nLLP A680\nSmall mol ligands found\nCPB A940\nStructure saved on /tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77/output_pdb_path.pdb\n\n2024-05-30 13:02:11,676 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/fix_altlocs/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/fix_altlocs/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_altloc.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 6866\n     Atoms ALIGNED in PDB_B: 6866\n     RMS: 1.0683071939348411e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:file_utils.py:391 Executing biobb_model.model.fix_altlocs Version: 4.1.0\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/3ebp.pdb to /tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77/3ebp.pdb -o /tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77/output_pdb_path.pdb --force_save --non_interactive altloc --select A339:A,A171:B,A768:A\n\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77/3ebp.pdb loaded\n PDB id: 3EBP \n Title: glycogen phosphorylase b/flavopiridol complex\n Experimental method: x-ray diffraction\n Keywords: glycogen phosphorylase, rational inhibitor design, glycogenolysis, diabetes type 2, allosteric enzyme, carbohydrate metabolism, glycogen metabolism, glycosyltransferase, nucleotide-binding, phosphoprotein, pyridoxal phosphate, transferase-transferase inhibitor complex\n Resolution (A): 2.0\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  1097\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  288\n Num. ligands or modified residues:  2\n Num. water mol.:  286\n Num. atoms:  6918\nModified residues found\nLLP A680\nSmall mol ligands found\nCPB A940\nRunning altloc. Options: --select A339:A,A171:B,A768:A\nDetected 3 residues with alternative location labels\nCYS A171\n  CB   A (0.50) B (0.50)\n  SG   A (0.50) B (0.50)\nASP A339\n  CG   A (0.50) B (0.50)\n  OD1  A (0.50) B (0.50)\n  OD2  A (0.50) B (0.50)\nHIS A768\n  CG   A (0.50) B (0.50)\n  ND1  A (0.50) B (0.50)\n  CD2  A (0.50) B (0.50)\n  CE1  A (0.50) B (0.50)\n  NE2  A (0.50) B (0.50)\nSelecting location A339:A,A171:B,A768:A\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  1097\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  288\nFinal Num. ligands or modified residues:  2\nFinal Num. water mol.:  286\nFinal Num. atoms:  6918\nModified residues found\nLLP A680\nSmall mol ligands found\nCPB A940\nStructure saved on /tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_altlocs/d3978bf4-9669-4f5a-a6fc-b7442c645d77&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_amides.py::TestFixAmides::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_amides.py::TestFixAmides::test_launch&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_amides.py::TestFixAmides::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-30 13:02:12,050 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_amides Version: 4.1.0\n2024-05-30 13:02:12,051 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/5s2z.pdb to /tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669\n2024-05-30 13:02:12,051 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669/5s2z.pdb -o /tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669/output_pdb_path.pdb --force_save amide --fix All\n\n2024-05-30 13:02:13,760 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-30 13:02:13,760 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669/5s2z.pdb loaded\n PDB id: 5S2Z \n Title: pandda analysis group deposition -- crystal structure of sars-cov-2 nsp3 macrodomain in complex with z126932614\n Experimental method: x-ray diffraction\n Keywords: sgc - diamond i04-1 fragment screening, pandda, xchemexplorer, sars- cov-2 nsp3 macrodomain, viral protein\n Resolution (A): 1.07\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  792\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  458\n Num. ligands or modified residues:  1\n Num. water mol.:  457\n Num. atoms:  2998\nModified residues found\nT6J A401\nRunning amide. Options: --fix All\nFound 2 unusual contact(s) involving amide atoms\n ASN B20.OD1  VAL B155.O      3.015 A\n ASN B20.OD1  PHE B156.O      2.894 A\nAmide residues fixed All (1)\nRechecking\nFound no unusual contact(s) involving amide atoms\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  792\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  458\nFinal Num. ligands or modified residues:  1\nFinal Num. water mol.:  457\nFinal Num. atoms:  2998\nModified residues found\nT6J A401\nStructure saved on /tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669/output_pdb_path.pdb\n\n2024-05-30 13:02:13,762 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/fix_amides/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/fix_amides/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_amide_pdb_path.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2984\n     Atoms ALIGNED in PDB_B: 2984\n     RMS: 7.386865969918367e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:file_utils.py:391 Executing biobb_model.model.fix_amides Version: 4.1.0\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/5s2z.pdb to /tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669/5s2z.pdb -o /tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669/output_pdb_path.pdb --force_save amide --fix All\n\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669/5s2z.pdb loaded\n PDB id: 5S2Z \n Title: pandda analysis group deposition -- crystal structure of sars-cov-2 nsp3 macrodomain in complex with z126932614\n Experimental method: x-ray diffraction\n Keywords: sgc - diamond i04-1 fragment screening, pandda, xchemexplorer, sars- cov-2 nsp3 macrodomain, viral protein\n Resolution (A): 1.07\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  792\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  458\n Num. ligands or modified residues:  1\n Num. water mol.:  457\n Num. atoms:  2998\nModified residues found\nT6J A401\nRunning amide. Options: --fix All\nFound 2 unusual contact(s) involving amide atoms\n ASN B20.OD1  VAL B155.O      3.015 A\n ASN B20.OD1  PHE B156.O      2.894 A\nAmide residues fixed All (1)\nRechecking\nFound no unusual contact(s) involving amide atoms\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  792\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  458\nFinal Num. ligands or modified residues:  1\nFinal Num. water mol.:  457\nFinal Num. atoms:  2998\nModified residues found\nT6J A401\nStructure saved on /tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_amides/6d305924-0379-4466-bb6c-e919d553d669&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_chirality.py::TestFixChirality::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_chirality.py::TestFixChirality::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_chirality.py::TestFixChirality::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-30 13:02:13,991 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_chirality Version: 4.1.0\n2024-05-30 13:02:13,992 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/3e2y.pdb to /tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6\n2024-05-30 13:02:13,992 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6/3e2y.pdb -o /tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6/output_pdb_path.pdb --force_save chiral --fix All\n\n2024-05-30 13:02:15,052 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-30 13:02:15,053 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6/3e2y.pdb loaded\n PDB id: 3E2Y \n Title: crystal structure of mouse kynurenine aminotransferase iii in complex with glutamine\n Experimental method: x-ray diffraction\n Keywords: alpha beta protein, plp dependent protein, aminotransferase, lyase, pyridoxal phosphate, transferase\n Resolution (A): 2.26\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  1239\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  419\n Num. ligands or modified residues:  8\n Num. water mol.:  411\n Num. atoms:  6993\nModified residues found\nGLN A456\nGLN B457\nSmall mol ligands found\nPMP A457\nGOL A458\nGOL A459\nPMP B456\nGOL B458\nGOL B459\nRunning chiral. Options: --fix All\nFound 2 residues with incorrect side-chain chirality\n THR A256  \n THR B286  \nChiral side chains fixed All (2)\nChecking for steric clashes\nNo severe clashes detected\n1 Steric apolar clashes detected\n THR A256.CG2 GLU A348.OE2    2.678 A\nNo polar_acceptor clashes detected\n1 Steric polar_donor clashes detected\n GLN A97.NE2  THR B286.N      3.001 A\nNo positive clashes detected\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  1239\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  419\nFinal Num. ligands or modified residues:  8\nFinal Num. water mol.:  411\nFinal Num. atoms:  6993\nModified residues found\nGLN A456\nGLN B457\nSmall mol ligands found\nPMP A457\nGOL A458\nGOL A459\nPMP B456\nGOL B458\nGOL B459\nStructure saved on /tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6/output_pdb_path.pdb\n\n2024-05-30 13:02:15,054 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/fix_chirality/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/fix_chirality/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_chirality_pdb_path.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 6917\n     Atoms ALIGNED in PDB_B: 6917\n     RMS: 6.2661067786844326e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:file_utils.py:391 Executing biobb_model.model.fix_chirality Version: 4.1.0\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/3e2y.pdb to /tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6/3e2y.pdb -o /tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6/output_pdb_path.pdb --force_save chiral --fix All\n\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6/3e2y.pdb loaded\n PDB id: 3E2Y \n Title: crystal structure of mouse kynurenine aminotransferase iii in complex with glutamine\n Experimental method: x-ray diffraction\n Keywords: alpha beta protein, plp dependent protein, aminotransferase, lyase, pyridoxal phosphate, transferase\n Resolution (A): 2.26\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  1239\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  419\n Num. ligands or modified residues:  8\n Num. water mol.:  411\n Num. atoms:  6993\nModified residues found\nGLN A456\nGLN B457\nSmall mol ligands found\nPMP A457\nGOL A458\nGOL A459\nPMP B456\nGOL B458\nGOL B459\nRunning chiral. Options: --fix All\nFound 2 residues with incorrect side-chain chirality\n THR A256  \n THR B286  \nChiral side chains fixed All (2)\nChecking for steric clashes\nNo severe clashes detected\n1 Steric apolar clashes detected\n THR A256.CG2 GLU A348.OE2    2.678 A\nNo polar_acceptor clashes detected\n1 Steric polar_donor clashes detected\n GLN A97.NE2  THR B286.N      3.001 A\nNo positive clashes detected\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  1239\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  419\nFinal Num. ligands or modified residues:  8\nFinal Num. water mol.:  411\nFinal Num. atoms:  6993\nModified residues found\nGLN A456\nGLN B457\nSmall mol ligands found\nPMP A457\nGOL A458\nGOL A459\nPMP B456\nGOL B458\nGOL B459\nStructure saved on /tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_chirality/a6daf703-cd2f-4933-843e-eff161ea5cf6&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_pdb.py::TestFixPdb::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_pdb.py::TestFixPdb::test_launch&#34;, &#34;duration&#34;: &#34;00:00:04&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_pdb.py::TestFixPdb::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:04&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-30 13:02:15,442 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_pdb Version: 4.1.0\n126 VVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFK-----IYSKH------TPINLVRDLPQGF-SALEPLVDLPIG----INIT------------------RFQTLLAL--------HRSYLT-PGDS------SSGWTAG------------------AAAYYVGYLQ------PRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRF-----PNITNLCPFGEVFNATRFASVYA------------WNRKR--------------------ISNCVADYSVL-YNSASFSTFKCYGV--------SPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNY---LYRLFRKSNLKPF\n    ||.|       |....|..|......|.    |.|........||.......|.|......|.|    ......|..     .|..|      .|..|..|....| ..|.||. .|.|    |..|                  .|.....|        ..|.|| |||.      ...|..|                  .|....|..|      ....||....|.....||.........|...||..    |.. .|.| ....|....|     .||....||.......|. .|..            |..||                    ......|||.. |.......|.....        .|....|.       ......|....|..  ..||.......| .||.|      |.|.|  ||....|   ||......|.|.|\n166 VVLK-------NEMARGYHYEDYGDYWR----RDYETEGSPDLEYSRDQLIKDVERIFAEIKPL----YEQLHAYVRTKLMDTYPFHISPTGCLPAHLLGDMWGRFWTNLYPLT-VPFGQKPNIDVTDAMLNQNWDAKRIFKEAEKFFVSIGLPNMTEGFWNNSMLTDPGDGRKVVCHPTAWDLGKGDFRIKMCTKVTMEDFLTAHHEMGHIQYDMAYASQPYLLRNGANEGFHEAVGEVMSLSVATPKHLKTM----GLL-SSDF-LEDNETEINFLFKQALNIVGTLPFTYMLEKWRW-MVFKGEIPKEEWMKKWWEMKRKIVGVVEPVPHDETYCDPASLFHVANDYSFIRYYTRTIFEFQFHEALCRIAKHDGPLHKCDI-------SNSTDAGEKLHQML--SVGKSQPWTSVL-KDFVG------SKNMD--VGPLLRYFEPLYTWLTEQNRKSF\n  Score=67\n\nNormalized score: 0.11185308848080133\nNot valid alignment\n19 STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYAD\n   ||.|..||.|||.||.|||.|..|||||||.|||||..||||.|..||.|||.|...||.||....|.||.|.|||||||.|||.||.|||||||||||.|||.|||||||||||.|.||||||||||||..||..|.||||||||||.||.||||||||||||||||||||||..||||||||||.|||..|.....|||.|||.|||..|.|||||||.||||||.|||..||..|||.||||||||||||||||||||.|||||||||||||||||..|.|||.||||||||||||.||||||.|||.||||||||...|.||||||||||||||||.|||||||.|||||||||||||||||||.||.||||||||||||||||.||||.|||||||..||||.||.||||||||||.||||.|||||||||||||||||||||||||..||||||||||.|||||||||||||||||||||||.||||||||||||...|||.||||..|||.||||||||||||.||.||..||..|||.|||..|...||.|||.|.|||.|||||.|||..||..|||||.||||||||\n 1 STTEDLAKKFLDDFNSEAENLSHQSSLASWEYNTNISDENVQKMDEAGAKWSDFYEKQSKLAKNFSLEEIHNDTVKLQLQILQQSGSPVLSEDKSKRLNSILNAMSTIYSTGKVCKPNNPQECLLLEPGLDNIMGTSKDYNERLWAWEGWRAEVGKQLRPLYEEYVVLKNEMARGYHYEDYGDYWRRDYETEGSPDLEYSRDQLIKDVERIFAEIKPLYEQLHAYVRTKLMDTYPFHISPTGCLPAHLLGDMWGRFWTNLYPLTVPFGQKPNIDVTDAMLNQNWDAKRIFKEAEKFFVSIGLPNMTEGFWNNSMLTDPGDGRKVVCHPTAWDLGKGDFRIKMCTKVTMEDFLTAHHEMGHIQYDMAYASQPYLLRNGANEGFHEAVGEVMSLSVATPKHLKTMGLLSSDFLEDNETEINFLFKQALNIVGTLPFTYMLEKWRWMVFKGEIPKEEWMKKWWEMKRKIVGVVEPVPHDETYCDPASLFHVANDYSFIRYYTRTIFEFQFHEALCRIAKHDGPLHKCDISNSTDAGEKLHQMLSVGKSQPWTSVLKDFVGSKNMDVGPLLRYFEPLYTWLTEQNRKSFVGWNTDWSPYAD\n  Score=2643\n\nNormalized score: 4.412353923205342\n334 NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP\n    ||||||||||||.|.|||||.||.||||||||||||||..||||||||||.||||||||.||||||||..||.||||||||||.||||||||||||.|||.|||..|.|....|||||.||..|...|.|||||||.........||. ....|||.||..|||..|.|.|||||||||||||||.||||||||\n  1 NLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCT-PPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGP\n  Score=792\n\nNormalized score: 4.103626943005182\n84 PLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLN--------------TILNTM--STIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERL--------WAWESWRSEV---------------GKQLRPLYEEYVVLKN----------EMARANHYEDYGDYWRGDYEVNGVDGY\n   |..|..|.|......|......|....|.|...|              |.||..  |..|....|...|....   ..||.....|   |||..|        .||.......               || |||....   ..|          .....|.|....||  |.|...|. ||\n 4 PFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQ---IAPGQTGVIA---DYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGK-LRPFERD---ISNVPFSPDGKPCTPPALNCYWPLNDY--GFYTTTGI-GY\n  Score=46.5\n\nNormalized score: 0.24093264248704663\nNot valid alignment\nReference summary:\n   A -&amp;gt; Q9BYF1\n   B -&amp;gt; P0DTC2\nFixed :)\n2024-05-30 13:02:19,659 [MainThread  ] [INFO ]  Removed: []\nChecking if empty file: /tmp/biobb/unitests_107/fix_pdb/output_fixpdb.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_107/fix_pdb/output_fixpdb.pdb\n        File_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_fixpdb.pdb\n        File_A hash: b&amp;#x27;g\\xebw_\\xb7\\xe0`\\x92\\xf8\\xc0\\xbd\\xc5\\xe6\\x86\\xbf\\xd6\\xc9\\x8f\\x17\\x82\\xfeV\\xd6\\xf7\\x89v\\xf6\\x11\\x80\\x96\\xfa_&amp;#x27;\n        File_B hash: b&amp;#x27;g\\xebw_\\xb7\\xe0`\\x92\\xf8\\xc0\\xbd\\xc5\\xe6\\x86\\xbf\\xd6\\xc9\\x8f\\x17\\x82\\xfeV\\xd6\\xf7\\x89v\\xf6\\x11\\x80\\x96\\xfa_&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_pdb/fix_pdb_log.out:file_utils.py:391 Executing biobb_model.model.fix_pdb Version: 4.1.0\nINFO     /tmp/biobb/unitests_107/fix_pdb/fix_pdb_log.out:file_utils.py:391 Removed: []\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_side_chain.py::TestFixSideChain::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_side_chain.py::TestFixSideChain::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_side_chain.py::TestFixSideChain::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-30 13:02:19,683 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_side_chain Version: 4.1.0\n2024-05-30 13:02:19,684 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea\n2024-05-30 13:02:19,684 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea/2ki5.pdb -o /tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea/output_pdb_path.pdb --force_save fixside --fix ALL\n\n2024-05-30 13:02:20,759 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-30 13:02:20,760 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea/2ki5.pdb loaded\n PDB id: 2KI5 \n Title: herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at 1.9a resolution\n Experimental method: x-ray diffraction\n Keywords: transferase (phosphotransferase) thymid, transferase (phosphotransferase) thymidine kinase; viridae; ds-dna enveloped viruses; herpesviridae; alphaherpesvirinae antiviral drug (aciclovir)\n Resolution (A): 1.9\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  908\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  296\n Num. ligands or modified residues:  4\n Num. water mol.:  292\n Num. atoms:  4961\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nRunning fixside. Options: --fix ALL\nFound 6 Residues with missing side chain atoms\n MET A46    CG,SD,CE\n PRO A154   CG,CD\n PRO A280   CG,CD\n MET B46    CG,SD,CE\n PRO B154   CG,CD\n ARG B220   CG,CD,NE,CZ,NH1,NH2\nFixing side chains\nMET A46\n  Adding new atom CG\n  Adding new atom SD\n  Adding new atom CE\nPRO A154\n  Adding new atom CG\n  Adding new atom CD\nPRO A280\n  Adding new atom CG\n  Adding new atom CD\nMET B46\n  Adding new atom CG\n  Adding new atom SD\n  Adding new atom CE\nPRO B154\n  Adding new atom CG\n  Adding new atom CD\nARG B220\n  Adding new atom CG\n  Adding new atom CD\n  Adding new atom NE\n  Adding new atom CZ\n  Adding new atom NH1\n  Adding new atom NH2\nFixed 6 side chain(s)\nChecking for steric clashes\n1 Steric severe clashes detected\n MET B46.CE   VAL B352.O      0.921 A\n5 Steric apolar clashes detected\n MET A46.CE   VAL A352.CG2    1.843 A\n MET A46.CE   THR A354.O      1.869 A\n MET B46.CE   VAL B352.O      0.921 A\n GLY B61.CA   ARG B220.NH1    2.301 A\n ARG B220.CZ  SO4 B3.O3       1.597 A\n3 Steric polar_acceptor clashes detected\n MET A46.SD   VAL A352.O      2.171 A\n MET A46.SD   THR A354.O      2.569 A\n MET B46.SD   VAL B352.O      2.291 A\n2 Steric polar_donor clashes detected\n GLY B61.N    ARG B220.NH1    2.443 A\n ARG B216.NH2 ARG B220.NH1    2.977 A\n1 Steric positive clashes detected\n ARG B216.NH2 ARG B220.NH1    2.977 A\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  908\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  296\nFinal Num. ligands or modified residues:  4\nFinal Num. water mol.:  292\nFinal Num. atoms:  4979\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nStructure saved on /tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea/output_pdb_path.pdb\n\n2024-05-30 13:02:20,761 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/fix_side_chain/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/fix_side_chain/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_pdb_path.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 4937\n     Atoms ALIGNED in PDB_B: 4937\n     RMS: 6.0339467652777484e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:file_utils.py:391 Executing biobb_model.model.fix_side_chain Version: 4.1.0\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea/2ki5.pdb -o /tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea/output_pdb_path.pdb --force_save fixside --fix ALL\n\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea/2ki5.pdb loaded\n PDB id: 2KI5 \n Title: herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at 1.9a resolution\n Experimental method: x-ray diffraction\n Keywords: transferase (phosphotransferase) thymid, transferase (phosphotransferase) thymidine kinase; viridae; ds-dna enveloped viruses; herpesviridae; alphaherpesvirinae antiviral drug (aciclovir)\n Resolution (A): 1.9\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  908\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  296\n Num. ligands or modified residues:  4\n Num. water mol.:  292\n Num. atoms:  4961\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nRunning fixside. Options: --fix ALL\nFound 6 Residues with missing side chain atoms\n MET A46    CG,SD,CE\n PRO A154   CG,CD\n PRO A280   CG,CD\n MET B46    CG,SD,CE\n PRO B154   CG,CD\n ARG B220   CG,CD,NE,CZ,NH1,NH2\nFixing side chains\nMET A46\n  Adding new atom CG\n  Adding new atom SD\n  Adding new atom CE\nPRO A154\n  Adding new atom CG\n  Adding new atom CD\nPRO A280\n  Adding new atom CG\n  Adding new atom CD\nMET B46\n  Adding new atom CG\n  Adding new atom SD\n  Adding new atom CE\nPRO B154\n  Adding new atom CG\n  Adding new atom CD\nARG B220\n  Adding new atom CG\n  Adding new atom CD\n  Adding new atom NE\n  Adding new atom CZ\n  Adding new atom NH1\n  Adding new atom NH2\nFixed 6 side chain(s)\nChecking for steric clashes\n1 Steric severe clashes detected\n MET B46.CE   VAL B352.O      0.921 A\n5 Steric apolar clashes detected\n MET A46.CE   VAL A352.CG2    1.843 A\n MET A46.CE   THR A354.O      1.869 A\n MET B46.CE   VAL B352.O      0.921 A\n GLY B61.CA   ARG B220.NH1    2.301 A\n ARG B220.CZ  SO4 B3.O3       1.597 A\n3 Steric polar_acceptor clashes detected\n MET A46.SD   VAL A352.O      2.171 A\n MET A46.SD   THR A354.O      2.569 A\n MET B46.SD   VAL B352.O      2.291 A\n2 Steric polar_donor clashes detected\n GLY B61.N    ARG B220.NH1    2.443 A\n ARG B216.NH2 ARG B220.NH1    2.977 A\n1 Steric positive clashes detected\n ARG B216.NH2 ARG B220.NH1    2.977 A\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  908\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  296\nFinal Num. ligands or modified residues:  4\nFinal Num. water mol.:  292\nFinal Num. atoms:  4979\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nStructure saved on /tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_side_chain/ca806262-a081-4fb0-8c80-3861ded4ddea&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_ssbonds.py::TestFixSSBonds::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_ssbonds.py::TestFixSSBonds::test_launch&#34;, &#34;duration&#34;: &#34;678 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_ssbonds.py::TestFixSSBonds::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;678 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-30 13:02:21,070 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_ssbonds Version: 4.1.0\n2024-05-30 13:02:21,213 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/1aki.pdb to /tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa\n2024-05-30 13:02:21,213 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa/1aki.pdb -o /tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa/output_pdb_path.pdb --force_save --non_interactive getss --mark All\n\n2024-05-30 13:02:21,677 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-30 13:02:21,677 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\nRunning getss. Options: --mark All\nDetected 4 Possible SS Bonds\n CYS A6.SG    CYS A127.SG     3.880\n CYS A30.SG   CYS A115.SG     4.005\n CYS A64.SG   CYS A80.SG      3.948\n CYS A76.SG   CYS A94.SG      4.073\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  207\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  78\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  78\nFinal Num. atoms:  1079\nStructure saved on /tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa/output_pdb_path.pdb\n\n2024-05-30 13:02:21,678 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/fix_ssbonds/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/fix_ssbonds/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_ssbonds.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 1079\n     Atoms ALIGNED in PDB_B: 1079\n     RMS: 1.212094551631224e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:file_utils.py:391 Executing biobb_model.model.fix_ssbonds Version: 4.1.0\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/1aki.pdb to /tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa/1aki.pdb -o /tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa/output_pdb_path.pdb --force_save --non_interactive getss --mark All\n\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\nRunning getss. Options: --mark All\nDetected 4 Possible SS Bonds\n CYS A6.SG    CYS A127.SG     3.880\n CYS A30.SG   CYS A115.SG     4.005\n CYS A64.SG   CYS A80.SG      3.948\n CYS A76.SG   CYS A94.SG      4.073\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  207\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  78\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  78\nFinal Num. atoms:  1079\nStructure saved on /tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_ssbonds/c012981f-4973-4ef0-a125-80a863a89caa&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_mutate.py::TestFixSideChain::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_mutate.py::TestFixSideChain::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_mutate.py::TestFixSideChain::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-30 13:02:21,750 [MainThread  ] [INFO ]  Executing biobb_model.model.mutate Version: 4.1.0\n2024-05-30 13:02:21,751 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20\n2024-05-30 13:02:21,751 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20/2ki5.pdb -o /tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20/output_mutated_pdb_path.pdb --force_save --non_interactive mutateside --mut Leu49Ile,B:arg51Lys\n\n2024-05-30 13:02:22,686 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-30 13:02:22,687 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20/2ki5.pdb loaded\n PDB id: 2KI5 \n Title: herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at 1.9a resolution\n Experimental method: x-ray diffraction\n Keywords: transferase (phosphotransferase) thymid, transferase (phosphotransferase) thymidine kinase; viridae; ds-dna enveloped viruses; herpesviridae; alphaherpesvirinae antiviral drug (aciclovir)\n Resolution (A): 1.9\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  908\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  296\n Num. ligands or modified residues:  4\n Num. water mol.:  292\n Num. atoms:  4961\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nRunning mutateside. Options: --mut Leu49Ile,B:arg51Lys\nMutations to perform\n*:LEU49ILE\nB:ARG51LYS\nReplacing LEU A49 into ILE\n  Deleting CD2\n  Renaming CG to CG1\n  Adding new atom CG2\nReplacing LEU B49 into ILE\n  Deleting CD2\n  Renaming CG to CG1\n  Adding new atom CG2\n\nReplacing ARG B51 into LYS\n  Deleting NE\n  Deleting CZ\n  Deleting NH1\n  Deleting NH2\n  Adding new atom CE\n  Adding new atom NZ\n\nChecking for steric clashes\nNo severe clashes detected\n4 Steric apolar clashes detected\n ILE A49.CG2  THR A350.OG1    2.815 A\n ILE B49.CG2  THR B350.OG1    2.611 A\n LYS B51.NZ   LEU B139.CG     2.403 A\n LYS B51.NZ   ILE B143.CD1    2.319 A\nNo polar_acceptor clashes detected\nNo polar_donor clashes detected\nNo positive clashes detected\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  908\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  296\nFinal Num. ligands or modified residues:  4\nFinal Num. water mol.:  292\nFinal Num. atoms:  4959\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nStructure saved on /tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20/output_mutated_pdb_path.pdb\n\n2024-05-30 13:02:22,688 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/mutate/output_mutated_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/mutate/output_mutated_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_mutated_pdb_path.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 4917\n     Atoms ALIGNED in PDB_B: 4917\n     RMS: 1.983345332028294e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:file_utils.py:391 Executing biobb_model.model.mutate Version: 4.1.0\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20/2ki5.pdb -o /tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20/output_mutated_pdb_path.pdb --force_save --non_interactive mutateside --mut Leu49Ile,B:arg51Lys\n\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20/2ki5.pdb loaded\n PDB id: 2KI5 \n Title: herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at 1.9a resolution\n Experimental method: x-ray diffraction\n Keywords: transferase (phosphotransferase) thymid, transferase (phosphotransferase) thymidine kinase; viridae; ds-dna enveloped viruses; herpesviridae; alphaherpesvirinae antiviral drug (aciclovir)\n Resolution (A): 1.9\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  908\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  296\n Num. ligands or modified residues:  4\n Num. water mol.:  292\n Num. atoms:  4961\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nRunning mutateside. Options: --mut Leu49Ile,B:arg51Lys\nMutations to perform\n*:LEU49ILE\nB:ARG51LYS\nReplacing LEU A49 into ILE\n  Deleting CD2\n  Renaming CG to CG1\n  Adding new atom CG2\nReplacing LEU B49 into ILE\n  Deleting CD2\n  Renaming CG to CG1\n  Adding new atom CG2\n\nReplacing ARG B51 into LYS\n  Deleting NE\n  Deleting CZ\n  Deleting NH1\n  Deleting NH2\n  Adding new atom CE\n  Adding new atom NZ\n\nChecking for steric clashes\nNo severe clashes detected\n4 Steric apolar clashes detected\n ILE A49.CG2  THR A350.OG1    2.815 A\n ILE B49.CG2  THR B350.OG1    2.611 A\n LYS B51.NZ   LEU B139.CG     2.403 A\n LYS B51.NZ   ILE B143.CD1    2.319 A\nNo polar_acceptor clashes detected\nNo polar_donor clashes detected\nNo positive clashes detected\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  908\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  296\nFinal Num. ligands or modified residues:  4\nFinal Num. water mol.:  292\nFinal Num. atoms:  4959\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nStructure saved on /tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20/output_mutated_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/mutate/5efb25a5-f94d-4c3b-8096-caa1b339cb20&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.10.14&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.2.1&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_model/test/unitests/test_model/test_checking_log.py::TestCheckingLog::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_checking_log.py::TestCheckingLog::test_launch&#34;, &#34;duration&#34;: &#34;00:00:18&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_checking_log.py::TestCheckingLog::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:18&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-31 13:33:04,503 [MainThread  ] [INFO ]  Executing biobb_model.model.checking_log Version: 4.2.0\n2024-05-31 13:33:04,504 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/checking_log/df53e321-bca8-437d-b785-79576ed953bc\n2024-05-31 13:33:04,504 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/checking_log/df53e321-bca8-437d-b785-79576ed953bc/2ki5.pdb checkall &amp;gt; /tmp/biobb/unitests_107/checking_log/df53e321-bca8-437d-b785-79576ed953bc/output_log_path.log\n\n2024-05-31 13:33:22,771 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-31 13:33:22,772 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/checking_log/df53e321-bca8-437d-b785-79576ed953bc&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/checking_log/output_log_path.log\nComparing ignoring lines containing this words: [&amp;#x27;loaded&amp;#x27;]\n     FILE_A: /tmp/biobb/unitests_107/checking_log/output_log_path.log\n     FILE_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/checking.log\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/checking_log/checking_log_log.out:file_utils.py:391 Executing biobb_model.model.checking_log Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/checking_log/checking_log_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/checking_log/df53e321-bca8-437d-b785-79576ed953bc\nINFO     /tmp/biobb/unitests_107/checking_log/checking_log_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/checking_log/df53e321-bca8-437d-b785-79576ed953bc/2ki5.pdb checkall &amp;gt; /tmp/biobb/unitests_107/checking_log/df53e321-bca8-437d-b785-79576ed953bc/output_log_path.log\n\nINFO     /tmp/biobb/unitests_107/checking_log/checking_log_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/checking_log/checking_log_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/checking_log/df53e321-bca8-437d-b785-79576ed953bc&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_altlocs.py::TestFixAltlocs::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_altlocs.py::TestFixAltlocs::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_altlocs.py::TestFixAltlocs::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-31 13:33:22,809 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_altlocs Version: 4.2.0\n2024-05-31 13:33:22,810 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/3ebp.pdb to /tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf\n2024-05-31 13:33:22,810 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf/3ebp.pdb -o /tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf/output_pdb_path.pdb --force_save --non_interactive altloc --select A339:A,A171:B,A768:A\n\n2024-05-31 13:33:23,620 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-31 13:33:23,620 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf/3ebp.pdb loaded\n PDB id: 3EBP \n Title: glycogen phosphorylase b/flavopiridol complex\n Experimental method: x-ray diffraction\n Keywords: glycogen phosphorylase, rational inhibitor design, glycogenolysis, diabetes type 2, allosteric enzyme, carbohydrate metabolism, glycogen metabolism, glycosyltransferase, nucleotide-binding, phosphoprotein, pyridoxal phosphate, transferase-transferase inhibitor complex\n Resolution (A): 2.0\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  1097\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  288\n Num. ligands or modified residues:  2\n Num. water mol.:  286\n Num. atoms:  6918\nModified residues found\nLLP A680\nSmall mol ligands found\nCPB A940\nRunning altloc. Options: --select A339:A,A171:B,A768:A\nDetected 3 residues with alternative location labels\nCYS A171\n  CB   A (0.50) B (0.50)\n  SG   A (0.50) B (0.50)\nASP A339\n  CG   A (0.50) B (0.50)\n  OD1  A (0.50) B (0.50)\n  OD2  A (0.50) B (0.50)\nHIS A768\n  CG   A (0.50) B (0.50)\n  ND1  A (0.50) B (0.50)\n  CD2  A (0.50) B (0.50)\n  CE1  A (0.50) B (0.50)\n  NE2  A (0.50) B (0.50)\nSelecting location A339:A,A171:B,A768:A\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  1097\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  288\nFinal Num. ligands or modified residues:  2\nFinal Num. water mol.:  286\nFinal Num. atoms:  6918\nModified residues found\nLLP A680\nSmall mol ligands found\nCPB A940\nStructure saved on /tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf/output_pdb_path.pdb\n\n2024-05-31 13:33:23,621 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/fix_altlocs/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/fix_altlocs/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_altloc.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 6866\n     Atoms ALIGNED in PDB_B: 6866\n     RMS: 1.0683071939348411e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:file_utils.py:391 Executing biobb_model.model.fix_altlocs Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/3ebp.pdb to /tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf/3ebp.pdb -o /tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf/output_pdb_path.pdb --force_save --non_interactive altloc --select A339:A,A171:B,A768:A\n\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf/3ebp.pdb loaded\n PDB id: 3EBP \n Title: glycogen phosphorylase b/flavopiridol complex\n Experimental method: x-ray diffraction\n Keywords: glycogen phosphorylase, rational inhibitor design, glycogenolysis, diabetes type 2, allosteric enzyme, carbohydrate metabolism, glycogen metabolism, glycosyltransferase, nucleotide-binding, phosphoprotein, pyridoxal phosphate, transferase-transferase inhibitor complex\n Resolution (A): 2.0\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  1097\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  288\n Num. ligands or modified residues:  2\n Num. water mol.:  286\n Num. atoms:  6918\nModified residues found\nLLP A680\nSmall mol ligands found\nCPB A940\nRunning altloc. Options: --select A339:A,A171:B,A768:A\nDetected 3 residues with alternative location labels\nCYS A171\n  CB   A (0.50) B (0.50)\n  SG   A (0.50) B (0.50)\nASP A339\n  CG   A (0.50) B (0.50)\n  OD1  A (0.50) B (0.50)\n  OD2  A (0.50) B (0.50)\nHIS A768\n  CG   A (0.50) B (0.50)\n  ND1  A (0.50) B (0.50)\n  CD2  A (0.50) B (0.50)\n  CE1  A (0.50) B (0.50)\n  NE2  A (0.50) B (0.50)\nSelecting location A339:A,A171:B,A768:A\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  1097\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  288\nFinal Num. ligands or modified residues:  2\nFinal Num. water mol.:  286\nFinal Num. atoms:  6918\nModified residues found\nLLP A680\nSmall mol ligands found\nCPB A940\nStructure saved on /tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/fix_altlocs/fix_altlocs_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_altlocs/c1154c16-2a38-4427-bdb9-255c4b48efcf&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_amides.py::TestFixAmides::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_amides.py::TestFixAmides::test_launch&#34;, &#34;duration&#34;: &#34;00:00:02&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_amides.py::TestFixAmides::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:02&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-31 13:33:23,961 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_amides Version: 4.2.0\n2024-05-31 13:33:23,962 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/5s2z.pdb to /tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e\n2024-05-31 13:33:23,962 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e/5s2z.pdb -o /tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e/output_pdb_path.pdb --force_save amide --fix All\n\n2024-05-31 13:33:25,740 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-31 13:33:25,740 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e/5s2z.pdb loaded\n PDB id: 5S2Z \n Title: pandda analysis group deposition -- crystal structure of sars-cov-2 nsp3 macrodomain in complex with z126932614\n Experimental method: x-ray diffraction\n Keywords: sgc - diamond i04-1 fragment screening, pandda, xchemexplorer, sars- cov-2 nsp3 macrodomain, viral protein\n Resolution (A): 1.07\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  792\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  458\n Num. ligands or modified residues:  1\n Num. water mol.:  457\n Num. atoms:  2998\nModified residues found\nT6J A401\nRunning amide. Options: --fix All\nFound 2 unusual contact(s) involving amide atoms\n ASN B20.OD1  VAL B155.O      3.015 A\n ASN B20.OD1  PHE B156.O      2.894 A\nAmide residues fixed All (1)\nRechecking\nFound no unusual contact(s) involving amide atoms\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  792\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  458\nFinal Num. ligands or modified residues:  1\nFinal Num. water mol.:  457\nFinal Num. atoms:  2998\nModified residues found\nT6J A401\nStructure saved on /tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e/output_pdb_path.pdb\n\n2024-05-31 13:33:25,741 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/fix_amides/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/fix_amides/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_amide_pdb_path.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2984\n     Atoms ALIGNED in PDB_B: 2984\n     RMS: 7.386865969918367e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:file_utils.py:391 Executing biobb_model.model.fix_amides Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/5s2z.pdb to /tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e/5s2z.pdb -o /tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e/output_pdb_path.pdb --force_save amide --fix All\n\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e/5s2z.pdb loaded\n PDB id: 5S2Z \n Title: pandda analysis group deposition -- crystal structure of sars-cov-2 nsp3 macrodomain in complex with z126932614\n Experimental method: x-ray diffraction\n Keywords: sgc - diamond i04-1 fragment screening, pandda, xchemexplorer, sars- cov-2 nsp3 macrodomain, viral protein\n Resolution (A): 1.07\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  792\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  458\n Num. ligands or modified residues:  1\n Num. water mol.:  457\n Num. atoms:  2998\nModified residues found\nT6J A401\nRunning amide. Options: --fix All\nFound 2 unusual contact(s) involving amide atoms\n ASN B20.OD1  VAL B155.O      3.015 A\n ASN B20.OD1  PHE B156.O      2.894 A\nAmide residues fixed All (1)\nRechecking\nFound no unusual contact(s) involving amide atoms\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  792\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  458\nFinal Num. ligands or modified residues:  1\nFinal Num. water mol.:  457\nFinal Num. atoms:  2998\nModified residues found\nT6J A401\nStructure saved on /tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/fix_amides/fix_amides_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_amides/e62fb9a1-d0af-4b82-98ae-66adec9a910e&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_chirality.py::TestFixChirality::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_chirality.py::TestFixChirality::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_chirality.py::TestFixChirality::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-31 13:33:25,938 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_chirality Version: 4.2.0\n2024-05-31 13:33:25,938 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/3e2y.pdb to /tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1\n2024-05-31 13:33:25,939 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1/3e2y.pdb -o /tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1/output_pdb_path.pdb --force_save chiral --fix All\n\n2024-05-31 13:33:27,005 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-31 13:33:27,005 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1/3e2y.pdb loaded\n PDB id: 3E2Y \n Title: crystal structure of mouse kynurenine aminotransferase iii in complex with glutamine\n Experimental method: x-ray diffraction\n Keywords: alpha beta protein, plp dependent protein, aminotransferase, lyase, pyridoxal phosphate, transferase\n Resolution (A): 2.26\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  1239\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  419\n Num. ligands or modified residues:  8\n Num. water mol.:  411\n Num. atoms:  6993\nModified residues found\nGLN A456\nGLN B457\nSmall mol ligands found\nPMP A457\nGOL A458\nGOL A459\nPMP B456\nGOL B458\nGOL B459\nRunning chiral. Options: --fix All\nFound 2 residues with incorrect side-chain chirality\n THR A256  \n THR B286  \nChiral side chains fixed All (2)\nChecking for steric clashes\nNo severe clashes detected\n1 Steric apolar clashes detected\n THR A256.CG2 GLU A348.OE2    2.678 A\nNo polar_acceptor clashes detected\n1 Steric polar_donor clashes detected\n GLN A97.NE2  THR B286.N      3.001 A\nNo positive clashes detected\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  1239\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  419\nFinal Num. ligands or modified residues:  8\nFinal Num. water mol.:  411\nFinal Num. atoms:  6993\nModified residues found\nGLN A456\nGLN B457\nSmall mol ligands found\nPMP A457\nGOL A458\nGOL A459\nPMP B456\nGOL B458\nGOL B459\nStructure saved on /tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1/output_pdb_path.pdb\n\n2024-05-31 13:33:27,006 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/fix_chirality/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/fix_chirality/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_chirality_pdb_path.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 6917\n     Atoms ALIGNED in PDB_B: 6917\n     RMS: 6.2661067786844326e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:file_utils.py:391 Executing biobb_model.model.fix_chirality Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/3e2y.pdb to /tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1/3e2y.pdb -o /tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1/output_pdb_path.pdb --force_save chiral --fix All\n\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1/3e2y.pdb loaded\n PDB id: 3E2Y \n Title: crystal structure of mouse kynurenine aminotransferase iii in complex with glutamine\n Experimental method: x-ray diffraction\n Keywords: alpha beta protein, plp dependent protein, aminotransferase, lyase, pyridoxal phosphate, transferase\n Resolution (A): 2.26\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  1239\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  419\n Num. ligands or modified residues:  8\n Num. water mol.:  411\n Num. atoms:  6993\nModified residues found\nGLN A456\nGLN B457\nSmall mol ligands found\nPMP A457\nGOL A458\nGOL A459\nPMP B456\nGOL B458\nGOL B459\nRunning chiral. Options: --fix All\nFound 2 residues with incorrect side-chain chirality\n THR A256  \n THR B286  \nChiral side chains fixed All (2)\nChecking for steric clashes\nNo severe clashes detected\n1 Steric apolar clashes detected\n THR A256.CG2 GLU A348.OE2    2.678 A\nNo polar_acceptor clashes detected\n1 Steric polar_donor clashes detected\n GLN A97.NE2  THR B286.N      3.001 A\nNo positive clashes detected\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  1239\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  419\nFinal Num. ligands or modified residues:  8\nFinal Num. water mol.:  411\nFinal Num. atoms:  6993\nModified residues found\nGLN A456\nGLN B457\nSmall mol ligands found\nPMP A457\nGOL A458\nGOL A459\nPMP B456\nGOL B458\nGOL B459\nStructure saved on /tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/fix_chirality/fix_chirality_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_chirality/eee7822d-e848-4da6-b484-e9ff9767bbc1&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_pdb.py::TestFixPdb::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_pdb.py::TestFixPdb::test_launch&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_pdb.py::TestFixPdb::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-31 13:33:27,357 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_pdb Version: 4.2.0\n126 VVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFK-----IYSKH------TPINLVRDLPQGF-SALEPLVDLPIG----INIT------------------RFQTLLAL--------HRSYLT-PGDS------SSGWTAG------------------AAAYYVGYLQ------PRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRF-----PNITNLCPFGEVFNATRFASVYA------------WNRKR--------------------ISNCVADYSVL-YNSASFSTFKCYGV--------SPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNY---LYRLFRKSNLKPF\n    ||.|       |....|..|......|.    |.|........||.......|.|......|.|    ......|..     .|..|      .|..|..|....| ..|.||. .|.|    |..|                  .|.....|        ..|.|| |||.      ...|..|                  .|....|..|      ....||....|.....||.........|...||..    |.. .|.| ....|....|     .||....||.......|. .|..            |..||                    ......|||.. |.......|.....        .|....|.       ......|....|..  ..||.......| .||.|      |.|.|  ||....|   ||......|.|.|\n166 VVLK-------NEMARGYHYEDYGDYWR----RDYETEGSPDLEYSRDQLIKDVERIFAEIKPL----YEQLHAYVRTKLMDTYPFHISPTGCLPAHLLGDMWGRFWTNLYPLT-VPFGQKPNIDVTDAMLNQNWDAKRIFKEAEKFFVSIGLPNMTEGFWNNSMLTDPGDGRKVVCHPTAWDLGKGDFRIKMCTKVTMEDFLTAHHEMGHIQYDMAYASQPYLLRNGANEGFHEAVGEVMSLSVATPKHLKTM----GLL-SSDF-LEDNETEINFLFKQALNIVGTLPFTYMLEKWRW-MVFKGEIPKEEWMKKWWEMKRKIVGVVEPVPHDETYCDPASLFHVANDYSFIRYYTRTIFEFQFHEALCRIAKHDGPLHKCDI-------SNSTDAGEKLHQML--SVGKSQPWTSVL-KDFVG------SKNMD--VGPLLRYFEPLYTWLTEQNRKSF\n  Score=67\n\nNormalized score: 0.11185308848080133\nNot valid alignment\n19 STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYAD\n   ||.|..||.|||.||.|||.|..|||||||.|||||..||||.|..||.|||.|...||.||....|.||.|.|||||||.|||.||.|||||||||||.|||.|||||||||||.|.||||||||||||..||..|.||||||||||.||.||||||||||||||||||||||..||||||||||.|||..|.....|||.|||.|||..|.|||||||.||||||.|||..||..|||.||||||||||||||||||||.|||||||||||||||||..|.|||.||||||||||||.||||||.|||.||||||||...|.||||||||||||||||.|||||||.|||||||||||||||||||.||.||||||||||||||||.||||.|||||||..||||.||.||||||||||.||||.|||||||||||||||||||||||||..||||||||||.|||||||||||||||||||||||.||||||||||||...|||.||||..|||.||||||||||||.||.||..||..|||.|||..|...||.|||.|.|||.|||||.|||..||..|||||.||||||||\n 1 STTEDLAKKFLDDFNSEAENLSHQSSLASWEYNTNISDENVQKMDEAGAKWSDFYEKQSKLAKNFSLEEIHNDTVKLQLQILQQSGSPVLSEDKSKRLNSILNAMSTIYSTGKVCKPNNPQECLLLEPGLDNIMGTSKDYNERLWAWEGWRAEVGKQLRPLYEEYVVLKNEMARGYHYEDYGDYWRRDYETEGSPDLEYSRDQLIKDVERIFAEIKPLYEQLHAYVRTKLMDTYPFHISPTGCLPAHLLGDMWGRFWTNLYPLTVPFGQKPNIDVTDAMLNQNWDAKRIFKEAEKFFVSIGLPNMTEGFWNNSMLTDPGDGRKVVCHPTAWDLGKGDFRIKMCTKVTMEDFLTAHHEMGHIQYDMAYASQPYLLRNGANEGFHEAVGEVMSLSVATPKHLKTMGLLSSDFLEDNETEINFLFKQALNIVGTLPFTYMLEKWRWMVFKGEIPKEEWMKKWWEMKRKIVGVVEPVPHDETYCDPASLFHVANDYSFIRYYTRTIFEFQFHEALCRIAKHDGPLHKCDISNSTDAGEKLHQMLSVGKSQPWTSVLKDFVGSKNMDVGPLLRYFEPLYTWLTEQNRKSFVGWNTDWSPYAD\n  Score=2643\n\nNormalized score: 4.412353923205342\n334 NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP\n    ||||||||||||.|.|||||.||.||||||||||||||..||||||||||.||||||||.||||||||..||.||||||||||.||||||||||||.|||.|||..|.|....|||||.||..|...|.|||||||.........||. ....|||.||..|||..|.|.|||||||||||||||.||||||||\n  1 NLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCT-PPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGP\n  Score=792\n\nNormalized score: 4.103626943005182\n84 PLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLN--------------TILNTM--STIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERL--------WAWESWRSEV---------------GKQLRPLYEEYVVLKN----------EMARANHYEDYGDYWRGDYEVNGVDGY\n   |..|..|.|......|......|....|.|...|              |.||..  |..|....|...|....   ..||.....|   |||..|        .||.......               || |||....   ..|          .....|.|....||  |.|...|. ||\n 4 PFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQ---IAPGQTGVIA---DYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGK-LRPFERD---ISNVPFSPDGKPCTPPALNCYWPLNDY--GFYTTTGI-GY\n  Score=46.5\n\nNormalized score: 0.24093264248704663\nNot valid alignment\nReference summary:\n   A -&amp;gt; Q9BYF1\n   B -&amp;gt; P0DTC2\nFixed :)\n2024-05-31 13:33:32,226 [MainThread  ] [INFO ]  Removed: []\nChecking if empty file: /tmp/biobb/unitests_107/fix_pdb/output_fixpdb.pdb\nComparing: \n        File_A: /tmp/biobb/unitests_107/fix_pdb/output_fixpdb.pdb\n        File_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_fixpdb.pdb\n        File_A hash: b&amp;#x27;g\\xebw_\\xb7\\xe0`\\x92\\xf8\\xc0\\xbd\\xc5\\xe6\\x86\\xbf\\xd6\\xc9\\x8f\\x17\\x82\\xfeV\\xd6\\xf7\\x89v\\xf6\\x11\\x80\\x96\\xfa_&amp;#x27;\n        File_B hash: b&amp;#x27;g\\xebw_\\xb7\\xe0`\\x92\\xf8\\xc0\\xbd\\xc5\\xe6\\x86\\xbf\\xd6\\xc9\\x8f\\x17\\x82\\xfeV\\xd6\\xf7\\x89v\\xf6\\x11\\x80\\x96\\xfa_&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_pdb/fix_pdb_log.out:file_utils.py:391 Executing biobb_model.model.fix_pdb Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/fix_pdb/fix_pdb_log.out:file_utils.py:391 Removed: []\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_side_chain.py::TestFixSideChain::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_side_chain.py::TestFixSideChain::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_side_chain.py::TestFixSideChain::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-31 13:33:32,253 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_side_chain Version: 4.2.0\n2024-05-31 13:33:32,253 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1\n2024-05-31 13:33:32,254 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1/2ki5.pdb -o /tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1/output_pdb_path.pdb --force_save fixside --fix ALL\n\n2024-05-31 13:33:33,368 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-31 13:33:33,369 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1/2ki5.pdb loaded\n PDB id: 2KI5 \n Title: herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at 1.9a resolution\n Experimental method: x-ray diffraction\n Keywords: transferase (phosphotransferase) thymid, transferase (phosphotransferase) thymidine kinase; viridae; ds-dna enveloped viruses; herpesviridae; alphaherpesvirinae antiviral drug (aciclovir)\n Resolution (A): 1.9\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  908\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  296\n Num. ligands or modified residues:  4\n Num. water mol.:  292\n Num. atoms:  4961\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nRunning fixside. Options: --fix ALL\nFound 6 Residues with missing side chain atoms\n MET A46    CG,SD,CE\n PRO A154   CG,CD\n PRO A280   CG,CD\n MET B46    CG,SD,CE\n PRO B154   CG,CD\n ARG B220   CG,CD,NE,CZ,NH1,NH2\nFixing side chains\nMET A46\n  Adding new atom CG\n  Adding new atom SD\n  Adding new atom CE\nPRO A154\n  Adding new atom CG\n  Adding new atom CD\nPRO A280\n  Adding new atom CG\n  Adding new atom CD\nMET B46\n  Adding new atom CG\n  Adding new atom SD\n  Adding new atom CE\nPRO B154\n  Adding new atom CG\n  Adding new atom CD\nARG B220\n  Adding new atom CG\n  Adding new atom CD\n  Adding new atom NE\n  Adding new atom CZ\n  Adding new atom NH1\n  Adding new atom NH2\nFixed 6 side chain(s)\nChecking for steric clashes\n1 Steric severe clashes detected\n MET B46.CE   VAL B352.O      0.921 A\n5 Steric apolar clashes detected\n MET A46.CE   VAL A352.CG2    1.843 A\n MET A46.CE   THR A354.O      1.869 A\n MET B46.CE   VAL B352.O      0.921 A\n GLY B61.CA   ARG B220.NH1    2.301 A\n ARG B220.CZ  SO4 B3.O3       1.597 A\n3 Steric polar_acceptor clashes detected\n MET A46.SD   VAL A352.O      2.171 A\n MET A46.SD   THR A354.O      2.569 A\n MET B46.SD   VAL B352.O      2.291 A\n2 Steric polar_donor clashes detected\n GLY B61.N    ARG B220.NH1    2.443 A\n ARG B216.NH2 ARG B220.NH1    2.977 A\n1 Steric positive clashes detected\n ARG B216.NH2 ARG B220.NH1    2.977 A\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  908\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  296\nFinal Num. ligands or modified residues:  4\nFinal Num. water mol.:  292\nFinal Num. atoms:  4979\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nStructure saved on /tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1/output_pdb_path.pdb\n\n2024-05-31 13:33:33,370 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/fix_side_chain/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/fix_side_chain/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_pdb_path.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 4937\n     Atoms ALIGNED in PDB_B: 4937\n     RMS: 6.0339467652777484e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:file_utils.py:391 Executing biobb_model.model.fix_side_chain Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1/2ki5.pdb -o /tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1/output_pdb_path.pdb --force_save fixside --fix ALL\n\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1/2ki5.pdb loaded\n PDB id: 2KI5 \n Title: herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at 1.9a resolution\n Experimental method: x-ray diffraction\n Keywords: transferase (phosphotransferase) thymid, transferase (phosphotransferase) thymidine kinase; viridae; ds-dna enveloped viruses; herpesviridae; alphaherpesvirinae antiviral drug (aciclovir)\n Resolution (A): 1.9\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  908\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  296\n Num. ligands or modified residues:  4\n Num. water mol.:  292\n Num. atoms:  4961\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nRunning fixside. Options: --fix ALL\nFound 6 Residues with missing side chain atoms\n MET A46    CG,SD,CE\n PRO A154   CG,CD\n PRO A280   CG,CD\n MET B46    CG,SD,CE\n PRO B154   CG,CD\n ARG B220   CG,CD,NE,CZ,NH1,NH2\nFixing side chains\nMET A46\n  Adding new atom CG\n  Adding new atom SD\n  Adding new atom CE\nPRO A154\n  Adding new atom CG\n  Adding new atom CD\nPRO A280\n  Adding new atom CG\n  Adding new atom CD\nMET B46\n  Adding new atom CG\n  Adding new atom SD\n  Adding new atom CE\nPRO B154\n  Adding new atom CG\n  Adding new atom CD\nARG B220\n  Adding new atom CG\n  Adding new atom CD\n  Adding new atom NE\n  Adding new atom CZ\n  Adding new atom NH1\n  Adding new atom NH2\nFixed 6 side chain(s)\nChecking for steric clashes\n1 Steric severe clashes detected\n MET B46.CE   VAL B352.O      0.921 A\n5 Steric apolar clashes detected\n MET A46.CE   VAL A352.CG2    1.843 A\n MET A46.CE   THR A354.O      1.869 A\n MET B46.CE   VAL B352.O      0.921 A\n GLY B61.CA   ARG B220.NH1    2.301 A\n ARG B220.CZ  SO4 B3.O3       1.597 A\n3 Steric polar_acceptor clashes detected\n MET A46.SD   VAL A352.O      2.171 A\n MET A46.SD   THR A354.O      2.569 A\n MET B46.SD   VAL B352.O      2.291 A\n2 Steric polar_donor clashes detected\n GLY B61.N    ARG B220.NH1    2.443 A\n ARG B216.NH2 ARG B220.NH1    2.977 A\n1 Steric positive clashes detected\n ARG B216.NH2 ARG B220.NH1    2.977 A\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  908\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  296\nFinal Num. ligands or modified residues:  4\nFinal Num. water mol.:  292\nFinal Num. atoms:  4979\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nStructure saved on /tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/fix_side_chain/fix_side_chain_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_side_chain/51321dbb-d8bd-41da-bca5-9cdc30c94fb1&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_fix_ssbonds.py::TestFixSSBonds::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_fix_ssbonds.py::TestFixSSBonds::test_launch&#34;, &#34;duration&#34;: &#34;534 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_fix_ssbonds.py::TestFixSSBonds::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;534 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-31 13:33:33,663 [MainThread  ] [INFO ]  Executing biobb_model.model.fix_ssbonds Version: 4.2.0\n2024-05-31 13:33:33,664 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/1aki.pdb to /tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d\n2024-05-31 13:33:33,664 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d/1aki.pdb -o /tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d/output_pdb_path.pdb --force_save --non_interactive getss --mark All\n\n2024-05-31 13:33:34,132 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-31 13:33:34,132 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\nRunning getss. Options: --mark All\nDetected 4 Possible SS Bonds\n CYS A6.SG    CYS A127.SG     3.880\n CYS A30.SG   CYS A115.SG     4.005\n CYS A64.SG   CYS A80.SG      3.948\n CYS A76.SG   CYS A94.SG      4.073\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  207\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  78\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  78\nFinal Num. atoms:  1079\nStructure saved on /tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d/output_pdb_path.pdb\n\n2024-05-31 13:33:34,133 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/fix_ssbonds/output_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/fix_ssbonds/output_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_ssbonds.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 1079\n     Atoms ALIGNED in PDB_B: 1079\n     RMS: 1.212094551631224e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:file_utils.py:391 Executing biobb_model.model.fix_ssbonds Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/1aki.pdb to /tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d/1aki.pdb -o /tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d/output_pdb_path.pdb --force_save --non_interactive getss --mark All\n\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\nRunning getss. Options: --mark All\nDetected 4 Possible SS Bonds\n CYS A6.SG    CYS A127.SG     3.880\n CYS A30.SG   CYS A115.SG     4.005\n CYS A64.SG   CYS A80.SG      3.948\n CYS A76.SG   CYS A94.SG      4.073\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  207\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  78\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  78\nFinal Num. atoms:  1079\nStructure saved on /tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d/output_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/fix_ssbonds/fix_ssbonds_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/fix_ssbonds/fe89c6be-1ada-4b29-bae7-aca8864c417d&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}], &#34;biobb_model/test/unitests/test_model/test_mutate.py::TestFixSideChain::test_launch&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_model/test/unitests/test_model/test_mutate.py::TestFixSideChain::test_launch&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_model/test/unitests/test_model/test_mutate.py::TestFixSideChain::test_launch&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-31 13:33:34,198 [MainThread  ] [INFO ]  Executing biobb_model.model.mutate Version: 4.2.0\n2024-05-31 13:33:34,199 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc\n2024-05-31 13:33:34,199 [MainThread  ] [INFO ]  check_structure -i /tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc/2ki5.pdb -o /tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc/output_mutated_pdb_path.pdb --force_save --non_interactive mutateside --mut Leu49Ile,B:arg51Lys\n\n2024-05-31 13:33:35,168 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-31 13:33:35,168 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc/2ki5.pdb loaded\n PDB id: 2KI5 \n Title: herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at 1.9a resolution\n Experimental method: x-ray diffraction\n Keywords: transferase (phosphotransferase) thymid, transferase (phosphotransferase) thymidine kinase; viridae; ds-dna enveloped viruses; herpesviridae; alphaherpesvirinae antiviral drug (aciclovir)\n Resolution (A): 1.9\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  908\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  296\n Num. ligands or modified residues:  4\n Num. water mol.:  292\n Num. atoms:  4961\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nRunning mutateside. Options: --mut Leu49Ile,B:arg51Lys\nMutations to perform\n*:LEU49ILE\nB:ARG51LYS\nReplacing LEU A49 into ILE\n  Deleting CD2\n  Renaming CG to CG1\n  Adding new atom CG2\nReplacing LEU B49 into ILE\n  Deleting CD2\n  Renaming CG to CG1\n  Adding new atom CG2\n\nReplacing ARG B51 into LYS\n  Deleting NE\n  Deleting CZ\n  Deleting NH1\n  Deleting NH2\n  Adding new atom CE\n  Adding new atom NZ\n\nChecking for steric clashes\nNo severe clashes detected\n4 Steric apolar clashes detected\n ILE A49.CG2  THR A350.OG1    2.815 A\n ILE B49.CG2  THR B350.OG1    2.611 A\n LYS B51.NZ   LEU B139.CG     2.403 A\n LYS B51.NZ   ILE B143.CD1    2.319 A\nNo polar_acceptor clashes detected\nNo polar_donor clashes detected\nNo positive clashes detected\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  908\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  296\nFinal Num. ligands or modified residues:  4\nFinal Num. water mol.:  292\nFinal Num. atoms:  4959\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nStructure saved on /tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc/output_mutated_pdb_path.pdb\n\n2024-05-31 13:33:35,169 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_107/mutate/output_mutated_pdb_path.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_107/mutate/output_mutated_pdb_path.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/reference/model/output_mutated_pdb_path.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 4917\n     Atoms ALIGNED in PDB_B: 4917\n     RMS: 1.983345332028294e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:file_utils.py:391 Executing biobb_model.model.mutate Version: 4.2.0\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_model/biobb_model/biobb_model/test/data/model/2ki5.pdb to /tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:cmd_wrapper.py:33 check_structure -i /tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc/2ki5.pdb -o /tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc/output_mutated_pdb_path.pdb --force_save --non_interactive mutateside --mut Leu49Ile,B:arg51Lys\n\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:cmd_wrapper.py:52 ================================================================================\n=                   BioBB structure checking utility v3.13.4                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc/2ki5.pdb loaded\n PDB id: 2KI5 \n Title: herpes simplex type-1 thymidine kinase in complex with the drug aciclovir at 1.9a resolution\n Experimental method: x-ray diffraction\n Keywords: transferase (phosphotransferase) thymid, transferase (phosphotransferase) thymidine kinase; viridae; ds-dna enveloped viruses; herpesviridae; alphaherpesvirinae antiviral drug (aciclovir)\n Resolution (A): 1.9\n\n Num. models: 1\n Num. chains: 2 (A: Protein, B: Protein)\n Num. residues:  908\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  296\n Num. ligands or modified residues:  4\n Num. water mol.:  292\n Num. atoms:  4961\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nRunning mutateside. Options: --mut Leu49Ile,B:arg51Lys\nMutations to perform\n*:LEU49ILE\nB:ARG51LYS\nReplacing LEU A49 into ILE\n  Deleting CD2\n  Renaming CG to CG1\n  Adding new atom CG2\nReplacing LEU B49 into ILE\n  Deleting CD2\n  Renaming CG to CG1\n  Adding new atom CG2\n\nReplacing ARG B51 into LYS\n  Deleting NE\n  Deleting CZ\n  Deleting NH1\n  Deleting NH2\n  Adding new atom CE\n  Adding new atom NZ\n\nChecking for steric clashes\nNo severe clashes detected\n4 Steric apolar clashes detected\n ILE A49.CG2  THR A350.OG1    2.815 A\n ILE B49.CG2  THR B350.OG1    2.611 A\n LYS B51.NZ   LEU B139.CG     2.403 A\n LYS B51.NZ   ILE B143.CD1    2.319 A\nNo polar_acceptor clashes detected\nNo polar_donor clashes detected\nNo positive clashes detected\nNo negative clashes detected\nFinal Num. models: 1\nFinal Num. chains: 2 (A: Protein, B: Protein)\nFinal Num. residues:  908\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 0\nFinal Num. HETATM residues:  296\nFinal Num. ligands or modified residues:  4\nFinal Num. water mol.:  292\nFinal Num. atoms:  4959\nSmall mol ligands found\nSO4 A4\nAC2 A1\nSO4 B3\nAC2 B2\nStructure saved on /tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc/output_mutated_pdb_path.pdb\n\nINFO     /tmp/biobb/unitests_107/mutate/mutate_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_107/mutate/638f194f-d3d3-43bd-871d-65ef5b3ad8cc&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_107\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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