From 72bb6cf33fe8f7e3c5771a34ec154ade4abe4421 Mon Sep 17 00:00:00 2001
From: gbayarri <genis.bayarri@irbbarcelona.org>
Date: Fri, 24 May 2024 09:47:31 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bioexcel?=
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MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
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 coverage/coverage.xml                                   | 2 +-
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 coverage/index.html                                     | 4 ++--
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 coverage/z_68fa7e1546d8c55d_test_imod_imove_py.html     | 4 ++--
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 junit/junit.xml                                         | 2 +-
 junit/report.html                                       | 6 +++---
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             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:12 +0000
+            created at 2024-05-24 09:47 +0000
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
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+            created at 2024-05-24 09:47 +0000
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             &nbsp; &nbsp; &nbsp;
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+            created at 2024-05-24 09:47 +0000
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
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+            created at 2024-05-24 09:47 +0000
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diff --git a/coverage/z_eefc2129b55d56d0_nolb_nma_py.html b/coverage/z_eefc2129b55d56d0_nolb_nma_py.html
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+++ b/coverage/z_eefc2129b55d56d0_nolb_nma_py.html
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             <a id="nextFileLink" class="nav" href="z_eefc2129b55d56d0_prody_anm_py.html">&#xbb; next</a>
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+            created at 2024-05-24 09:47 +0000
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+            created at 2024-05-24 09:47 +0000
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diff --git a/coverage/z_eefc2129b55d56d0_prody_anm_py.html b/coverage/z_eefc2129b55d56d0_prody_anm_py.html
index 8564c05..8059219 100644
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+++ b/coverage/z_eefc2129b55d56d0_prody_anm_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_68fa7e1546d8c55d_test_concoord_disco_py.html">&#xbb; next</a>
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+            created at 2024-05-24 09:47 +0000
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+            created at 2024-05-24 09:47 +0000
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diff --git a/flake8/index.html b/flake8/index.html
index 1410ee2..3390022 100644
--- a/flake8/index.html
+++ b/flake8/index.html
@@ -9,7 +9,7 @@
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       <div id="page">
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-         <p id="versions">Generated on 2024-05-07 09:12
+         <p id="versions">Generated on 2024-05-24 09:47
             with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.11.1, pyflakes: 3.2.0
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diff --git a/junit/junit.xml b/junit/junit.xml
index 6553cc0..ea94956 100644
--- a/junit/junit.xml
+++ b/junit/junit.xml
@@ -1 +1 @@
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index bacd3d4..c12cab3 100644
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@@ -7,7 +7,7 @@
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   <body>
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-    <p>Report generated on 07-May-2024 at 09:12:53 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 24-May-2024 at 09:47:17 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
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         <h2>Summary</h2>
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-        <p class="run-count">7 tests took 00:00:08.</p>
+        <p class="run-count">7 tests took 00:00:07.</p>
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@@ -108,7 +108,7 @@ <h2>Summary</h2>
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-    <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;8.2.0&#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_flexdyn/test/unitests/test_flexdyn/test_concoord_disco.py::TestConcoordDisco::test_concoord_disco&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_concoord_disco.py::TestConcoordDisco::test_concoord_disco&#34;, &#34;duration&#34;: &#34;00:00:06&#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_flexdyn/test/unitests/test_flexdyn/test_concoord_disco.py::TestConcoordDisco::test_concoord_disco&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:06&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:12:45,478 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.concoord_disco Version: 4.1.0\n2024-05-07 09:12:45,479 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_21/concoord_disco/8077b4ea-7005-49e7-a99c-e5ad1396ee63\n2024-05-07 09:12:45,480 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/dist.dat to /tmp/biobb/unitests_21/concoord_disco/8077b4ea-7005-49e7-a99c-e5ad1396ee63\n2024-05-07 09:12:45,481 [MainThread  ] [INFO ]  cd  /tmp/biobb/unitests_21/concoord_disco/8077b4ea-7005-49e7-a99c-e5ad1396ee63 ; disco -p structure.pdb -d dist.dat -or concoord_disco_rmsd.dat -of concoord_disco_bfactor.pdb -on concoord_disco.pdb -n 20\n\n2024-05-07 09:12:51,525 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 09:12:51,526 [MainThread  ] [INFO ]  Determining system size...\n-------------------------------------------------\ndisco - version 2.1.2 - build date: Thu Jan 24 11:26:08 CET 2013                                \nProcess started with PID:  2170574\non host: biobb-runners\nnumber of threads =    4\nin directory: /tmp/biobb/unitests_21/concoord_disco/8077b4ea-7005-49e7-a99c-e5ad1396ee63\non: 07/05/0024 at: 09:12:45\n-------------------------------------------------\ncommand line options:\ninput coordinates...................: structure.pdb                           \ndistance constraints................: dist.dat                                \nnr of structures to be generated....:      20\nmaximum nr of iterations............:    2500\nmaximum nr of trials................:      25\nmaximal sum of violations...........:    1.00000\noutput NMR-PDB file.................: concoord_disco.pdb                      \noutput RMSD values..................: concoord_disco_rmsd.dat                 \noutput atomic fluctuations..........: concoord_disco_bfactor.pdb              \nchirality corrections will be performed on the fly\nNr. of rounds of bound smoothing....:       0\nDamping factor (converted)..........:    1.00000\nprocessing input...\nnumber of atoms.....................:     775\nnumber of residues..................:     144\nnumber of chiral centers to check...:     106\nnumber of planar groups to check....:     124\nsorting distances...\nnumber of read distances............:   25223\nnumber of angles....................:     966\ntotal number of read distances......:   25223\nNr of input violations:      44\nSum of input violations: 0.10774E-03 nm\nSum of input bumps: 0.00000E+00 nm\nperc. of total nr of distances......:    8.41\nUncertainty sum/average:  0.13517E+05 0.53589E+00 nm\nParallel operation, number of threads =    4\nOverride by setting the environment variable OMP_NUM_THREADS\ngenerated structure.................:       1 with RMSD  2.87 A\nNr. of violations...................:     203\nSum of violations...................:    0.34908\ngenerated structure.................:       2 with RMSD  2.39 A\nNr. of violations...................:     183\nSum of violations...................:    0.32294\ngenerated structure.................:       3 with RMSD  2.14 A\nNr. of violations...................:     180\nSum of violations...................:    0.33313\nGiving up, best violation sum was...:  12.66167\nstructure rejected (no convergence after    606 steps)\nGiving up, best violation sum was...:   0.89863\nstructure rejected (no convergence after    603 steps)\nGiving up, best violation sum was...:  13.30915\nstructure rejected (no convergence after    940 steps)\ngenerated structure.................:       4 with RMSD  2.47 A\nNr. of violations...................:     191\nSum of violations...................:    0.36691\ngenerated structure.................:       5 with RMSD  1.43 A\nNr. of violations...................:     148\nSum of violations...................:    0.22789\ngenerated structure.................:       6 with RMSD  2.82 A\nNr. of violations...................:     199\nSum of violations...................:    0.34200\ngenerated structure.................:       7 with RMSD  2.07 A\nNr. of violations...................:     164\nSum of violations...................:    0.26734\ngenerated structure.................:       8 with RMSD  2.51 A\nNr. of violations...................:     182\nSum of violations...................:    0.32628\nGiving up, best violation sum was...:   6.15732\nstructure rejected (no convergence after   1070 steps)\ngenerated structure.................:       9 with RMSD  3.57 A\nNr. of violations...................:     185\nSum of violations...................:    0.32794\nGiving up, best violation sum was...:   7.77156\nstructure rejected (no convergence after    990 steps)\nGiving up, best violation sum was...:   4.55957\nstructure rejected (no convergence after    610 steps)\nGiving up, best violation sum was...:   2.89941\nstructure rejected (no convergence after    601 steps)\ngenerated structure.................:      10 with RMSD  1.77 A\nNr. of violations...................:     189\nSum of violations...................:    0.31135\nGiving up, best violation sum was...:  12.75521\nstructure rejected (no convergence after    750 steps)\nGiving up, best violation sum was...:  14.66847\nstructure rejected (no convergence after   1159 steps)\ngenerated structure.................:      11 with RMSD  3.39 A\nNr. of violations...................:     211\nSum of violations...................:    0.30720\ngenerated structure.................:      12 with RMSD  1.74 A\nNr. of violations...................:     189\nSum of violations...................:    0.34857\nGiving up, best violation sum was...:   0.94540\nstructure rejected (no convergence after    609 steps)\nGiving up, best violation sum was...:   1.17588\nstructure rejected (no convergence after    609 steps)\nGiving up, best violation sum was...:   1.02614\nstructure rejected (no convergence after    606 steps)\ngenerated structure.................:      13 with RMSD  2.39 A\nNr. of violations...................:     197\nSum of violations...................:    0.37360\nGiving up, best violation sum was...:   0.92332\nstructure rejected (no convergence after    610 steps)\nGiving up, best violation sum was...:  14.51781\nstructure rejected (no convergence after    730 steps)\ngenerated structure.................:      14 with RMSD  2.51 A\nNr. of violations...................:     199\nSum of violations...................:    0.32411\nGiving up, best violation sum was...:   9.83401\nstructure rejected (no convergence after    830 steps)\ngenerated structure.................:      15 with RMSD  3.34 A\nNr. of violations...................:     173\nSum of violations...................:    0.32189\nGiving up, best violation sum was...:  10.80298\nstructure rejected (no convergence after    566 steps)\nGiving up, best violation sum was...:   7.94726\nstructure rejected (no convergence after    581 steps)\nGiving up, best violation sum was...:   1.34604\nstructure rejected (no convergence after    610 steps)\nstructure rejected (no convergence after    193 steps)\ngenerated structure.................:      16 with RMSD  3.37 A\nNr. of violations...................:     206\nSum of violations...................:    0.35689\ngenerated structure.................:      17 with RMSD  2.79 A\nNr. of violations...................:     176\nSum of violations...................:    0.32207\ngenerated structure.................:      18 with RMSD  2.44 A\nNr. of violations...................:     193\nSum of violations...................:    0.36618\ngenerated structure.................:      19 with RMSD  2.16 A\nNr. of violations...................:     189\nSum of violations...................:    0.31926\nGiving up, best violation sum was...:  11.34416\nstructure rejected (no convergence after   1530 steps)\ngenerated structure.................:      20 with RMSD  2.03 A\nNr. of violations...................:     197\nSum of violations...................:    0.36505\nnormal termination\nCPU time: user=     19.74s, system=      0.00s\n\n2024-05-07 09:12:51,528 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/concoord_disco/8077b4ea-7005-49e7-a99c-e5ad1396ee63&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/concoord_disco/concoord_disco.pdb\nChecking if empty file: /tmp/biobb/unitests_21/concoord_disco/concoord_disco_rmsd.dat\nChecking if empty file: /tmp/biobb/unitests_21/concoord_disco/concoord_disco_bfactor.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/concoord_disco/concoord_disco_log.out:file_utils.py:390 Executing biobb_flexdyn.flexdyn.concoord_disco Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/concoord_disco/concoord_disco_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_21/concoord_disco/8077b4ea-7005-49e7-a99c-e5ad1396ee63\nINFO     /tmp/biobb/unitests_21/concoord_disco/concoord_disco_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/dist.dat to /tmp/biobb/unitests_21/concoord_disco/8077b4ea-7005-49e7-a99c-e5ad1396ee63\nINFO     /tmp/biobb/unitests_21/concoord_disco/concoord_disco_log.out:cmd_wrapper.py:33 cd  /tmp/biobb/unitests_21/concoord_disco/8077b4ea-7005-49e7-a99c-e5ad1396ee63 ; disco -p structure.pdb -d dist.dat -or concoord_disco_rmsd.dat -of concoord_disco_bfactor.pdb -on concoord_disco.pdb -n 20\n\nINFO     /tmp/biobb/unitests_21/concoord_disco/concoord_disco_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_21/concoord_disco/concoord_disco_log.out:cmd_wrapper.py:52 Determining system size...\n-------------------------------------------------\ndisco - version 2.1.2 - build date: Thu Jan 24 11:26:08 CET 2013                                \nProcess started with PID:  2170574\non host: biobb-runners\nnumber of threads =    4\nin directory: /tmp/biobb/unitests_21/concoord_disco/8077b4ea-7005-49e7-a99c-e5ad1396ee63\non: 07/05/0024 at: 09:12:45\n-------------------------------------------------\ncommand line options:\ninput coordinates...................: structure.pdb                           \ndistance constraints................: dist.dat                                \nnr of structures to be generated....:      20\nmaximum nr of iterations............:    2500\nmaximum nr of trials................:      25\nmaximal sum of violations...........:    1.00000\noutput NMR-PDB file.................: concoord_disco.pdb                      \noutput RMSD values..................: concoord_disco_rmsd.dat                 \noutput atomic fluctuations..........: concoord_disco_bfactor.pdb              \nchirality corrections will be performed on the fly\nNr. of rounds of bound smoothing....:       0\nDamping factor (converted)..........:    1.00000\nprocessing input...\nnumber of atoms.....................:     775\nnumber of residues..................:     144\nnumber of chiral centers to check...:     106\nnumber of planar groups to check....:     124\nsorting distances...\nnumber of read distances............:   25223\nnumber of angles....................:     966\ntotal number of read distances......:   25223\nNr of input violations:      44\nSum of input violations: 0.10774E-03 nm\nSum of input bumps: 0.00000E+00 nm\nperc. of total nr of distances......:    8.41\nUncertainty sum/average:  0.13517E+05 0.53589E+00 nm\nParallel operation, number of threads =    4\nOverride by setting the environment variable OMP_NUM_THREADS\ngenerated structure.................:       1 with RMSD  2.87 A\nNr. of violations...................:     203\nSum of violations...................:    0.34908\ngenerated structure.................:       2 with RMSD  2.39 A\nNr. of violations...................:     183\nSum of violations...................:    0.32294\ngenerated structure.................:       3 with RMSD  2.14 A\nNr. of violations...................:     180\nSum of violations...................:    0.33313\nGiving up, best violation sum was...:  12.66167\nstructure rejected (no convergence after    606 steps)\nGiving up, best violation sum was...:   0.89863\nstructure rejected (no convergence after    603 steps)\nGiving up, best violation sum was...:  13.30915\nstructure rejected (no convergence after    940 steps)\ngenerated structure.................:       4 with RMSD  2.47 A\nNr. of violations...................:     191\nSum of violations...................:    0.36691\ngenerated structure.................:       5 with RMSD  1.43 A\nNr. of violations...................:     148\nSum of violations...................:    0.22789\ngenerated structure.................:       6 with RMSD  2.82 A\nNr. of violations...................:     199\nSum of violations...................:    0.34200\ngenerated structure.................:       7 with RMSD  2.07 A\nNr. of violations...................:     164\nSum of violations...................:    0.26734\ngenerated structure.................:       8 with RMSD  2.51 A\nNr. of violations...................:     182\nSum of violations...................:    0.32628\nGiving up, best violation sum was...:   6.15732\nstructure rejected (no convergence after   1070 steps)\ngenerated structure.................:       9 with RMSD  3.57 A\nNr. of violations...................:     185\nSum of violations...................:    0.32794\nGiving up, best violation sum was...:   7.77156\nstructure rejected (no convergence after    990 steps)\nGiving up, best violation sum was...:   4.55957\nstructure rejected (no convergence after    610 steps)\nGiving up, best violation sum was...:   2.89941\nstructure rejected (no convergence after    601 steps)\ngenerated structure.................:      10 with RMSD  1.77 A\nNr. of violations...................:     189\nSum of violations...................:    0.31135\nGiving up, best violation sum was...:  12.75521\nstructure rejected (no convergence after    750 steps)\nGiving up, best violation sum was...:  14.66847\nstructure rejected (no convergence after   1159 steps)\ngenerated structure.................:      11 with RMSD  3.39 A\nNr. of violations...................:     211\nSum of violations...................:    0.30720\ngenerated structure.................:      12 with RMSD  1.74 A\nNr. of violations...................:     189\nSum of violations...................:    0.34857\nGiving up, best violation sum was...:   0.94540\nstructure rejected (no convergence after    609 steps)\nGiving up, best violation sum was...:   1.17588\nstructure rejected (no convergence after    609 steps)\nGiving up, best violation sum was...:   1.02614\nstructure rejected (no convergence after    606 steps)\ngenerated structure.................:      13 with RMSD  2.39 A\nNr. of violations...................:     197\nSum of violations...................:    0.37360\nGiving up, best violation sum was...:   0.92332\nstructure rejected (no convergence after    610 steps)\nGiving up, best violation sum was...:  14.51781\nstructure rejected (no convergence after    730 steps)\ngenerated structure.................:      14 with RMSD  2.51 A\nNr. of violations...................:     199\nSum of violations...................:    0.32411\nGiving up, best violation sum was...:   9.83401\nstructure rejected (no convergence after    830 steps)\ngenerated structure.................:      15 with RMSD  3.34 A\nNr. of violations...................:     173\nSum of violations...................:    0.32189\nGiving up, best violation sum was...:  10.80298\nstructure rejected (no convergence after    566 steps)\nGiving up, best violation sum was...:   7.94726\nstructure rejected (no convergence after    581 steps)\nGiving up, best violation sum was...:   1.34604\nstructure rejected (no convergence after    610 steps)\nstructure rejected (no convergence after    193 steps)\ngenerated structure.................:      16 with RMSD  3.37 A\nNr. of violations...................:     206\nSum of violations...................:    0.35689\ngenerated structure.................:      17 with RMSD  2.79 A\nNr. of violations...................:     176\nSum of violations...................:    0.32207\ngenerated structure.................:      18 with RMSD  2.44 A\nNr. of violations...................:     193\nSum of violations...................:    0.36618\ngenerated structure.................:      19 with RMSD  2.16 A\nNr. of violations...................:     189\nSum of violations...................:    0.31926\nGiving up, best violation sum was...:  11.34416\nstructure rejected (no convergence after   1530 steps)\ngenerated structure.................:      20 with RMSD  2.03 A\nNr. of violations...................:     197\nSum of violations...................:    0.36505\nnormal termination\nCPU time: user=     19.74s, system=      0.00s\n\nINFO     /tmp/biobb/unitests_21/concoord_disco/concoord_disco_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/concoord_disco/8077b4ea-7005-49e7-a99c-e5ad1396ee63&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_concoord_dist.py::TestConcoordDist::test_concoord_dist&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_concoord_dist.py::TestConcoordDist::test_concoord_dist&#34;, &#34;duration&#34;: &#34;175 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_flexdyn/test/unitests/test_flexdyn/test_concoord_dist.py::TestConcoordDist::test_concoord_dist&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;175 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 -----------------------------\n2024-05-07 09:12:51,568 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.concoord_dist Version: 4.1.0\n2024-05-07 09:12:51,568 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_21/concoord_dist/53f43315-1bcd-4298-b189-27dae28c0118\n2024-05-07 09:12:51,569 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_21/concoord_dist/a4ef06cf-c9e7-4c82-bd11-dde196a45266.stdin to /tmp/biobb/unitests_21/concoord_dist/53f43315-1bcd-4298-b189-27dae28c0118\n2024-05-07 09:12:51,569 [MainThread  ] [INFO ]  cd  /tmp/biobb/unitests_21/concoord_dist/53f43315-1bcd-4298-b189-27dae28c0118 ; dist -op concoord_dist.pdb -og concoord_dist.gro -od concoord_dist.dat -p structure.pdb -c 4.0 -m 50 -damp 1.0 &amp;lt; a4ef06cf-c9e7-4c82-bd11-dde196a45266.stdin\n\n2024-05-07 09:12:51,683 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 09:12:51,683 [MainThread  ] [INFO ]  Select a set of Van der Waals parameters:\n1: OPLS-UA (united atoms) parameters\n2: OPLS-AA (all atoms) parameters\n3: PROLSQ repel parameters\n4: Yamber2 parameters\n5: Li et al. parameters\n6: OPLS-X parameters (recommended for NMR structure determination)\nSelected parameter set 1\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/ATOMS_oplsua.DAT to ATOMS.DAT in current working directory\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/MARGINS_oplsua.DAT to MARGINS.DAT in current working directory\nSelect a set of bond/angle parameters:\n1: Concoord default parameters\n2: Engh-Huber parameters\nSelected parameter set 1\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/BONDS.DAT.noeh to BONDS.DAT in current working directory\n-------------------------------------------------\ndist.exe - build date: Thu Jan 24 11:26:08 CET 2013                                \nProcess started with PID:  2170584\non host: biobb-runners\nin directory: /tmp/biobb/unitests_21/concoord_dist/53f43315-1bcd-4298-b189-27dae28c0118\non: 07/05/0024 at: 09:12:51\n-------------------------------------------------\ncommand line options:\npdb input coordinate file...........: structure.pdb                           \nWARNING WARNING WARNING WARNING WARNING WARNING\nWarning: no dssp calculation will be performed. Expect poor results!\nWARNING WARNING WARNING WARNING WARNING WARNING\nnon-bonded cut-off radius...........:   4.00 A + VDW sum\nminimal nr. of distances per atom...:     50\noutput distances....................: concoord_dist.dat                       \noutput coordinates (PDB)............: concoord_dist.pdb                       \noutput coordinates (GROMOS87).......: concoord_dist.gro                       \nhydrogen atoms (if any) will be removed\nnon-bonded contacts of starting structure will be preserved\nprocessing input...\ntotal number of atoms       :      775\nnumber of residues          :      144\nnumber of atoms to be used  :      775\ncounted    640 intra-residue bonds\ncounted     84 peptide bonds\ncounted      0 disulphide bonds\ncounted      0 histidine-heme bonds\ncounted    724 bonds in total\ncounted    966 1-3 pairs (angles)\ncounted     36 ring restrictions\ncounted      0 omega restrictions\ncounted   1037 other 1-4 restrictions\ncounted      0 hydrogen bonds\ncounted      4 salt bridges\ncounted    142 hydrogen bonds\ncounted    868 side chain restrictions\ncounted      0 sheet restrictions\ncounted  18104 other close pairs\ncounted   3878 more restrictions\ntotal nr of non-bonded pairs:  19118\ntotal number of constraints :   26254\n 1 warning(s) encountered. Please investigate!\n\n2024-05-07 09:12:51,683 [MainThread  ] [INFO ]  remark: distance between atom      31 and      27 (3.11) smaller than VdWsum (3.75)    C    C 0.290\nremark: distance between atom     124 and     122 (2.94) smaller than VdWsum (3.43) CH2E    O 0.141\nremark: distance between atom     159 and     157 (2.90) smaller than VdWsum (3.36)    C    O 0.102\nremark: distance between atom     328 and     324 (3.13) smaller than VdWsum (3.50)  NH1    C 0.022\nremark: distance between atom     383 and     377 (3.22) smaller than VdWsum (3.58) CH2E  NH1 0.008\nremark: distance between atom     383 and     379 (3.36) smaller than VdWsum (3.83) CH2E    C 0.113\nremark: distance between atom     392 and     388 (2.86) smaller than VdWsum (3.36)   OC    C 0.146\nremark: distance between atom     452 and     448 (3.26) smaller than VdWsum (3.78) CH3E    C 0.161\nremark: distance between atom     560 and     555 (3.27) smaller than VdWsum (3.65) CR1E    C 0.028\nremark: distance between atom      18 and      12 (2.93) smaller than VdWsum (3.36)    C    O 0.077\nremark: distance between atom      27 and      19 (2.84) smaller than VdWsum (3.36)    C    O 0.163\nremark: distance between atom      76 and      68 (2.86) smaller than VdWsum (3.36)    C    O 0.147\nremark: distance between atom      84 and      77 (2.85) smaller than VdWsum (3.36)    C    O 0.154\nremark: distance between atom      87 and      48 (2.87) smaller than VdWsum (3.43) CH2E    O 0.210\nremark: distance between atom     101 and      93 (2.83) smaller than VdWsum (3.36)    C    O 0.177\nremark: distance between atom     103 and      68 (2.99) smaller than VdWsum (3.43) CH2E    O 0.097\nremark: distance between atom     108 and      92 (3.11) smaller than VdWsum (3.50)  NH1    C 0.038\nremark: distance between atom     127 and      94 (3.03) smaller than VdWsum (3.58)  NH3 CH2E 0.202\nremark: distance between atom     139 and     131 (2.66) smaller than VdWsum (3.43) CH2E    O 0.421\nremark: distance between atom     140 and     131 (2.74) smaller than VdWsum (3.26)   C5    O 0.169\nremark: distance between atom     154 and     150 (2.79) smaller than VdWsum (3.58)  NH1 CH2E 0.442\nremark: distance between atom     158 and     148 (2.90) smaller than VdWsum (3.43) CH2E    O 0.186\nremark: distance between atom     162 and     147 (3.07) smaller than VdWsum (3.50)  NH1    C 0.080\nremark: distance between atom     170 and     167 (3.14) smaller than VdWsum (3.50)  NH1    C 0.015\nremark: distance between atom     172 and     165 (2.74) smaller than VdWsum (3.36)    C    O 0.264\nremark: distance between atom     177 and     164 (2.97) smaller than VdWsum (3.50)  NH1    C 0.182\nremark: distance between atom     189 and     184 (2.96) smaller than VdWsum (3.36)    C    O 0.048\nremark: distance between atom     221 and     213 (3.00) smaller than VdWsum (3.36)    C    O 0.003\nremark: distance between atom     224 and     190 (2.95) smaller than VdWsum (3.43) CH2E    O 0.134\nremark: distance between atom     234 and     230 (2.92) smaller than VdWsum (3.36)    C    O 0.088\nremark: distance between atom     237 and     206 (2.99) smaller than VdWsum (3.43) CH2E    O 0.096\nremark: distance between atom     239 and     176 (3.26) smaller than VdWsum (3.80) CH3E CH3E 0.189\nremark: distance between atom     242 and     235 (2.98) smaller than VdWsum (3.36)    C    O 0.029\nremark: distance between atom     250 and     243 (2.87) smaller than VdWsum (3.36)    C    O 0.133\nremark: distance between atom     257 and     251 (2.95) smaller than VdWsum (3.36)    C    O 0.055\nremark: distance between atom     318 and     292 (2.95) smaller than VdWsum (3.43) CH2E    O 0.133\nremark: distance between atom     322 and     307 (3.13) smaller than VdWsum (3.50)  NH1    C 0.019\nremark: distance between atom     322 and     318 (3.19) smaller than VdWsum (3.58)  NH1 CH2E 0.040\nremark: distance between atom     340 and     324 (3.05) smaller than VdWsum (3.50)  NH1    C 0.100\nremark: distance between atom     342 and     335 (2.96) smaller than VdWsum (3.36)    C    O 0.043\nremark: distance between atom     364 and     357 (3.15) smaller than VdWsum (3.53)  NH1 CH3E 0.028\nremark: distance between atom     370 and     361 (2.94) smaller than VdWsum (3.36)    C    O 0.065\nremark: distance between atom     377 and     360 (3.09) smaller than VdWsum (3.50)  NH1    C 0.058\nremark: distance between atom     388 and     380 (2.92) smaller than VdWsum (3.36)    C    O 0.085\nremark: distance between atom     394 and     391 (3.01) smaller than VdWsum (3.50)  NH1    C 0.139\nremark: distance between atom     433 and     423 (2.97) smaller than VdWsum (3.36)    C    O 0.037\nremark: distance between atom     444 and     434 (2.95) smaller than VdWsum (3.36)    C    O 0.055\nremark: distance between atom     456 and     449 (2.96) smaller than VdWsum (3.36)    C    O 0.046\nremark: distance between atom     478 and     304 (3.42) smaller than VdWsum (3.80) CH3E CH3E 0.027\nremark: distance between atom     481 and     474 (2.96) smaller than VdWsum (3.36)    C    O 0.044\nremark: distance between atom     492 and     489 (3.00) smaller than VdWsum (3.36)    C    O 0.009\nremark: distance between atom     499 and     488 (3.14) smaller than VdWsum (3.50)  NH1    C 0.006\nremark: distance between atom     508 and     253 (2.65) smaller than VdWsum (3.00)  NC2  OH1 0.000\nremark: distance between atom     534 and     524 (2.98) smaller than VdWsum (3.36)    C    O 0.026\nremark: distance between atom     553 and     542 (3.14) smaller than VdWsum (3.50)  NH1    C 0.010\nremark: distance between atom     575 and     568 (2.95) smaller than VdWsum (3.36)    C    O 0.060\nremark: distance between atom     618 and     612 (3.00) smaller than VdWsum (3.36)    C    O 0.004\nremark: distance between atom     657 and     647 (3.00) smaller than VdWsum (3.36)    C    O 0.002\nremark: distance between atom     660 and     619 (2.95) smaller than VdWsum (3.43) CH2E    O 0.133\nremark: distance between atom     672 and     670 (3.10) smaller than VdWsum (3.53)  NH1 CH3E 0.078\nremark: distance between atom     730 and     407 (2.57) smaller than VdWsum (3.01)  OH1    O 0.097\nremark: distance between atom     735 and     520 (2.58) smaller than VdWsum (3.00)  OH1  NC2 0.066\nremark: distance between atom     737 and      72 (2.58) smaller than VdWsum (3.01)  OH1   OC 0.084\nremark: distance between atom     744 and     125 (3.09) smaller than VdWsum (3.49)  OH1 CH2E 0.051\n\n2024-05-07 09:12:51,686 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/concoord_dist/53f43315-1bcd-4298-b189-27dae28c0118&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_21/concoord_dist/a4ef06cf-c9e7-4c82-bd11-dde196a45266.stdin&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/concoord_dist/concoord_dist.pdb\nChecking if empty file: /tmp/biobb/unitests_21/concoord_dist/concoord_dist.gro\nChecking if empty file: /tmp/biobb/unitests_21/concoord_dist/concoord_dist.dat\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_21/concoord_dist/concoord_dist.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/reference/flexdyn/dist.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 775\n     Atoms ALIGNED in PDB_B: 775\n     RMS: 6.91545531105067e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/concoord_dist/concoord_dist_log.out:file_utils.py:390 Executing biobb_flexdyn.flexdyn.concoord_dist Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/concoord_dist/concoord_dist_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_21/concoord_dist/53f43315-1bcd-4298-b189-27dae28c0118\nINFO     /tmp/biobb/unitests_21/concoord_dist/concoord_dist_log.out:file_utils.py:390 Copy: /tmp/biobb/unitests_21/concoord_dist/a4ef06cf-c9e7-4c82-bd11-dde196a45266.stdin to /tmp/biobb/unitests_21/concoord_dist/53f43315-1bcd-4298-b189-27dae28c0118\nINFO     /tmp/biobb/unitests_21/concoord_dist/concoord_dist_log.out:cmd_wrapper.py:33 cd  /tmp/biobb/unitests_21/concoord_dist/53f43315-1bcd-4298-b189-27dae28c0118 ; dist -op concoord_dist.pdb -og concoord_dist.gro -od concoord_dist.dat -p structure.pdb -c 4.0 -m 50 -damp 1.0 &amp;lt; a4ef06cf-c9e7-4c82-bd11-dde196a45266.stdin\n\nINFO     /tmp/biobb/unitests_21/concoord_dist/concoord_dist_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_21/concoord_dist/concoord_dist_log.out:cmd_wrapper.py:52 Select a set of Van der Waals parameters:\n1: OPLS-UA (united atoms) parameters\n2: OPLS-AA (all atoms) parameters\n3: PROLSQ repel parameters\n4: Yamber2 parameters\n5: Li et al. parameters\n6: OPLS-X parameters (recommended for NMR structure determination)\nSelected parameter set 1\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/ATOMS_oplsua.DAT to ATOMS.DAT in current working directory\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/MARGINS_oplsua.DAT to MARGINS.DAT in current working directory\nSelect a set of bond/angle parameters:\n1: Concoord default parameters\n2: Engh-Huber parameters\nSelected parameter set 1\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/BONDS.DAT.noeh to BONDS.DAT in current working directory\n-------------------------------------------------\ndist.exe - build date: Thu Jan 24 11:26:08 CET 2013                                \nProcess started with PID:  2170584\non host: biobb-runners\nin directory: /tmp/biobb/unitests_21/concoord_dist/53f43315-1bcd-4298-b189-27dae28c0118\non: 07/05/0024 at: 09:12:51\n-------------------------------------------------\ncommand line options:\npdb input coordinate file...........: structure.pdb                           \nWARNING WARNING WARNING WARNING WARNING WARNING\nWarning: no dssp calculation will be performed. Expect poor results!\nWARNING WARNING WARNING WARNING WARNING WARNING\nnon-bonded cut-off radius...........:   4.00 A + VDW sum\nminimal nr. of distances per atom...:     50\noutput distances....................: concoord_dist.dat                       \noutput coordinates (PDB)............: concoord_dist.pdb                       \noutput coordinates (GROMOS87).......: concoord_dist.gro                       \nhydrogen atoms (if any) will be removed\nnon-bonded contacts of starting structure will be preserved\nprocessing input...\ntotal number of atoms       :      775\nnumber of residues          :      144\nnumber of atoms to be used  :      775\ncounted    640 intra-residue bonds\ncounted     84 peptide bonds\ncounted      0 disulphide bonds\ncounted      0 histidine-heme bonds\ncounted    724 bonds in total\ncounted    966 1-3 pairs (angles)\ncounted     36 ring restrictions\ncounted      0 omega restrictions\ncounted   1037 other 1-4 restrictions\ncounted      0 hydrogen bonds\ncounted      4 salt bridges\ncounted    142 hydrogen bonds\ncounted    868 side chain restrictions\ncounted      0 sheet restrictions\ncounted  18104 other close pairs\ncounted   3878 more restrictions\ntotal nr of non-bonded pairs:  19118\ntotal number of constraints :   26254\n 1 warning(s) encountered. Please investigate!\n\nINFO     /tmp/biobb/unitests_21/concoord_dist/concoord_dist_log.err:cmd_wrapper.py:60 remark: distance between atom      31 and      27 (3.11) smaller than VdWsum (3.75)    C    C 0.290\nremark: distance between atom     124 and     122 (2.94) smaller than VdWsum (3.43) CH2E    O 0.141\nremark: distance between atom     159 and     157 (2.90) smaller than VdWsum (3.36)    C    O 0.102\nremark: distance between atom     328 and     324 (3.13) smaller than VdWsum (3.50)  NH1    C 0.022\nremark: distance between atom     383 and     377 (3.22) smaller than VdWsum (3.58) CH2E  NH1 0.008\nremark: distance between atom     383 and     379 (3.36) smaller than VdWsum (3.83) CH2E    C 0.113\nremark: distance between atom     392 and     388 (2.86) smaller than VdWsum (3.36)   OC    C 0.146\nremark: distance between atom     452 and     448 (3.26) smaller than VdWsum (3.78) CH3E    C 0.161\nremark: distance between atom     560 and     555 (3.27) smaller than VdWsum (3.65) CR1E    C 0.028\nremark: distance between atom      18 and      12 (2.93) smaller than VdWsum (3.36)    C    O 0.077\nremark: distance between atom      27 and      19 (2.84) smaller than VdWsum (3.36)    C    O 0.163\nremark: distance between atom      76 and      68 (2.86) smaller than VdWsum (3.36)    C    O 0.147\nremark: distance between atom      84 and      77 (2.85) smaller than VdWsum (3.36)    C    O 0.154\nremark: distance between atom      87 and      48 (2.87) smaller than VdWsum (3.43) CH2E    O 0.210\nremark: distance between atom     101 and      93 (2.83) smaller than VdWsum (3.36)    C    O 0.177\nremark: distance between atom     103 and      68 (2.99) smaller than VdWsum (3.43) CH2E    O 0.097\nremark: distance between atom     108 and      92 (3.11) smaller than VdWsum (3.50)  NH1    C 0.038\nremark: distance between atom     127 and      94 (3.03) smaller than VdWsum (3.58)  NH3 CH2E 0.202\nremark: distance between atom     139 and     131 (2.66) smaller than VdWsum (3.43) CH2E    O 0.421\nremark: distance between atom     140 and     131 (2.74) smaller than VdWsum (3.26)   C5    O 0.169\nremark: distance between atom     154 and     150 (2.79) smaller than VdWsum (3.58)  NH1 CH2E 0.442\nremark: distance between atom     158 and     148 (2.90) smaller than VdWsum (3.43) CH2E    O 0.186\nremark: distance between atom     162 and     147 (3.07) smaller than VdWsum (3.50)  NH1    C 0.080\nremark: distance between atom     170 and     167 (3.14) smaller than VdWsum (3.50)  NH1    C 0.015\nremark: distance between atom     172 and     165 (2.74) smaller than VdWsum (3.36)    C    O 0.264\nremark: distance between atom     177 and     164 (2.97) smaller than VdWsum (3.50)  NH1    C 0.182\nremark: distance between atom     189 and     184 (2.96) smaller than VdWsum (3.36)    C    O 0.048\nremark: distance between atom     221 and     213 (3.00) smaller than VdWsum (3.36)    C    O 0.003\nremark: distance between atom     224 and     190 (2.95) smaller than VdWsum (3.43) CH2E    O 0.134\nremark: distance between atom     234 and     230 (2.92) smaller than VdWsum (3.36)    C    O 0.088\nremark: distance between atom     237 and     206 (2.99) smaller than VdWsum (3.43) CH2E    O 0.096\nremark: distance between atom     239 and     176 (3.26) smaller than VdWsum (3.80) CH3E CH3E 0.189\nremark: distance between atom     242 and     235 (2.98) smaller than VdWsum (3.36)    C    O 0.029\nremark: distance between atom     250 and     243 (2.87) smaller than VdWsum (3.36)    C    O 0.133\nremark: distance between atom     257 and     251 (2.95) smaller than VdWsum (3.36)    C    O 0.055\nremark: distance between atom     318 and     292 (2.95) smaller than VdWsum (3.43) CH2E    O 0.133\nremark: distance between atom     322 and     307 (3.13) smaller than VdWsum (3.50)  NH1    C 0.019\nremark: distance between atom     322 and     318 (3.19) smaller than VdWsum (3.58)  NH1 CH2E 0.040\nremark: distance between atom     340 and     324 (3.05) smaller than VdWsum (3.50)  NH1    C 0.100\nremark: distance between atom     342 and     335 (2.96) smaller than VdWsum (3.36)    C    O 0.043\nremark: distance between atom     364 and     357 (3.15) smaller than VdWsum (3.53)  NH1 CH3E 0.028\nremark: distance between atom     370 and     361 (2.94) smaller than VdWsum (3.36)    C    O 0.065\nremark: distance between atom     377 and     360 (3.09) smaller than VdWsum (3.50)  NH1    C 0.058\nremark: distance between atom     388 and     380 (2.92) smaller than VdWsum (3.36)    C    O 0.085\nremark: distance between atom     394 and     391 (3.01) smaller than VdWsum (3.50)  NH1    C 0.139\nremark: distance between atom     433 and     423 (2.97) smaller than VdWsum (3.36)    C    O 0.037\nremark: distance between atom     444 and     434 (2.95) smaller than VdWsum (3.36)    C    O 0.055\nremark: distance between atom     456 and     449 (2.96) smaller than VdWsum (3.36)    C    O 0.046\nremark: distance between atom     478 and     304 (3.42) smaller than VdWsum (3.80) CH3E CH3E 0.027\nremark: distance between atom     481 and     474 (2.96) smaller than VdWsum (3.36)    C    O 0.044\nremark: distance between atom     492 and     489 (3.00) smaller than VdWsum (3.36)    C    O 0.009\nremark: distance between atom     499 and     488 (3.14) smaller than VdWsum (3.50)  NH1    C 0.006\nremark: distance between atom     508 and     253 (2.65) smaller than VdWsum (3.00)  NC2  OH1 0.000\nremark: distance between atom     534 and     524 (2.98) smaller than VdWsum (3.36)    C    O 0.026\nremark: distance between atom     553 and     542 (3.14) smaller than VdWsum (3.50)  NH1    C 0.010\nremark: distance between atom     575 and     568 (2.95) smaller than VdWsum (3.36)    C    O 0.060\nremark: distance between atom     618 and     612 (3.00) smaller than VdWsum (3.36)    C    O 0.004\nremark: distance between atom     657 and     647 (3.00) smaller than VdWsum (3.36)    C    O 0.002\nremark: distance between atom     660 and     619 (2.95) smaller than VdWsum (3.43) CH2E    O 0.133\nremark: distance between atom     672 and     670 (3.10) smaller than VdWsum (3.53)  NH1 CH3E 0.078\nremark: distance between atom     730 and     407 (2.57) smaller than VdWsum (3.01)  OH1    O 0.097\nremark: distance between atom     735 and     520 (2.58) smaller than VdWsum (3.00)  OH1  NC2 0.066\nremark: distance between atom     737 and      72 (2.58) smaller than VdWsum (3.01)  OH1   OC 0.084\nremark: distance between atom     744 and     125 (3.09) smaller than VdWsum (3.49)  OH1 CH2E 0.051\n\nINFO     /tmp/biobb/unitests_21/concoord_dist/concoord_dist_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/concoord_dist/53f43315-1bcd-4298-b189-27dae28c0118&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_21/concoord_dist/a4ef06cf-c9e7-4c82-bd11-dde196a45266.stdin&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imc.py::TestImodImc::test_imod_imc&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imc.py::TestImodImc::test_imod_imc&#34;, &#34;duration&#34;: &#34;44 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_flexdyn/test/unitests/test_flexdyn/test_imod_imc.py::TestImodImc::test_imod_imc&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;44 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 -----------------------------\n2024-05-07 09:12:51,744 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.imod_imc Version: 4.1.0\n2024-05-07 09:12:51,745 [MainThread  ] [INFO ]  Creating aa443a40-1dde-45eb-b8ee-25085e1ac3be temporary folder\n2024-05-07 09:12:51,745 [MainThread  ] [INFO ]  cd aa443a40-1dde-45eb-b8ee-25085e1ac3be ; imc structure_cleaned.pdb imod_imode_evecs.dat -o imod_ensemble -c 10 -n 10 -a 6.0\n\n2024-05-07 09:12:51,772 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 09:12:51,772 [MainThread  ] [INFO ]  imc&amp;gt;\nimc&amp;gt; Monte-Carlo IC-NMA based program v1.11\nimc&amp;gt;\nimc&amp;gt; Reading Input PDB file\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimc&amp;gt; Formatting pdb names\nimc&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimc&amp;gt; Selected model number of (pseudo)atoms: 716\nimc&amp;gt; Opening output trajectory file: imod_ensemble.pdb\nimc&amp;gt; Number of Dihedral angles: 168\nimc&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimc&amp;gt; Predicted number of ICs (Eckart): 168\nimc&amp;gt; Number of ICs predicted by seg_props(): 168\nimc&amp;gt; Ptraj info: imod_imode_evecs.dat  vectors=20  components=168\nimc&amp;gt; Number of used modes: 10\nimc&amp;gt; Monte-Carlo stage using Ef= 1.000000\nimc&amp;gt; Frame     1  Etot= 2.814298 0.00 sec\rimc&amp;gt; Frame     2  Etot= 1.481835 0.00 sec\rimc&amp;gt; Frame     3  Etot= 2.017057 0.00 sec\rimc&amp;gt; Frame     4  Etot= 3.779804 0.00 sec\rimc&amp;gt; Frame     5  Etot= 2.140620 0.01 sec\rimc&amp;gt; Frame     6  Etot= 2.771852 0.00 sec\rimc&amp;gt; Frame     7  Etot= 4.756513 0.00 sec\rimc&amp;gt; Frame     8  Etot= 1.985850 0.00 sec\rimc&amp;gt; Frame     9  Etot= 5.451007 0.00 sec\rimc&amp;gt; Frame    10  Etot= 9.098349 0.00 sec\r\nimc&amp;gt;           Total        0.01 sec\nimc&amp;gt;\nimc&amp;gt; ACEPTANCE RATIO(%): 39.746025\nimc&amp;gt;\nimc&amp;gt; Success!\nimc&amp;gt; Written MC-trajectory: imod_ensemble.pdb (10 frames)\nimc&amp;gt; Bye!\n\n2024-05-07 09:12:51,773 [MainThread  ] [INFO ]  Removed: [&amp;#x27;aa443a40-1dde-45eb-b8ee-25085e1ac3be&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/imod_imc/imod_imc_output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/imod_imc/imod_imc_log.out:file_utils.py:390 Executing biobb_flexdyn.flexdyn.imod_imc Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/imod_imc/imod_imc_log.out:file_utils.py:390 Creating aa443a40-1dde-45eb-b8ee-25085e1ac3be temporary folder\nINFO     /tmp/biobb/unitests_21/imod_imc/imod_imc_log.out:cmd_wrapper.py:33 cd aa443a40-1dde-45eb-b8ee-25085e1ac3be ; imc structure_cleaned.pdb imod_imode_evecs.dat -o imod_ensemble -c 10 -n 10 -a 6.0\n\nINFO     /tmp/biobb/unitests_21/imod_imc/imod_imc_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_21/imod_imc/imod_imc_log.out:cmd_wrapper.py:52 imc&amp;gt;\nimc&amp;gt; Monte-Carlo IC-NMA based program v1.11\nimc&amp;gt;\nimc&amp;gt; Reading Input PDB file\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimc&amp;gt; Formatting pdb names\nimc&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimc&amp;gt; Selected model number of (pseudo)atoms: 716\nimc&amp;gt; Opening output trajectory file: imod_ensemble.pdb\nimc&amp;gt; Number of Dihedral angles: 168\nimc&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimc&amp;gt; Predicted number of ICs (Eckart): 168\nimc&amp;gt; Number of ICs predicted by seg_props(): 168\nimc&amp;gt; Ptraj info: imod_imode_evecs.dat  vectors=20  components=168\nimc&amp;gt; Number of used modes: 10\nimc&amp;gt; Monte-Carlo stage using Ef= 1.000000\nimc&amp;gt; Frame     1  Etot= 2.814298 0.00 sec\rimc&amp;gt; Frame     2  Etot= 1.481835 0.00 sec\rimc&amp;gt; Frame     3  Etot= 2.017057 0.00 sec\rimc&amp;gt; Frame     4  Etot= 3.779804 0.00 sec\rimc&amp;gt; Frame     5  Etot= 2.140620 0.01 sec\rimc&amp;gt; Frame     6  Etot= 2.771852 0.00 sec\rimc&amp;gt; Frame     7  Etot= 4.756513 0.00 sec\rimc&amp;gt; Frame     8  Etot= 1.985850 0.00 sec\rimc&amp;gt; Frame     9  Etot= 5.451007 0.00 sec\rimc&amp;gt; Frame    10  Etot= 9.098349 0.00 sec\r\nimc&amp;gt;           Total        0.01 sec\nimc&amp;gt;\nimc&amp;gt; ACEPTANCE RATIO(%): 39.746025\nimc&amp;gt;\nimc&amp;gt; Success!\nimc&amp;gt; Written MC-trajectory: imod_ensemble.pdb (10 frames)\nimc&amp;gt; Bye!\n\nINFO     /tmp/biobb/unitests_21/imod_imc/imod_imc_log.out:file_utils.py:390 Removed: [&amp;#x27;aa443a40-1dde-45eb-b8ee-25085e1ac3be&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imode.py::TestImodImode::test_imod_imode&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imode.py::TestImodImode::test_imod_imode&#34;, &#34;duration&#34;: &#34;57 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_flexdyn/test/unitests/test_flexdyn/test_imod_imode.py::TestImodImode::test_imod_imode&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;57 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 -----------------------------\n2024-05-07 09:12:51,790 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.imod_imode Version: 4.1.0\n2024-05-07 09:12:51,790 [MainThread  ] [INFO ]  Creating a2453e7c-6a56-4d2e-a0d9-f8e5e4adf103 temporary folder\n2024-05-07 09:12:51,790 [MainThread  ] [INFO ]  cd a2453e7c-6a56-4d2e-a0d9-f8e5e4adf103 ; imode_gcc structure.pdb -o imods_evecs -m 2\n\n2024-05-07 09:12:51,830 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 09:12:51,831 [MainThread  ] [INFO ]  imode&amp;gt;\nimode&amp;gt; Welcome to the NMA in Internal Coordinates tool v1.20\nimode&amp;gt;\nParser&amp;gt; Using eigensolver: 1 \nimode&amp;gt; Reading PDB file: structure.pdb\nimode&amp;gt; Deleting Hydrogen atoms (if any)...\nimode&amp;gt; Deleting Water molecules (if any)...\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimode&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimode&amp;gt; Selected model residues: 85\nimode&amp;gt; Selected model (pseudo)atoms: 716\nimode&amp;gt; Number of Dihedral angles: 168\nimode&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimode&amp;gt; Predicted number of ICs (Eckart): 168\nimode&amp;gt; Number of ICs predicted by seg_props(): 168\nimode&amp;gt; Range of computed modes: 1-20\nimode&amp;gt; Creating pairwise interaction potential:\nimode&amp;gt; Inverse Exponential (37284 nipas) cutoff= 10.0, k= 1.000000, x0= 3.8 (0.006926 s)\nimode&amp;gt; Packed-Hessian/Kinetic matrices mem.= 0.114 Mb (rank= 168)\nimode&amp;gt; Fast Hessian Matrix Building O(n^2) [hessianMFAx()] 0.005672 s\nimode&amp;gt; Fast Kinetic-Energy matrix Building O(n^2) [kineticMFAx()] 0.000794 s\nimode&amp;gt; Eigenvector matrix mem. = 0.027 Mb\nimode&amp;gt; Diagonalization with ARPACK-based dsdrv1_AP_BP_W_mon()... 0.011424 s\nimode&amp;gt; Showing the first 10 eigenvalues:\nimode&amp;gt;\nimode&amp;gt; MODE   EIGENVALUE\nimode&amp;gt;    1  2.05448e-05\nimode&amp;gt;    2  5.46551e-05\nimode&amp;gt;    3  1.57342e-04\nimode&amp;gt;    4  3.81292e-04\nimode&amp;gt;    5  6.05538e-04\nimode&amp;gt;    6  1.41292e-03\nimode&amp;gt;    7  2.48869e-03\nimode&amp;gt;    8  3.14694e-03\nimode&amp;gt;    9  4.44243e-03\nimode&amp;gt;   10  5.40564e-03\nimode&amp;gt;\nimode&amp;gt;\nimode&amp;gt; SAVED FILES:\nimode&amp;gt; Log file:                                                imods_evecs.log\nimode&amp;gt; Model PDB:                                         imods_evecs_model.pdb\nimode&amp;gt; ICS eigenvectors:                                    imods_evecs_ic.evec\nimode&amp;gt;\nimode&amp;gt; Bye!\n\n2024-05-07 09:12:51,831 [MainThread  ] [INFO ]  Removed: [&amp;#x27;a2453e7c-6a56-4d2e-a0d9-f8e5e4adf103&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/imod_imode/imod_imode_evecs.dat\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/imod_imode/imod_imode_log.out:file_utils.py:390 Executing biobb_flexdyn.flexdyn.imod_imode Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/imod_imode/imod_imode_log.out:file_utils.py:390 Creating a2453e7c-6a56-4d2e-a0d9-f8e5e4adf103 temporary folder\nINFO     /tmp/biobb/unitests_21/imod_imode/imod_imode_log.out:cmd_wrapper.py:33 cd a2453e7c-6a56-4d2e-a0d9-f8e5e4adf103 ; imode_gcc structure.pdb -o imods_evecs -m 2\n\nINFO     /tmp/biobb/unitests_21/imod_imode/imod_imode_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_21/imod_imode/imod_imode_log.out:cmd_wrapper.py:52 imode&amp;gt;\nimode&amp;gt; Welcome to the NMA in Internal Coordinates tool v1.20\nimode&amp;gt;\nParser&amp;gt; Using eigensolver: 1 \nimode&amp;gt; Reading PDB file: structure.pdb\nimode&amp;gt; Deleting Hydrogen atoms (if any)...\nimode&amp;gt; Deleting Water molecules (if any)...\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimode&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimode&amp;gt; Selected model residues: 85\nimode&amp;gt; Selected model (pseudo)atoms: 716\nimode&amp;gt; Number of Dihedral angles: 168\nimode&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimode&amp;gt; Predicted number of ICs (Eckart): 168\nimode&amp;gt; Number of ICs predicted by seg_props(): 168\nimode&amp;gt; Range of computed modes: 1-20\nimode&amp;gt; Creating pairwise interaction potential:\nimode&amp;gt; Inverse Exponential (37284 nipas) cutoff= 10.0, k= 1.000000, x0= 3.8 (0.006926 s)\nimode&amp;gt; Packed-Hessian/Kinetic matrices mem.= 0.114 Mb (rank= 168)\nimode&amp;gt; Fast Hessian Matrix Building O(n^2) [hessianMFAx()] 0.005672 s\nimode&amp;gt; Fast Kinetic-Energy matrix Building O(n^2) [kineticMFAx()] 0.000794 s\nimode&amp;gt; Eigenvector matrix mem. = 0.027 Mb\nimode&amp;gt; Diagonalization with ARPACK-based dsdrv1_AP_BP_W_mon()... 0.011424 s\nimode&amp;gt; Showing the first 10 eigenvalues:\nimode&amp;gt;\nimode&amp;gt; MODE   EIGENVALUE\nimode&amp;gt;    1  2.05448e-05\nimode&amp;gt;    2  5.46551e-05\nimode&amp;gt;    3  1.57342e-04\nimode&amp;gt;    4  3.81292e-04\nimode&amp;gt;    5  6.05538e-04\nimode&amp;gt;    6  1.41292e-03\nimode&amp;gt;    7  2.48869e-03\nimode&amp;gt;    8  3.14694e-03\nimode&amp;gt;    9  4.44243e-03\nimode&amp;gt;   10  5.40564e-03\nimode&amp;gt;\nimode&amp;gt;\nimode&amp;gt; SAVED FILES:\nimode&amp;gt; Log file:                                                imods_evecs.log\nimode&amp;gt; Model PDB:                                         imods_evecs_model.pdb\nimode&amp;gt; ICS eigenvectors:                                    imods_evecs_ic.evec\nimode&amp;gt;\nimode&amp;gt; Bye!\n\nINFO     /tmp/biobb/unitests_21/imod_imode/imod_imode_log.out:file_utils.py:390 Removed: [&amp;#x27;a2453e7c-6a56-4d2e-a0d9-f8e5e4adf103&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imove.py::TestImodImove::test_imod_imove&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imove.py::TestImodImove::test_imod_imove&#34;, &#34;duration&#34;: &#34;447 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_flexdyn/test/unitests/test_flexdyn/test_imod_imove.py::TestImodImove::test_imod_imove&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;447 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 -----------------------------\n2024-05-07 09:12:51,849 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.imod_imove Version: 4.1.0\n2024-05-07 09:12:51,849 [MainThread  ] [INFO ]  Creating 93b7705c-5f93-4dc7-8408-a49f0b3042f1 temporary folder\n2024-05-07 09:12:51,850 [MainThread  ] [INFO ]  cd 93b7705c-5f93-4dc7-8408-a49f0b3042f1 ; imove structure_cleaned.pdb imod_imode_evecs.dat imod_imove_output.pdb 1 -c 11\n\n2024-05-07 09:12:51,877 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 09:12:51,877 [MainThread  ] [INFO ]  imove&amp;gt;\nimove&amp;gt; Welcome to the Internal Coordinates Motion Tool v1.14\nimove&amp;gt;\nimove&amp;gt; Input PDB-file structure_cleaned.pdb\nimove&amp;gt; Multi-PDB output file imod_imove_output.pdb\nimove&amp;gt; Number of frames to be generated 11\nimove&amp;gt; Normal Mode choosen 1\nimove&amp;gt; Reading PDB file structure_cleaned.pdb\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimove&amp;gt; Formatting residues names\nimove&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimove&amp;gt; Ptraj info: imod_imode_evecs.dat  vectors=20  components=168\nimove&amp;gt; Maximum internal coordinate amplitude: 761.802917\nimove&amp;gt; Selected model number of residues: 85\nimove&amp;gt; Number of Dihedral angles: 168\nimove&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimove&amp;gt; Predicted number of ICs (Eckart): 168\nimove&amp;gt; Number of ICs predicted by seg_props(): 168\nimove&amp;gt; Moving analiticaly (moving internal coordinates)\nimove&amp;gt; Added frame    -5 to Multi-PDB\nimove&amp;gt; Added frame    -4 to Multi-PDB\nimove&amp;gt; Added frame    -3 to Multi-PDB\nimove&amp;gt; Added frame    -2 to Multi-PDB\nimove&amp;gt; Added frame    -1 to Multi-PDB\nimove&amp;gt; Added frame     0 to Multi-PDB &amp;lt;-- 1st model (structure_cleaned.pdb)\nimove&amp;gt; Added frame     1 to Multi-PDB\nimove&amp;gt; Added frame     2 to Multi-PDB\nimove&amp;gt; Added frame     3 to Multi-PDB\nimove&amp;gt; Added frame     4 to Multi-PDB\nimove&amp;gt; Added frame     5 to Multi-PDB\nimove&amp;gt;\nimove&amp;gt; Success!\nimove&amp;gt; Written movie: imod_imove_output.pdb (11 frames)\nimove&amp;gt; Bye!\n\n2024-05-07 09:12:51,878 [MainThread  ] [INFO ]  Removed: [&amp;#x27;93b7705c-5f93-4dc7-8408-a49f0b3042f1&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/imod_imove/imod_imove_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_21/imod_imove/imod_imove_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/reference/flexdyn/imod_imove_output.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 716\n     Atoms ALIGNED in PDB_B: 716\n     RMS: 3.73364302621313e-05\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/imod_imove/imod_imove_log.out:file_utils.py:390 Executing biobb_flexdyn.flexdyn.imod_imove Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/imod_imove/imod_imove_log.out:file_utils.py:390 Creating 93b7705c-5f93-4dc7-8408-a49f0b3042f1 temporary folder\nINFO     /tmp/biobb/unitests_21/imod_imove/imod_imove_log.out:cmd_wrapper.py:33 cd 93b7705c-5f93-4dc7-8408-a49f0b3042f1 ; imove structure_cleaned.pdb imod_imode_evecs.dat imod_imove_output.pdb 1 -c 11\n\nINFO     /tmp/biobb/unitests_21/imod_imove/imod_imove_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_21/imod_imove/imod_imove_log.out:cmd_wrapper.py:52 imove&amp;gt;\nimove&amp;gt; Welcome to the Internal Coordinates Motion Tool v1.14\nimove&amp;gt;\nimove&amp;gt; Input PDB-file structure_cleaned.pdb\nimove&amp;gt; Multi-PDB output file imod_imove_output.pdb\nimove&amp;gt; Number of frames to be generated 11\nimove&amp;gt; Normal Mode choosen 1\nimove&amp;gt; Reading PDB file structure_cleaned.pdb\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimove&amp;gt; Formatting residues names\nimove&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimove&amp;gt; Ptraj info: imod_imode_evecs.dat  vectors=20  components=168\nimove&amp;gt; Maximum internal coordinate amplitude: 761.802917\nimove&amp;gt; Selected model number of residues: 85\nimove&amp;gt; Number of Dihedral angles: 168\nimove&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimove&amp;gt; Predicted number of ICs (Eckart): 168\nimove&amp;gt; Number of ICs predicted by seg_props(): 168\nimove&amp;gt; Moving analiticaly (moving internal coordinates)\nimove&amp;gt; Added frame    -5 to Multi-PDB\nimove&amp;gt; Added frame    -4 to Multi-PDB\nimove&amp;gt; Added frame    -3 to Multi-PDB\nimove&amp;gt; Added frame    -2 to Multi-PDB\nimove&amp;gt; Added frame    -1 to Multi-PDB\nimove&amp;gt; Added frame     0 to Multi-PDB &amp;lt;-- 1st model (structure_cleaned.pdb)\nimove&amp;gt; Added frame     1 to Multi-PDB\nimove&amp;gt; Added frame     2 to Multi-PDB\nimove&amp;gt; Added frame     3 to Multi-PDB\nimove&amp;gt; Added frame     4 to Multi-PDB\nimove&amp;gt; Added frame     5 to Multi-PDB\nimove&amp;gt;\nimove&amp;gt; Success!\nimove&amp;gt; Written movie: imod_imove_output.pdb (11 frames)\nimove&amp;gt; Bye!\n\nINFO     /tmp/biobb/unitests_21/imod_imove/imod_imove_log.out:file_utils.py:390 Removed: [&amp;#x27;93b7705c-5f93-4dc7-8408-a49f0b3042f1&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_nolb.py::TestNolb_nma::test_nolb_nma&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_nolb.py::TestNolb_nma::test_nolb_nma&#34;, &#34;duration&#34;: &#34;437 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_flexdyn/test/unitests/test_flexdyn/test_nolb.py::TestNolb_nma::test_nolb_nma&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;437 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 -----------------------------\n2024-05-07 09:12:52,299 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.nolb_nma Version: 4.1.0\n2024-05-07 09:12:52,299 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_21/nolb_nma/5541dde1-fe49-4a97-ab72-f535634ed705\n2024-05-07 09:12:52,300 [MainThread  ] [INFO ]  NOLB 5541dde1-fe49-4a97-ab72-f535634ed705/structure.pdb -o /tmp/biobb/unitests_21/nolb_nma/5541dde1-fe49-4a97-ab72-f535634ed705/nolb_ensemble -m -s 20 -c 5.0 --rmsd 1.0 --dist 1 --nSteps 5000 --tol 0.001\n\n2024-05-07 09:12:52,715 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 09:12:52,716 [MainThread  ] [INFO ]  *******************************************************************\n*-----------------------------------------------------------------*\n*-----------NOLB : a Non-Linear rigid block NMA method------------*\n*----------Authors: Alexandre Hoffmann &amp;amp; Sergei Grudinin----------*\n*-Copyright (c): Nano-D team, Inria/CNRS Grenoble, France, 2019.--*\n*--------------- e-mail: sergei.grudinin@inria.fr ----------------*\n*---- http://team.inria.fr/nano-d/software/nolb-normal-modes/ ----*\n*-----------------------------------------------------------------*\n*******************************************************************\nHostname......................................................... : biobb-runners\nRun at........................................................... : Tue May  7 09:12:52 2024\nCommand-line arguments........................................... : NOLB 5541dde1-fe49-4a97-ab72-f535634ed705/structure.pdb -o /tmp/biobb/unitests_21/nolb_nma/5541dde1-fe49-4a97-ab72-f535634ed705/nolb_ensemble -m -s 20 -c 5.0 --rmsd 1.0 --dist 1 --nSteps 5000 --tol 0.001 \n=====================Reading input PDB file======================\nInput PDB file................................................... : 5541dde1-fe49-4a97-ab72-f535634ed705/structure.pdb\nNumber of chains read............................................ : 2\nNumber of atoms read............................................. : 716\nFound............................................................ : 724 covalent bonds\n................................................................. : 966 angles\n======================Constructing Hessian=======================\nNumber of disconnected atoms..................................... : 0\nNumber of interactions........................................... : 16156\nInteraction cutoff distance...................................... : 5 A\nMemory required for the Hessian matrix........................... : 3.32803 Mb\nAll-atom Hessian size : ......................................... : 2148 x 2148\n============================Doing NMA============================\nMemory required for the RTB projection matrix.................... : 0.196655 Mb\nReduced Hessian size : .......................................... : 510 x 510\nNumber of computed modes......................................... : 10 \nNull-space size.................................................. : 1 \nLowest mode frequency............................................ : 7.08086e-05 \nHighest mode frequency........................................... : 0.0017141 \nFrequencies :\n            [ 1]................................................. : 7.08086e-05 \n            [ 2]................................................. : 9.22104e-05 \n            [ 3]................................................. : 0.000160579 \n            [ 4]................................................. : 0.000271988 \n            [ 5]................................................. : 0.000359596 \n            [ 6]................................................. : 0.000917588 \n            [ 7]................................................. : 0.00102481 \n            [ 8]................................................. : 0.00123429 \n            [ 9]................................................. : 0.0013176 \n            [10]................................................. : 0.0017141 \n===================Writing output Decoy files====================\nNumber of files.................................................. : 20\nOutput RMSD...................................................... : 1 A\nUsing outputfilename............................................. : /tmp/biobb/unitests_21/nolb_nma/5541dde1-fe49-4a97-ab72-f535634ed705/nolb_ensemble_nlb_decoys.pdb\nCurrent energy................................................... : 0.000802458\nN minimization steps............................................. : 17\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.838698\nCurrent energy................................................... : 0.000492936\nN minimization steps............................................. : 36\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.660651\nCurrent energy................................................... : 0.000204576\nN minimization steps............................................. : 18\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.138729\nCurrent energy................................................... : 0.000755071\nN minimization steps............................................. : 28\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.304596\nCurrent energy................................................... : 0.000423189\nN minimization steps............................................. : 24\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.289287\nCurrent energy................................................... : 0.000490861\nN minimization steps............................................. : 26\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.348679\nCurrent energy................................................... : 0.000536261\nN minimization steps............................................. : 33\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.373157\nCurrent energy................................................... : 0.000600031\nN minimization steps............................................. : 49\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.724211\nCurrent energy................................................... : 0.000574138\nN minimization steps............................................. : 34\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.361212\nCurrent energy................................................... : 0.000721136\nN minimization steps............................................. : 69\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.924134\nCurrent energy................................................... : 0.00116361\nN minimization steps............................................. : 50\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.834636\nCurrent energy................................................... : 0.000324975\nN minimization steps............................................. : 17\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.127239\nCurrent energy................................................... : 0.000960058\nN minimization steps............................................. : 52\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.618944\nCurrent energy................................................... : 0.000619613\nN minimization steps............................................. : 65\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.55831\nCurrent energy................................................... : 0.000841583\nN minimization steps............................................. : 56\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.569489\nCurrent energy................................................... : 0.000284024\nN minimization steps............................................. : 25\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.23718\nCurrent energy................................................... : 0.000582824\nN minimization steps............................................. : 21\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.154705\nCurrent energy................................................... : 0.000723304\nN minimization steps............................................. : 66\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.793648\nCurrent energy................................................... : 0.00122979\nN minimization steps............................................. : 57\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.887673\nCurrent energy................................................... : 0.000270424\nN minimization steps............................................. : 18\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.0829017\n=================================================================\n=========================== Timing : ============================\n=================================================================\nParsing arguments................................................ : 0.000215888 s\nReading input PDB file........................................... : 0.0018925 s\nConstructing Hessian............................................. : 0.0102495 s\nDoing NMA........................................................ : 0.0571819 s\nWriting output Decoy files....................................... : 0.336817 s\n.................................................................\nTotal time : .................................................... : 0.406357 s\n=================================================================\n\nMain Reference: Alexandre Hoffmann &amp;amp; Sergei Grudinin. NOLB : Nonlinear rigid block normal mode analysis method. Journal of Chemical Theory and Computation, 2017, 13 (5), pp.2123-2134. DOI: 10.1021/acs.jctc.7b00197.\n\nReference for clustering and decoy generation: Emilie Neveu, Petr Popov, Alexandre Hoffmann, Angelo Migliosi, Xavier Besseron, Gregoire Danoy, Pascal Bouvry, Sergei Grudinin. RapidRMSD: Rapid determination of RMSDs corresponding to motions of flexible molecules. Bioinformatics, Oxford University Press (OUP), 2018. DOI: 10.1093/bioinformatics/bty160.\n\n\n2024-05-07 09:12:52,719 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/nolb_nma/5541dde1-fe49-4a97-ab72-f535634ed705&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/nolb_nma/nolb_output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/nolb_nma/nolb_nma_log.out:file_utils.py:390 Executing biobb_flexdyn.flexdyn.nolb_nma Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/nolb_nma/nolb_nma_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_21/nolb_nma/5541dde1-fe49-4a97-ab72-f535634ed705\nINFO     /tmp/biobb/unitests_21/nolb_nma/nolb_nma_log.out:cmd_wrapper.py:33 NOLB 5541dde1-fe49-4a97-ab72-f535634ed705/structure.pdb -o /tmp/biobb/unitests_21/nolb_nma/5541dde1-fe49-4a97-ab72-f535634ed705/nolb_ensemble -m -s 20 -c 5.0 --rmsd 1.0 --dist 1 --nSteps 5000 --tol 0.001\n\nINFO     /tmp/biobb/unitests_21/nolb_nma/nolb_nma_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_21/nolb_nma/nolb_nma_log.out:cmd_wrapper.py:52 *******************************************************************\n*-----------------------------------------------------------------*\n*-----------NOLB : a Non-Linear rigid block NMA method------------*\n*----------Authors: Alexandre Hoffmann &amp;amp; Sergei Grudinin----------*\n*-Copyright (c): Nano-D team, Inria/CNRS Grenoble, France, 2019.--*\n*--------------- e-mail: sergei.grudinin@inria.fr ----------------*\n*---- http://team.inria.fr/nano-d/software/nolb-normal-modes/ ----*\n*-----------------------------------------------------------------*\n*******************************************************************\nHostname......................................................... : biobb-runners\nRun at........................................................... : Tue May  7 09:12:52 2024\nCommand-line arguments........................................... : NOLB 5541dde1-fe49-4a97-ab72-f535634ed705/structure.pdb -o /tmp/biobb/unitests_21/nolb_nma/5541dde1-fe49-4a97-ab72-f535634ed705/nolb_ensemble -m -s 20 -c 5.0 --rmsd 1.0 --dist 1 --nSteps 5000 --tol 0.001 \n=====================Reading input PDB file======================\nInput PDB file................................................... : 5541dde1-fe49-4a97-ab72-f535634ed705/structure.pdb\nNumber of chains read............................................ : 2\nNumber of atoms read............................................. : 716\nFound............................................................ : 724 covalent bonds\n................................................................. : 966 angles\n======================Constructing Hessian=======================\nNumber of disconnected atoms..................................... : 0\nNumber of interactions........................................... : 16156\nInteraction cutoff distance...................................... : 5 A\nMemory required for the Hessian matrix........................... : 3.32803 Mb\nAll-atom Hessian size : ......................................... : 2148 x 2148\n============================Doing NMA============================\nMemory required for the RTB projection matrix.................... : 0.196655 Mb\nReduced Hessian size : .......................................... : 510 x 510\nNumber of computed modes......................................... : 10 \nNull-space size.................................................. : 1 \nLowest mode frequency............................................ : 7.08086e-05 \nHighest mode frequency........................................... : 0.0017141 \nFrequencies :\n            [ 1]................................................. : 7.08086e-05 \n            [ 2]................................................. : 9.22104e-05 \n            [ 3]................................................. : 0.000160579 \n            [ 4]................................................. : 0.000271988 \n            [ 5]................................................. : 0.000359596 \n            [ 6]................................................. : 0.000917588 \n            [ 7]................................................. : 0.00102481 \n            [ 8]................................................. : 0.00123429 \n            [ 9]................................................. : 0.0013176 \n            [10]................................................. : 0.0017141 \n===================Writing output Decoy files====================\nNumber of files.................................................. : 20\nOutput RMSD...................................................... : 1 A\nUsing outputfilename............................................. : /tmp/biobb/unitests_21/nolb_nma/5541dde1-fe49-4a97-ab72-f535634ed705/nolb_ensemble_nlb_decoys.pdb\nCurrent energy................................................... : 0.000802458\nN minimization steps............................................. : 17\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.838698\nCurrent energy................................................... : 0.000492936\nN minimization steps............................................. : 36\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.660651\nCurrent energy................................................... : 0.000204576\nN minimization steps............................................. : 18\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.138729\nCurrent energy................................................... : 0.000755071\nN minimization steps............................................. : 28\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.304596\nCurrent energy................................................... : 0.000423189\nN minimization steps............................................. : 24\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.289287\nCurrent energy................................................... : 0.000490861\nN minimization steps............................................. : 26\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.348679\nCurrent energy................................................... : 0.000536261\nN minimization steps............................................. : 33\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.373157\nCurrent energy................................................... : 0.000600031\nN minimization steps............................................. : 49\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.724211\nCurrent energy................................................... : 0.000574138\nN minimization steps............................................. : 34\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.361212\nCurrent energy................................................... : 0.000721136\nN minimization steps............................................. : 69\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.924134\nCurrent energy................................................... : 0.00116361\nN minimization steps............................................. : 50\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.834636\nCurrent energy................................................... : 0.000324975\nN minimization steps............................................. : 17\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.127239\nCurrent energy................................................... : 0.000960058\nN minimization steps............................................. : 52\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.618944\nCurrent energy................................................... : 0.000619613\nN minimization steps............................................. : 65\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.55831\nCurrent energy................................................... : 0.000841583\nN minimization steps............................................. : 56\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.569489\nCurrent energy................................................... : 0.000284024\nN minimization steps............................................. : 25\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.23718\nCurrent energy................................................... : 0.000582824\nN minimization steps............................................. : 21\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.154705\nCurrent energy................................................... : 0.000723304\nN minimization steps............................................. : 66\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.793648\nCurrent energy................................................... : 0.00122979\nN minimization steps............................................. : 57\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.887673\nCurrent energy................................................... : 0.000270424\nN minimization steps............................................. : 18\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.0829017\n=================================================================\n=========================== Timing : ============================\n=================================================================\nParsing arguments................................................ : 0.000215888 s\nReading input PDB file........................................... : 0.0018925 s\nConstructing Hessian............................................. : 0.0102495 s\nDoing NMA........................................................ : 0.0571819 s\nWriting output Decoy files....................................... : 0.336817 s\n.................................................................\nTotal time : .................................................... : 0.406357 s\n=================================================================\n\nMain Reference: Alexandre Hoffmann &amp;amp; Sergei Grudinin. NOLB : Nonlinear rigid block normal mode analysis method. Journal of Chemical Theory and Computation, 2017, 13 (5), pp.2123-2134. DOI: 10.1021/acs.jctc.7b00197.\n\nReference for clustering and decoy generation: Emilie Neveu, Petr Popov, Alexandre Hoffmann, Angelo Migliosi, Xavier Besseron, Gregoire Danoy, Pascal Bouvry, Sergei Grudinin. RapidRMSD: Rapid determination of RMSDs corresponding to motions of flexible molecules. Bioinformatics, Oxford University Press (OUP), 2018. DOI: 10.1093/bioinformatics/bty160.\n\n\nINFO     /tmp/biobb/unitests_21/nolb_nma/nolb_nma_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/nolb_nma/5541dde1-fe49-4a97-ab72-f535634ed705&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_prody_anm.py::TestProdyANM::test_prody_anm&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_prody_anm.py::TestProdyANM::test_prody_anm&#34;, &#34;duration&#34;: &#34;315 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_flexdyn/test/unitests/test_flexdyn/test_prody_anm.py::TestProdyANM::test_prody_anm&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;315 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 -----------------------------\n2024-05-07 09:12:52,738 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.prody_anm Version: 4.1.0\n2024-05-07 09:12:52,739 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_21/prody_anm/23f1371f-f677-4905-9a57-d14e6cfad5a3\n2024-05-07 09:12:52,855 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/prody_anm/23f1371f-f677-4905-9a57-d14e6cfad5a3&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/prody_anm/prody_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_21/prody_anm/prody_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/reference/flexdyn/prody_output.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 85\n     Atoms ALIGNED in PDB_B: 85\n     RMS: 8.764934491121054e-15\n     RMS_CUTOFF: 1\n\n----------------------------- Captured stderr call -----------------------------\n@&amp;gt; 775 atoms and 1 coordinate set(s) were parsed in 0.02s.\n@&amp;gt; Hessian was built in 0.02s.\n@&amp;gt; 20 modes were calculated in 0.03s.\n@&amp;gt; Parameter: rmsd = 4.00 A\n@&amp;gt; Parameter: n_confs = 20\n@&amp;gt; Modes are scaled by 2.6167870077633855.\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/prody_anm/prody_anm_log.out:file_utils.py:390 Executing biobb_flexdyn.flexdyn.prody_anm Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/prody_anm/prody_anm_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_21/prody_anm/23f1371f-f677-4905-9a57-d14e6cfad5a3\nDEBUG    .prody:logger.py:135 775 atoms and 1 coordinate set(s) were parsed in 0.02s.\nDEBUG    .prody:logger.py:135 Hessian was built in 0.02s.\nDEBUG    .prody:logger.py:135 20 modes were calculated in 0.03s.\nINFO     .prody:logger.py:123 Parameter: rmsd = 4.00 A\nINFO     .prody:logger.py:123 Parameter: n_confs = 20\nINFO     .prody:logger.py:123 Modes are scaled by 2.6167870077633855.\nINFO     /tmp/biobb/unitests_21/prody_anm/prody_anm_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/prody_anm/23f1371f-f677-4905-9a57-d14e6cfad5a3&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\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_flexdyn/test/unitests/test_flexdyn/test_concoord_disco.py::TestConcoordDisco::test_concoord_disco&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_concoord_disco.py::TestConcoordDisco::test_concoord_disco&#34;, &#34;duration&#34;: &#34;00:00:06&#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_flexdyn/test/unitests/test_flexdyn/test_concoord_disco.py::TestConcoordDisco::test_concoord_disco&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:06&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:47:10,640 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.concoord_disco Version: 4.1.0\n2024-05-24 09:47:10,640 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_43/concoord_disco/4290e9e5-b287-4809-b5f2-7ad0b1caf3f0\n2024-05-24 09:47:10,642 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/dist.dat to /tmp/biobb/unitests_43/concoord_disco/4290e9e5-b287-4809-b5f2-7ad0b1caf3f0\n2024-05-24 09:47:10,643 [MainThread  ] [INFO ]  cd  /tmp/biobb/unitests_43/concoord_disco/4290e9e5-b287-4809-b5f2-7ad0b1caf3f0 ; disco -p structure.pdb -d dist.dat -or concoord_disco_rmsd.dat -of concoord_disco_bfactor.pdb -on concoord_disco.pdb -n 20\n\n2024-05-24 09:47:16,485 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-24 09:47:16,486 [MainThread  ] [INFO ]  Determining system size...\n-------------------------------------------------\ndisco - version 2.1.2 - build date: Thu Jan 24 11:26:08 CET 2013                                \nProcess started with PID:  2423610\non host: biobb-runners\nnumber of threads =    4\nin directory: /tmp/biobb/unitests_43/concoord_disco/4290e9e5-b287-4809-b5f2-7ad0b1caf3f0\non: 24/05/0024 at: 09:47:10\n-------------------------------------------------\ncommand line options:\ninput coordinates...................: structure.pdb                           \ndistance constraints................: dist.dat                                \nnr of structures to be generated....:      20\nmaximum nr of iterations............:    2500\nmaximum nr of trials................:      25\nmaximal sum of violations...........:    1.00000\noutput NMR-PDB file.................: concoord_disco.pdb                      \noutput RMSD values..................: concoord_disco_rmsd.dat                 \noutput atomic fluctuations..........: concoord_disco_bfactor.pdb              \nchirality corrections will be performed on the fly\nNr. of rounds of bound smoothing....:       0\nDamping factor (converted)..........:    1.00000\nprocessing input...\nnumber of atoms.....................:     775\nnumber of residues..................:     144\nnumber of chiral centers to check...:     106\nnumber of planar groups to check....:     124\nsorting distances...\nnumber of read distances............:   25223\nnumber of angles....................:     966\ntotal number of read distances......:   25223\nNr of input violations:      44\nSum of input violations: 0.10774E-03 nm\nSum of input bumps: 0.00000E+00 nm\nperc. of total nr of distances......:    8.41\nUncertainty sum/average:  0.13517E+05 0.53589E+00 nm\nParallel operation, number of threads =    4\nOverride by setting the environment variable OMP_NUM_THREADS\ngenerated structure.................:       1 with RMSD  2.87 A\nNr. of violations...................:     203\nSum of violations...................:    0.34908\ngenerated structure.................:       2 with RMSD  2.39 A\nNr. of violations...................:     183\nSum of violations...................:    0.32294\ngenerated structure.................:       3 with RMSD  2.14 A\nNr. of violations...................:     180\nSum of violations...................:    0.33313\nGiving up, best violation sum was...:  12.66167\nstructure rejected (no convergence after    606 steps)\nGiving up, best violation sum was...:   0.89863\nstructure rejected (no convergence after    603 steps)\nGiving up, best violation sum was...:  13.30915\nstructure rejected (no convergence after    940 steps)\ngenerated structure.................:       4 with RMSD  2.47 A\nNr. of violations...................:     191\nSum of violations...................:    0.36691\ngenerated structure.................:       5 with RMSD  1.43 A\nNr. of violations...................:     148\nSum of violations...................:    0.22789\ngenerated structure.................:       6 with RMSD  2.82 A\nNr. of violations...................:     199\nSum of violations...................:    0.34200\ngenerated structure.................:       7 with RMSD  2.07 A\nNr. of violations...................:     164\nSum of violations...................:    0.26734\ngenerated structure.................:       8 with RMSD  2.51 A\nNr. of violations...................:     182\nSum of violations...................:    0.32628\nGiving up, best violation sum was...:   6.15732\nstructure rejected (no convergence after   1070 steps)\ngenerated structure.................:       9 with RMSD  3.57 A\nNr. of violations...................:     185\nSum of violations...................:    0.32794\nGiving up, best violation sum was...:   7.77156\nstructure rejected (no convergence after    990 steps)\nGiving up, best violation sum was...:   4.55957\nstructure rejected (no convergence after    610 steps)\nGiving up, best violation sum was...:   2.89941\nstructure rejected (no convergence after    601 steps)\ngenerated structure.................:      10 with RMSD  1.77 A\nNr. of violations...................:     189\nSum of violations...................:    0.31135\nGiving up, best violation sum was...:  14.66847\nstructure rejected (no convergence after   1159 steps)\nGiving up, best violation sum was...:  12.75521\nstructure rejected (no convergence after    750 steps)\ngenerated structure.................:      11 with RMSD  3.39 A\nNr. of violations...................:     211\nSum of violations...................:    0.30720\ngenerated structure.................:      12 with RMSD  1.74 A\nNr. of violations...................:     189\nSum of violations...................:    0.34857\nGiving up, best violation sum was...:   0.94540\nstructure rejected (no convergence after    609 steps)\nGiving up, best violation sum was...:   1.02614\nstructure rejected (no convergence after    606 steps)\nGiving up, best violation sum was...:   1.17588\nstructure rejected (no convergence after    609 steps)\ngenerated structure.................:      13 with RMSD  2.39 A\nNr. of violations...................:     197\nSum of violations...................:    0.37360\nGiving up, best violation sum was...:   0.92332\nstructure rejected (no convergence after    610 steps)\nGiving up, best violation sum was...:  14.51781\nstructure rejected (no convergence after    730 steps)\ngenerated structure.................:      14 with RMSD  2.51 A\nNr. of violations...................:     199\nSum of violations...................:    0.32411\nGiving up, best violation sum was...:   9.83401\nstructure rejected (no convergence after    830 steps)\ngenerated structure.................:      15 with RMSD  3.34 A\nNr. of violations...................:     173\nSum of violations...................:    0.32189\nGiving up, best violation sum was...:  10.80298\nstructure rejected (no convergence after    566 steps)\nGiving up, best violation sum was...:   7.94726\nstructure rejected (no convergence after    581 steps)\nGiving up, best violation sum was...:   1.34604\nstructure rejected (no convergence after    610 steps)\nstructure rejected (no convergence after    193 steps)\ngenerated structure.................:      16 with RMSD  3.37 A\nNr. of violations...................:     206\nSum of violations...................:    0.35689\ngenerated structure.................:      17 with RMSD  2.79 A\nNr. of violations...................:     176\nSum of violations...................:    0.32207\ngenerated structure.................:      18 with RMSD  2.44 A\nNr. of violations...................:     193\nSum of violations...................:    0.36618\ngenerated structure.................:      19 with RMSD  2.16 A\nNr. of violations...................:     189\nSum of violations...................:    0.31926\nGiving up, best violation sum was...:  11.34416\nstructure rejected (no convergence after   1530 steps)\ngenerated structure.................:      20 with RMSD  1.97 A\nNr. of violations...................:     189\nSum of violations...................:    0.33658\nnormal termination\nCPU time: user=     18.60s, system=      0.00s\n\n2024-05-24 09:47:16,488 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_43/concoord_disco/4290e9e5-b287-4809-b5f2-7ad0b1caf3f0&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_43/concoord_disco/concoord_disco.pdb\nChecking if empty file: /tmp/biobb/unitests_43/concoord_disco/concoord_disco_rmsd.dat\nChecking if empty file: /tmp/biobb/unitests_43/concoord_disco/concoord_disco_bfactor.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_43/concoord_disco/concoord_disco_log.out:file_utils.py:391 Executing biobb_flexdyn.flexdyn.concoord_disco Version: 4.1.0\nINFO     /tmp/biobb/unitests_43/concoord_disco/concoord_disco_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_43/concoord_disco/4290e9e5-b287-4809-b5f2-7ad0b1caf3f0\nINFO     /tmp/biobb/unitests_43/concoord_disco/concoord_disco_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/dist.dat to /tmp/biobb/unitests_43/concoord_disco/4290e9e5-b287-4809-b5f2-7ad0b1caf3f0\nINFO     /tmp/biobb/unitests_43/concoord_disco/concoord_disco_log.out:cmd_wrapper.py:33 cd  /tmp/biobb/unitests_43/concoord_disco/4290e9e5-b287-4809-b5f2-7ad0b1caf3f0 ; disco -p structure.pdb -d dist.dat -or concoord_disco_rmsd.dat -of concoord_disco_bfactor.pdb -on concoord_disco.pdb -n 20\n\nINFO     /tmp/biobb/unitests_43/concoord_disco/concoord_disco_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_43/concoord_disco/concoord_disco_log.out:cmd_wrapper.py:52 Determining system size...\n-------------------------------------------------\ndisco - version 2.1.2 - build date: Thu Jan 24 11:26:08 CET 2013                                \nProcess started with PID:  2423610\non host: biobb-runners\nnumber of threads =    4\nin directory: /tmp/biobb/unitests_43/concoord_disco/4290e9e5-b287-4809-b5f2-7ad0b1caf3f0\non: 24/05/0024 at: 09:47:10\n-------------------------------------------------\ncommand line options:\ninput coordinates...................: structure.pdb                           \ndistance constraints................: dist.dat                                \nnr of structures to be generated....:      20\nmaximum nr of iterations............:    2500\nmaximum nr of trials................:      25\nmaximal sum of violations...........:    1.00000\noutput NMR-PDB file.................: concoord_disco.pdb                      \noutput RMSD values..................: concoord_disco_rmsd.dat                 \noutput atomic fluctuations..........: concoord_disco_bfactor.pdb              \nchirality corrections will be performed on the fly\nNr. of rounds of bound smoothing....:       0\nDamping factor (converted)..........:    1.00000\nprocessing input...\nnumber of atoms.....................:     775\nnumber of residues..................:     144\nnumber of chiral centers to check...:     106\nnumber of planar groups to check....:     124\nsorting distances...\nnumber of read distances............:   25223\nnumber of angles....................:     966\ntotal number of read distances......:   25223\nNr of input violations:      44\nSum of input violations: 0.10774E-03 nm\nSum of input bumps: 0.00000E+00 nm\nperc. of total nr of distances......:    8.41\nUncertainty sum/average:  0.13517E+05 0.53589E+00 nm\nParallel operation, number of threads =    4\nOverride by setting the environment variable OMP_NUM_THREADS\ngenerated structure.................:       1 with RMSD  2.87 A\nNr. of violations...................:     203\nSum of violations...................:    0.34908\ngenerated structure.................:       2 with RMSD  2.39 A\nNr. of violations...................:     183\nSum of violations...................:    0.32294\ngenerated structure.................:       3 with RMSD  2.14 A\nNr. of violations...................:     180\nSum of violations...................:    0.33313\nGiving up, best violation sum was...:  12.66167\nstructure rejected (no convergence after    606 steps)\nGiving up, best violation sum was...:   0.89863\nstructure rejected (no convergence after    603 steps)\nGiving up, best violation sum was...:  13.30915\nstructure rejected (no convergence after    940 steps)\ngenerated structure.................:       4 with RMSD  2.47 A\nNr. of violations...................:     191\nSum of violations...................:    0.36691\ngenerated structure.................:       5 with RMSD  1.43 A\nNr. of violations...................:     148\nSum of violations...................:    0.22789\ngenerated structure.................:       6 with RMSD  2.82 A\nNr. of violations...................:     199\nSum of violations...................:    0.34200\ngenerated structure.................:       7 with RMSD  2.07 A\nNr. of violations...................:     164\nSum of violations...................:    0.26734\ngenerated structure.................:       8 with RMSD  2.51 A\nNr. of violations...................:     182\nSum of violations...................:    0.32628\nGiving up, best violation sum was...:   6.15732\nstructure rejected (no convergence after   1070 steps)\ngenerated structure.................:       9 with RMSD  3.57 A\nNr. of violations...................:     185\nSum of violations...................:    0.32794\nGiving up, best violation sum was...:   7.77156\nstructure rejected (no convergence after    990 steps)\nGiving up, best violation sum was...:   4.55957\nstructure rejected (no convergence after    610 steps)\nGiving up, best violation sum was...:   2.89941\nstructure rejected (no convergence after    601 steps)\ngenerated structure.................:      10 with RMSD  1.77 A\nNr. of violations...................:     189\nSum of violations...................:    0.31135\nGiving up, best violation sum was...:  14.66847\nstructure rejected (no convergence after   1159 steps)\nGiving up, best violation sum was...:  12.75521\nstructure rejected (no convergence after    750 steps)\ngenerated structure.................:      11 with RMSD  3.39 A\nNr. of violations...................:     211\nSum of violations...................:    0.30720\ngenerated structure.................:      12 with RMSD  1.74 A\nNr. of violations...................:     189\nSum of violations...................:    0.34857\nGiving up, best violation sum was...:   0.94540\nstructure rejected (no convergence after    609 steps)\nGiving up, best violation sum was...:   1.02614\nstructure rejected (no convergence after    606 steps)\nGiving up, best violation sum was...:   1.17588\nstructure rejected (no convergence after    609 steps)\ngenerated structure.................:      13 with RMSD  2.39 A\nNr. of violations...................:     197\nSum of violations...................:    0.37360\nGiving up, best violation sum was...:   0.92332\nstructure rejected (no convergence after    610 steps)\nGiving up, best violation sum was...:  14.51781\nstructure rejected (no convergence after    730 steps)\ngenerated structure.................:      14 with RMSD  2.51 A\nNr. of violations...................:     199\nSum of violations...................:    0.32411\nGiving up, best violation sum was...:   9.83401\nstructure rejected (no convergence after    830 steps)\ngenerated structure.................:      15 with RMSD  3.34 A\nNr. of violations...................:     173\nSum of violations...................:    0.32189\nGiving up, best violation sum was...:  10.80298\nstructure rejected (no convergence after    566 steps)\nGiving up, best violation sum was...:   7.94726\nstructure rejected (no convergence after    581 steps)\nGiving up, best violation sum was...:   1.34604\nstructure rejected (no convergence after    610 steps)\nstructure rejected (no convergence after    193 steps)\ngenerated structure.................:      16 with RMSD  3.37 A\nNr. of violations...................:     206\nSum of violations...................:    0.35689\ngenerated structure.................:      17 with RMSD  2.79 A\nNr. of violations...................:     176\nSum of violations...................:    0.32207\ngenerated structure.................:      18 with RMSD  2.44 A\nNr. of violations...................:     193\nSum of violations...................:    0.36618\ngenerated structure.................:      19 with RMSD  2.16 A\nNr. of violations...................:     189\nSum of violations...................:    0.31926\nGiving up, best violation sum was...:  11.34416\nstructure rejected (no convergence after   1530 steps)\ngenerated structure.................:      20 with RMSD  1.97 A\nNr. of violations...................:     189\nSum of violations...................:    0.33658\nnormal termination\nCPU time: user=     18.60s, system=      0.00s\n\nINFO     /tmp/biobb/unitests_43/concoord_disco/concoord_disco_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_43/concoord_disco/4290e9e5-b287-4809-b5f2-7ad0b1caf3f0&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_43\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_concoord_dist.py::TestConcoordDist::test_concoord_dist&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_concoord_dist.py::TestConcoordDist::test_concoord_dist&#34;, &#34;duration&#34;: &#34;169 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_flexdyn/test/unitests/test_flexdyn/test_concoord_dist.py::TestConcoordDist::test_concoord_dist&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;169 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 -----------------------------\n2024-05-24 09:47:16,520 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.concoord_dist Version: 4.1.0\n2024-05-24 09:47:16,520 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_43/concoord_dist/a9c79d7d-1a5b-4481-bdd0-b32edff48416\n2024-05-24 09:47:16,521 [MainThread  ] [INFO ]  Copy: /tmp/biobb/unitests_43/concoord_dist/25aa70a0-e950-4422-a757-d8751da5723d.stdin to /tmp/biobb/unitests_43/concoord_dist/a9c79d7d-1a5b-4481-bdd0-b32edff48416\n2024-05-24 09:47:16,521 [MainThread  ] [INFO ]  cd  /tmp/biobb/unitests_43/concoord_dist/a9c79d7d-1a5b-4481-bdd0-b32edff48416 ; dist -op concoord_dist.pdb -og concoord_dist.gro -od concoord_dist.dat -p structure.pdb -c 4.0 -m 50 -damp 1.0 &amp;lt; 25aa70a0-e950-4422-a757-d8751da5723d.stdin\n\n2024-05-24 09:47:16,633 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-24 09:47:16,633 [MainThread  ] [INFO ]  Select a set of Van der Waals parameters:\n1: OPLS-UA (united atoms) parameters\n2: OPLS-AA (all atoms) parameters\n3: PROLSQ repel parameters\n4: Yamber2 parameters\n5: Li et al. parameters\n6: OPLS-X parameters (recommended for NMR structure determination)\nSelected parameter set 1\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/ATOMS_oplsua.DAT to ATOMS.DAT in current working directory\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/MARGINS_oplsua.DAT to MARGINS.DAT in current working directory\nSelect a set of bond/angle parameters:\n1: Concoord default parameters\n2: Engh-Huber parameters\nSelected parameter set 1\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/BONDS.DAT.noeh to BONDS.DAT in current working directory\n-------------------------------------------------\ndist.exe - build date: Thu Jan 24 11:26:08 CET 2013                                \nProcess started with PID:  2423620\non host: biobb-runners\nin directory: /tmp/biobb/unitests_43/concoord_dist/a9c79d7d-1a5b-4481-bdd0-b32edff48416\non: 24/05/0024 at: 09:47:16\n-------------------------------------------------\ncommand line options:\npdb input coordinate file...........: structure.pdb                           \nWARNING WARNING WARNING WARNING WARNING WARNING\nWarning: no dssp calculation will be performed. Expect poor results!\nWARNING WARNING WARNING WARNING WARNING WARNING\nnon-bonded cut-off radius...........:   4.00 A + VDW sum\nminimal nr. of distances per atom...:     50\noutput distances....................: concoord_dist.dat                       \noutput coordinates (PDB)............: concoord_dist.pdb                       \noutput coordinates (GROMOS87).......: concoord_dist.gro                       \nhydrogen atoms (if any) will be removed\nnon-bonded contacts of starting structure will be preserved\nprocessing input...\ntotal number of atoms       :      775\nnumber of residues          :      144\nnumber of atoms to be used  :      775\ncounted    640 intra-residue bonds\ncounted     84 peptide bonds\ncounted      0 disulphide bonds\ncounted      0 histidine-heme bonds\ncounted    724 bonds in total\ncounted    966 1-3 pairs (angles)\ncounted     36 ring restrictions\ncounted      0 omega restrictions\ncounted   1037 other 1-4 restrictions\ncounted      0 hydrogen bonds\ncounted      4 salt bridges\ncounted    142 hydrogen bonds\ncounted    868 side chain restrictions\ncounted      0 sheet restrictions\ncounted  18104 other close pairs\ncounted   3878 more restrictions\ntotal nr of non-bonded pairs:  19118\ntotal number of constraints :   26254\n 1 warning(s) encountered. Please investigate!\n\n2024-05-24 09:47:16,633 [MainThread  ] [INFO ]  remark: distance between atom      31 and      27 (3.11) smaller than VdWsum (3.75)    C    C 0.290\nremark: distance between atom     124 and     122 (2.94) smaller than VdWsum (3.43) CH2E    O 0.141\nremark: distance between atom     159 and     157 (2.90) smaller than VdWsum (3.36)    C    O 0.102\nremark: distance between atom     328 and     324 (3.13) smaller than VdWsum (3.50)  NH1    C 0.022\nremark: distance between atom     383 and     377 (3.22) smaller than VdWsum (3.58) CH2E  NH1 0.008\nremark: distance between atom     383 and     379 (3.36) smaller than VdWsum (3.83) CH2E    C 0.113\nremark: distance between atom     392 and     388 (2.86) smaller than VdWsum (3.36)   OC    C 0.146\nremark: distance between atom     452 and     448 (3.26) smaller than VdWsum (3.78) CH3E    C 0.161\nremark: distance between atom     560 and     555 (3.27) smaller than VdWsum (3.65) CR1E    C 0.028\nremark: distance between atom      18 and      12 (2.93) smaller than VdWsum (3.36)    C    O 0.077\nremark: distance between atom      27 and      19 (2.84) smaller than VdWsum (3.36)    C    O 0.163\nremark: distance between atom      76 and      68 (2.86) smaller than VdWsum (3.36)    C    O 0.147\nremark: distance between atom      84 and      77 (2.85) smaller than VdWsum (3.36)    C    O 0.154\nremark: distance between atom      87 and      48 (2.87) smaller than VdWsum (3.43) CH2E    O 0.210\nremark: distance between atom     101 and      93 (2.83) smaller than VdWsum (3.36)    C    O 0.177\nremark: distance between atom     103 and      68 (2.99) smaller than VdWsum (3.43) CH2E    O 0.097\nremark: distance between atom     108 and      92 (3.11) smaller than VdWsum (3.50)  NH1    C 0.038\nremark: distance between atom     127 and      94 (3.03) smaller than VdWsum (3.58)  NH3 CH2E 0.202\nremark: distance between atom     139 and     131 (2.66) smaller than VdWsum (3.43) CH2E    O 0.421\nremark: distance between atom     140 and     131 (2.74) smaller than VdWsum (3.26)   C5    O 0.169\nremark: distance between atom     154 and     150 (2.79) smaller than VdWsum (3.58)  NH1 CH2E 0.442\nremark: distance between atom     158 and     148 (2.90) smaller than VdWsum (3.43) CH2E    O 0.186\nremark: distance between atom     162 and     147 (3.07) smaller than VdWsum (3.50)  NH1    C 0.080\nremark: distance between atom     170 and     167 (3.14) smaller than VdWsum (3.50)  NH1    C 0.015\nremark: distance between atom     172 and     165 (2.74) smaller than VdWsum (3.36)    C    O 0.264\nremark: distance between atom     177 and     164 (2.97) smaller than VdWsum (3.50)  NH1    C 0.182\nremark: distance between atom     189 and     184 (2.96) smaller than VdWsum (3.36)    C    O 0.048\nremark: distance between atom     221 and     213 (3.00) smaller than VdWsum (3.36)    C    O 0.003\nremark: distance between atom     224 and     190 (2.95) smaller than VdWsum (3.43) CH2E    O 0.134\nremark: distance between atom     234 and     230 (2.92) smaller than VdWsum (3.36)    C    O 0.088\nremark: distance between atom     237 and     206 (2.99) smaller than VdWsum (3.43) CH2E    O 0.096\nremark: distance between atom     239 and     176 (3.26) smaller than VdWsum (3.80) CH3E CH3E 0.189\nremark: distance between atom     242 and     235 (2.98) smaller than VdWsum (3.36)    C    O 0.029\nremark: distance between atom     250 and     243 (2.87) smaller than VdWsum (3.36)    C    O 0.133\nremark: distance between atom     257 and     251 (2.95) smaller than VdWsum (3.36)    C    O 0.055\nremark: distance between atom     318 and     292 (2.95) smaller than VdWsum (3.43) CH2E    O 0.133\nremark: distance between atom     322 and     307 (3.13) smaller than VdWsum (3.50)  NH1    C 0.019\nremark: distance between atom     322 and     318 (3.19) smaller than VdWsum (3.58)  NH1 CH2E 0.040\nremark: distance between atom     340 and     324 (3.05) smaller than VdWsum (3.50)  NH1    C 0.100\nremark: distance between atom     342 and     335 (2.96) smaller than VdWsum (3.36)    C    O 0.043\nremark: distance between atom     364 and     357 (3.15) smaller than VdWsum (3.53)  NH1 CH3E 0.028\nremark: distance between atom     370 and     361 (2.94) smaller than VdWsum (3.36)    C    O 0.065\nremark: distance between atom     377 and     360 (3.09) smaller than VdWsum (3.50)  NH1    C 0.058\nremark: distance between atom     388 and     380 (2.92) smaller than VdWsum (3.36)    C    O 0.085\nremark: distance between atom     394 and     391 (3.01) smaller than VdWsum (3.50)  NH1    C 0.139\nremark: distance between atom     433 and     423 (2.97) smaller than VdWsum (3.36)    C    O 0.037\nremark: distance between atom     444 and     434 (2.95) smaller than VdWsum (3.36)    C    O 0.055\nremark: distance between atom     456 and     449 (2.96) smaller than VdWsum (3.36)    C    O 0.046\nremark: distance between atom     478 and     304 (3.42) smaller than VdWsum (3.80) CH3E CH3E 0.027\nremark: distance between atom     481 and     474 (2.96) smaller than VdWsum (3.36)    C    O 0.044\nremark: distance between atom     492 and     489 (3.00) smaller than VdWsum (3.36)    C    O 0.009\nremark: distance between atom     499 and     488 (3.14) smaller than VdWsum (3.50)  NH1    C 0.006\nremark: distance between atom     508 and     253 (2.65) smaller than VdWsum (3.00)  NC2  OH1 0.000\nremark: distance between atom     534 and     524 (2.98) smaller than VdWsum (3.36)    C    O 0.026\nremark: distance between atom     553 and     542 (3.14) smaller than VdWsum (3.50)  NH1    C 0.010\nremark: distance between atom     575 and     568 (2.95) smaller than VdWsum (3.36)    C    O 0.060\nremark: distance between atom     618 and     612 (3.00) smaller than VdWsum (3.36)    C    O 0.004\nremark: distance between atom     657 and     647 (3.00) smaller than VdWsum (3.36)    C    O 0.002\nremark: distance between atom     660 and     619 (2.95) smaller than VdWsum (3.43) CH2E    O 0.133\nremark: distance between atom     672 and     670 (3.10) smaller than VdWsum (3.53)  NH1 CH3E 0.078\nremark: distance between atom     730 and     407 (2.57) smaller than VdWsum (3.01)  OH1    O 0.097\nremark: distance between atom     735 and     520 (2.58) smaller than VdWsum (3.00)  OH1  NC2 0.066\nremark: distance between atom     737 and      72 (2.58) smaller than VdWsum (3.01)  OH1   OC 0.084\nremark: distance between atom     744 and     125 (3.09) smaller than VdWsum (3.49)  OH1 CH2E 0.051\n\n2024-05-24 09:47:16,635 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_43/concoord_dist/a9c79d7d-1a5b-4481-bdd0-b32edff48416&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_43/concoord_dist/25aa70a0-e950-4422-a757-d8751da5723d.stdin&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_43/concoord_dist/concoord_dist.pdb\nChecking if empty file: /tmp/biobb/unitests_43/concoord_dist/concoord_dist.gro\nChecking if empty file: /tmp/biobb/unitests_43/concoord_dist/concoord_dist.dat\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_43/concoord_dist/concoord_dist.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/reference/flexdyn/dist.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 775\n     Atoms ALIGNED in PDB_B: 775\n     RMS: 6.91545531105067e-15\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_43/concoord_dist/concoord_dist_log.out:file_utils.py:391 Executing biobb_flexdyn.flexdyn.concoord_dist Version: 4.1.0\nINFO     /tmp/biobb/unitests_43/concoord_dist/concoord_dist_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_43/concoord_dist/a9c79d7d-1a5b-4481-bdd0-b32edff48416\nINFO     /tmp/biobb/unitests_43/concoord_dist/concoord_dist_log.out:file_utils.py:391 Copy: /tmp/biobb/unitests_43/concoord_dist/25aa70a0-e950-4422-a757-d8751da5723d.stdin to /tmp/biobb/unitests_43/concoord_dist/a9c79d7d-1a5b-4481-bdd0-b32edff48416\nINFO     /tmp/biobb/unitests_43/concoord_dist/concoord_dist_log.out:cmd_wrapper.py:33 cd  /tmp/biobb/unitests_43/concoord_dist/a9c79d7d-1a5b-4481-bdd0-b32edff48416 ; dist -op concoord_dist.pdb -og concoord_dist.gro -od concoord_dist.dat -p structure.pdb -c 4.0 -m 50 -damp 1.0 &amp;lt; 25aa70a0-e950-4422-a757-d8751da5723d.stdin\n\nINFO     /tmp/biobb/unitests_43/concoord_dist/concoord_dist_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_43/concoord_dist/concoord_dist_log.out:cmd_wrapper.py:52 Select a set of Van der Waals parameters:\n1: OPLS-UA (united atoms) parameters\n2: OPLS-AA (all atoms) parameters\n3: PROLSQ repel parameters\n4: Yamber2 parameters\n5: Li et al. parameters\n6: OPLS-X parameters (recommended for NMR structure determination)\nSelected parameter set 1\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/ATOMS_oplsua.DAT to ATOMS.DAT in current working directory\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/MARGINS_oplsua.DAT to MARGINS.DAT in current working directory\nSelect a set of bond/angle parameters:\n1: Concoord default parameters\n2: Engh-Huber parameters\nSelected parameter set 1\ncopying /home/user/micromamba/envs/test_environment/share/concoord/lib/BONDS.DAT.noeh to BONDS.DAT in current working directory\n-------------------------------------------------\ndist.exe - build date: Thu Jan 24 11:26:08 CET 2013                                \nProcess started with PID:  2423620\non host: biobb-runners\nin directory: /tmp/biobb/unitests_43/concoord_dist/a9c79d7d-1a5b-4481-bdd0-b32edff48416\non: 24/05/0024 at: 09:47:16\n-------------------------------------------------\ncommand line options:\npdb input coordinate file...........: structure.pdb                           \nWARNING WARNING WARNING WARNING WARNING WARNING\nWarning: no dssp calculation will be performed. Expect poor results!\nWARNING WARNING WARNING WARNING WARNING WARNING\nnon-bonded cut-off radius...........:   4.00 A + VDW sum\nminimal nr. of distances per atom...:     50\noutput distances....................: concoord_dist.dat                       \noutput coordinates (PDB)............: concoord_dist.pdb                       \noutput coordinates (GROMOS87).......: concoord_dist.gro                       \nhydrogen atoms (if any) will be removed\nnon-bonded contacts of starting structure will be preserved\nprocessing input...\ntotal number of atoms       :      775\nnumber of residues          :      144\nnumber of atoms to be used  :      775\ncounted    640 intra-residue bonds\ncounted     84 peptide bonds\ncounted      0 disulphide bonds\ncounted      0 histidine-heme bonds\ncounted    724 bonds in total\ncounted    966 1-3 pairs (angles)\ncounted     36 ring restrictions\ncounted      0 omega restrictions\ncounted   1037 other 1-4 restrictions\ncounted      0 hydrogen bonds\ncounted      4 salt bridges\ncounted    142 hydrogen bonds\ncounted    868 side chain restrictions\ncounted      0 sheet restrictions\ncounted  18104 other close pairs\ncounted   3878 more restrictions\ntotal nr of non-bonded pairs:  19118\ntotal number of constraints :   26254\n 1 warning(s) encountered. Please investigate!\n\nINFO     /tmp/biobb/unitests_43/concoord_dist/concoord_dist_log.err:cmd_wrapper.py:60 remark: distance between atom      31 and      27 (3.11) smaller than VdWsum (3.75)    C    C 0.290\nremark: distance between atom     124 and     122 (2.94) smaller than VdWsum (3.43) CH2E    O 0.141\nremark: distance between atom     159 and     157 (2.90) smaller than VdWsum (3.36)    C    O 0.102\nremark: distance between atom     328 and     324 (3.13) smaller than VdWsum (3.50)  NH1    C 0.022\nremark: distance between atom     383 and     377 (3.22) smaller than VdWsum (3.58) CH2E  NH1 0.008\nremark: distance between atom     383 and     379 (3.36) smaller than VdWsum (3.83) CH2E    C 0.113\nremark: distance between atom     392 and     388 (2.86) smaller than VdWsum (3.36)   OC    C 0.146\nremark: distance between atom     452 and     448 (3.26) smaller than VdWsum (3.78) CH3E    C 0.161\nremark: distance between atom     560 and     555 (3.27) smaller than VdWsum (3.65) CR1E    C 0.028\nremark: distance between atom      18 and      12 (2.93) smaller than VdWsum (3.36)    C    O 0.077\nremark: distance between atom      27 and      19 (2.84) smaller than VdWsum (3.36)    C    O 0.163\nremark: distance between atom      76 and      68 (2.86) smaller than VdWsum (3.36)    C    O 0.147\nremark: distance between atom      84 and      77 (2.85) smaller than VdWsum (3.36)    C    O 0.154\nremark: distance between atom      87 and      48 (2.87) smaller than VdWsum (3.43) CH2E    O 0.210\nremark: distance between atom     101 and      93 (2.83) smaller than VdWsum (3.36)    C    O 0.177\nremark: distance between atom     103 and      68 (2.99) smaller than VdWsum (3.43) CH2E    O 0.097\nremark: distance between atom     108 and      92 (3.11) smaller than VdWsum (3.50)  NH1    C 0.038\nremark: distance between atom     127 and      94 (3.03) smaller than VdWsum (3.58)  NH3 CH2E 0.202\nremark: distance between atom     139 and     131 (2.66) smaller than VdWsum (3.43) CH2E    O 0.421\nremark: distance between atom     140 and     131 (2.74) smaller than VdWsum (3.26)   C5    O 0.169\nremark: distance between atom     154 and     150 (2.79) smaller than VdWsum (3.58)  NH1 CH2E 0.442\nremark: distance between atom     158 and     148 (2.90) smaller than VdWsum (3.43) CH2E    O 0.186\nremark: distance between atom     162 and     147 (3.07) smaller than VdWsum (3.50)  NH1    C 0.080\nremark: distance between atom     170 and     167 (3.14) smaller than VdWsum (3.50)  NH1    C 0.015\nremark: distance between atom     172 and     165 (2.74) smaller than VdWsum (3.36)    C    O 0.264\nremark: distance between atom     177 and     164 (2.97) smaller than VdWsum (3.50)  NH1    C 0.182\nremark: distance between atom     189 and     184 (2.96) smaller than VdWsum (3.36)    C    O 0.048\nremark: distance between atom     221 and     213 (3.00) smaller than VdWsum (3.36)    C    O 0.003\nremark: distance between atom     224 and     190 (2.95) smaller than VdWsum (3.43) CH2E    O 0.134\nremark: distance between atom     234 and     230 (2.92) smaller than VdWsum (3.36)    C    O 0.088\nremark: distance between atom     237 and     206 (2.99) smaller than VdWsum (3.43) CH2E    O 0.096\nremark: distance between atom     239 and     176 (3.26) smaller than VdWsum (3.80) CH3E CH3E 0.189\nremark: distance between atom     242 and     235 (2.98) smaller than VdWsum (3.36)    C    O 0.029\nremark: distance between atom     250 and     243 (2.87) smaller than VdWsum (3.36)    C    O 0.133\nremark: distance between atom     257 and     251 (2.95) smaller than VdWsum (3.36)    C    O 0.055\nremark: distance between atom     318 and     292 (2.95) smaller than VdWsum (3.43) CH2E    O 0.133\nremark: distance between atom     322 and     307 (3.13) smaller than VdWsum (3.50)  NH1    C 0.019\nremark: distance between atom     322 and     318 (3.19) smaller than VdWsum (3.58)  NH1 CH2E 0.040\nremark: distance between atom     340 and     324 (3.05) smaller than VdWsum (3.50)  NH1    C 0.100\nremark: distance between atom     342 and     335 (2.96) smaller than VdWsum (3.36)    C    O 0.043\nremark: distance between atom     364 and     357 (3.15) smaller than VdWsum (3.53)  NH1 CH3E 0.028\nremark: distance between atom     370 and     361 (2.94) smaller than VdWsum (3.36)    C    O 0.065\nremark: distance between atom     377 and     360 (3.09) smaller than VdWsum (3.50)  NH1    C 0.058\nremark: distance between atom     388 and     380 (2.92) smaller than VdWsum (3.36)    C    O 0.085\nremark: distance between atom     394 and     391 (3.01) smaller than VdWsum (3.50)  NH1    C 0.139\nremark: distance between atom     433 and     423 (2.97) smaller than VdWsum (3.36)    C    O 0.037\nremark: distance between atom     444 and     434 (2.95) smaller than VdWsum (3.36)    C    O 0.055\nremark: distance between atom     456 and     449 (2.96) smaller than VdWsum (3.36)    C    O 0.046\nremark: distance between atom     478 and     304 (3.42) smaller than VdWsum (3.80) CH3E CH3E 0.027\nremark: distance between atom     481 and     474 (2.96) smaller than VdWsum (3.36)    C    O 0.044\nremark: distance between atom     492 and     489 (3.00) smaller than VdWsum (3.36)    C    O 0.009\nremark: distance between atom     499 and     488 (3.14) smaller than VdWsum (3.50)  NH1    C 0.006\nremark: distance between atom     508 and     253 (2.65) smaller than VdWsum (3.00)  NC2  OH1 0.000\nremark: distance between atom     534 and     524 (2.98) smaller than VdWsum (3.36)    C    O 0.026\nremark: distance between atom     553 and     542 (3.14) smaller than VdWsum (3.50)  NH1    C 0.010\nremark: distance between atom     575 and     568 (2.95) smaller than VdWsum (3.36)    C    O 0.060\nremark: distance between atom     618 and     612 (3.00) smaller than VdWsum (3.36)    C    O 0.004\nremark: distance between atom     657 and     647 (3.00) smaller than VdWsum (3.36)    C    O 0.002\nremark: distance between atom     660 and     619 (2.95) smaller than VdWsum (3.43) CH2E    O 0.133\nremark: distance between atom     672 and     670 (3.10) smaller than VdWsum (3.53)  NH1 CH3E 0.078\nremark: distance between atom     730 and     407 (2.57) smaller than VdWsum (3.01)  OH1    O 0.097\nremark: distance between atom     735 and     520 (2.58) smaller than VdWsum (3.00)  OH1  NC2 0.066\nremark: distance between atom     737 and      72 (2.58) smaller than VdWsum (3.01)  OH1   OC 0.084\nremark: distance between atom     744 and     125 (3.09) smaller than VdWsum (3.49)  OH1 CH2E 0.051\n\nINFO     /tmp/biobb/unitests_43/concoord_dist/concoord_dist_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_43/concoord_dist/a9c79d7d-1a5b-4481-bdd0-b32edff48416&amp;#x27;, &amp;#x27;/tmp/biobb/unitests_43/concoord_dist/25aa70a0-e950-4422-a757-d8751da5723d.stdin&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_43\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imc.py::TestImodImc::test_imod_imc&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imc.py::TestImodImc::test_imod_imc&#34;, &#34;duration&#34;: &#34;43 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_flexdyn/test/unitests/test_flexdyn/test_imod_imc.py::TestImodImc::test_imod_imc&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;43 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 -----------------------------\n2024-05-24 09:47:16,690 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.imod_imc Version: 4.1.0\n2024-05-24 09:47:16,690 [MainThread  ] [INFO ]  Creating 73d000f2-49bd-47d0-bf70-aaa114a38ee6 temporary folder\n2024-05-24 09:47:16,690 [MainThread  ] [INFO ]  cd 73d000f2-49bd-47d0-bf70-aaa114a38ee6 ; imc structure_cleaned.pdb imod_imode_evecs.dat -o imod_ensemble -c 10 -n 10 -a 6.0\n\n2024-05-24 09:47:16,717 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-24 09:47:16,717 [MainThread  ] [INFO ]  imc&amp;gt;\nimc&amp;gt; Monte-Carlo IC-NMA based program v1.11\nimc&amp;gt;\nimc&amp;gt; Reading Input PDB file\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimc&amp;gt; Formatting pdb names\nimc&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimc&amp;gt; Selected model number of (pseudo)atoms: 716\nimc&amp;gt; Opening output trajectory file: imod_ensemble.pdb\nimc&amp;gt; Number of Dihedral angles: 168\nimc&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimc&amp;gt; Predicted number of ICs (Eckart): 168\nimc&amp;gt; Number of ICs predicted by seg_props(): 168\nimc&amp;gt; Ptraj info: imod_imode_evecs.dat  vectors=20  components=168\nimc&amp;gt; Number of used modes: 10\nimc&amp;gt; Monte-Carlo stage using Ef= 1.000000\nimc&amp;gt; Frame     1  Etot= 4.281294 0.00 sec\rimc&amp;gt; Frame     2  Etot= 2.652164 0.00 sec\rimc&amp;gt; Frame     3  Etot= 5.444238 0.00 sec\rimc&amp;gt; Frame     4  Etot= 0.979999 0.00 sec\rimc&amp;gt; Frame     5  Etot= 3.171644 0.01 sec\rimc&amp;gt; Frame     6  Etot= 2.332981 0.00 sec\rimc&amp;gt; Frame     7  Etot= 1.976528 0.00 sec\rimc&amp;gt; Frame     8  Etot= 1.639353 0.00 sec\rimc&amp;gt; Frame     9  Etot= 2.429815 0.00 sec\rimc&amp;gt; Frame    10  Etot= 3.521556 0.00 sec\r\nimc&amp;gt;           Total        0.01 sec\nimc&amp;gt;\nimc&amp;gt; ACEPTANCE RATIO(%): 40.515945\nimc&amp;gt;\nimc&amp;gt; Success!\nimc&amp;gt; Written MC-trajectory: imod_ensemble.pdb (10 frames)\nimc&amp;gt; Bye!\n\n2024-05-24 09:47:16,717 [MainThread  ] [INFO ]  Removed: [&amp;#x27;73d000f2-49bd-47d0-bf70-aaa114a38ee6&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_43/imod_imc/imod_imc_output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_43/imod_imc/imod_imc_log.out:file_utils.py:391 Executing biobb_flexdyn.flexdyn.imod_imc Version: 4.1.0\nINFO     /tmp/biobb/unitests_43/imod_imc/imod_imc_log.out:file_utils.py:391 Creating 73d000f2-49bd-47d0-bf70-aaa114a38ee6 temporary folder\nINFO     /tmp/biobb/unitests_43/imod_imc/imod_imc_log.out:cmd_wrapper.py:33 cd 73d000f2-49bd-47d0-bf70-aaa114a38ee6 ; imc structure_cleaned.pdb imod_imode_evecs.dat -o imod_ensemble -c 10 -n 10 -a 6.0\n\nINFO     /tmp/biobb/unitests_43/imod_imc/imod_imc_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_43/imod_imc/imod_imc_log.out:cmd_wrapper.py:52 imc&amp;gt;\nimc&amp;gt; Monte-Carlo IC-NMA based program v1.11\nimc&amp;gt;\nimc&amp;gt; Reading Input PDB file\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimc&amp;gt; Formatting pdb names\nimc&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimc&amp;gt; Selected model number of (pseudo)atoms: 716\nimc&amp;gt; Opening output trajectory file: imod_ensemble.pdb\nimc&amp;gt; Number of Dihedral angles: 168\nimc&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimc&amp;gt; Predicted number of ICs (Eckart): 168\nimc&amp;gt; Number of ICs predicted by seg_props(): 168\nimc&amp;gt; Ptraj info: imod_imode_evecs.dat  vectors=20  components=168\nimc&amp;gt; Number of used modes: 10\nimc&amp;gt; Monte-Carlo stage using Ef= 1.000000\nimc&amp;gt; Frame     1  Etot= 4.281294 0.00 sec\rimc&amp;gt; Frame     2  Etot= 2.652164 0.00 sec\rimc&amp;gt; Frame     3  Etot= 5.444238 0.00 sec\rimc&amp;gt; Frame     4  Etot= 0.979999 0.00 sec\rimc&amp;gt; Frame     5  Etot= 3.171644 0.01 sec\rimc&amp;gt; Frame     6  Etot= 2.332981 0.00 sec\rimc&amp;gt; Frame     7  Etot= 1.976528 0.00 sec\rimc&amp;gt; Frame     8  Etot= 1.639353 0.00 sec\rimc&amp;gt; Frame     9  Etot= 2.429815 0.00 sec\rimc&amp;gt; Frame    10  Etot= 3.521556 0.00 sec\r\nimc&amp;gt;           Total        0.01 sec\nimc&amp;gt;\nimc&amp;gt; ACEPTANCE RATIO(%): 40.515945\nimc&amp;gt;\nimc&amp;gt; Success!\nimc&amp;gt; Written MC-trajectory: imod_ensemble.pdb (10 frames)\nimc&amp;gt; Bye!\n\nINFO     /tmp/biobb/unitests_43/imod_imc/imod_imc_log.out:file_utils.py:391 Removed: [&amp;#x27;73d000f2-49bd-47d0-bf70-aaa114a38ee6&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_43\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imode.py::TestImodImode::test_imod_imode&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imode.py::TestImodImode::test_imod_imode&#34;, &#34;duration&#34;: &#34;53 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_flexdyn/test/unitests/test_flexdyn/test_imod_imode.py::TestImodImode::test_imod_imode&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;53 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 -----------------------------\n2024-05-24 09:47:16,733 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.imod_imode Version: 4.1.0\n2024-05-24 09:47:16,734 [MainThread  ] [INFO ]  Creating b5c71add-8b45-456b-8c8e-d08a115fadc9 temporary folder\n2024-05-24 09:47:16,734 [MainThread  ] [INFO ]  cd b5c71add-8b45-456b-8c8e-d08a115fadc9 ; imode_gcc structure.pdb -o imods_evecs -m 2\n\n2024-05-24 09:47:16,768 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-24 09:47:16,768 [MainThread  ] [INFO ]  imode&amp;gt;\nimode&amp;gt; Welcome to the NMA in Internal Coordinates tool v1.20\nimode&amp;gt;\nParser&amp;gt; Using eigensolver: 1 \nimode&amp;gt; Reading PDB file: structure.pdb\nimode&amp;gt; Deleting Hydrogen atoms (if any)...\nimode&amp;gt; Deleting Water molecules (if any)...\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimode&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimode&amp;gt; Selected model residues: 85\nimode&amp;gt; Selected model (pseudo)atoms: 716\nimode&amp;gt; Number of Dihedral angles: 168\nimode&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimode&amp;gt; Predicted number of ICs (Eckart): 168\nimode&amp;gt; Number of ICs predicted by seg_props(): 168\nimode&amp;gt; Range of computed modes: 1-20\nimode&amp;gt; Creating pairwise interaction potential:\nimode&amp;gt; Inverse Exponential (37284 nipas) cutoff= 10.0, k= 1.000000, x0= 3.8 (0.006752 s)\nimode&amp;gt; Packed-Hessian/Kinetic matrices mem.= 0.114 Mb (rank= 168)\nimode&amp;gt; Fast Hessian Matrix Building O(n^2) [hessianMFAx()] 0.005479 s\nimode&amp;gt; Fast Kinetic-Energy matrix Building O(n^2) [kineticMFAx()] 0.000837 s\nimode&amp;gt; Eigenvector matrix mem. = 0.027 Mb\nimode&amp;gt; Diagonalization with ARPACK-based dsdrv1_AP_BP_W_mon()... 0.011752 s\nimode&amp;gt; Showing the first 10 eigenvalues:\nimode&amp;gt;\nimode&amp;gt; MODE   EIGENVALUE\nimode&amp;gt;    1  2.05448e-05\nimode&amp;gt;    2  5.46551e-05\nimode&amp;gt;    3  1.57342e-04\nimode&amp;gt;    4  3.81292e-04\nimode&amp;gt;    5  6.05538e-04\nimode&amp;gt;    6  1.41292e-03\nimode&amp;gt;    7  2.48869e-03\nimode&amp;gt;    8  3.14694e-03\nimode&amp;gt;    9  4.44243e-03\nimode&amp;gt;   10  5.40564e-03\nimode&amp;gt;\nimode&amp;gt;\nimode&amp;gt; SAVED FILES:\nimode&amp;gt; Log file:                                                imods_evecs.log\nimode&amp;gt; Model PDB:                                         imods_evecs_model.pdb\nimode&amp;gt; ICS eigenvectors:                                    imods_evecs_ic.evec\nimode&amp;gt;\nimode&amp;gt; Bye!\n\n2024-05-24 09:47:16,771 [MainThread  ] [INFO ]  Removed: [&amp;#x27;b5c71add-8b45-456b-8c8e-d08a115fadc9&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_43/imod_imode/imod_imode_evecs.dat\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_43/imod_imode/imod_imode_log.out:file_utils.py:391 Executing biobb_flexdyn.flexdyn.imod_imode Version: 4.1.0\nINFO     /tmp/biobb/unitests_43/imod_imode/imod_imode_log.out:file_utils.py:391 Creating b5c71add-8b45-456b-8c8e-d08a115fadc9 temporary folder\nINFO     /tmp/biobb/unitests_43/imod_imode/imod_imode_log.out:cmd_wrapper.py:33 cd b5c71add-8b45-456b-8c8e-d08a115fadc9 ; imode_gcc structure.pdb -o imods_evecs -m 2\n\nINFO     /tmp/biobb/unitests_43/imod_imode/imod_imode_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_43/imod_imode/imod_imode_log.out:cmd_wrapper.py:52 imode&amp;gt;\nimode&amp;gt; Welcome to the NMA in Internal Coordinates tool v1.20\nimode&amp;gt;\nParser&amp;gt; Using eigensolver: 1 \nimode&amp;gt; Reading PDB file: structure.pdb\nimode&amp;gt; Deleting Hydrogen atoms (if any)...\nimode&amp;gt; Deleting Water molecules (if any)...\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimode&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimode&amp;gt; Selected model residues: 85\nimode&amp;gt; Selected model (pseudo)atoms: 716\nimode&amp;gt; Number of Dihedral angles: 168\nimode&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimode&amp;gt; Predicted number of ICs (Eckart): 168\nimode&amp;gt; Number of ICs predicted by seg_props(): 168\nimode&amp;gt; Range of computed modes: 1-20\nimode&amp;gt; Creating pairwise interaction potential:\nimode&amp;gt; Inverse Exponential (37284 nipas) cutoff= 10.0, k= 1.000000, x0= 3.8 (0.006752 s)\nimode&amp;gt; Packed-Hessian/Kinetic matrices mem.= 0.114 Mb (rank= 168)\nimode&amp;gt; Fast Hessian Matrix Building O(n^2) [hessianMFAx()] 0.005479 s\nimode&amp;gt; Fast Kinetic-Energy matrix Building O(n^2) [kineticMFAx()] 0.000837 s\nimode&amp;gt; Eigenvector matrix mem. = 0.027 Mb\nimode&amp;gt; Diagonalization with ARPACK-based dsdrv1_AP_BP_W_mon()... 0.011752 s\nimode&amp;gt; Showing the first 10 eigenvalues:\nimode&amp;gt;\nimode&amp;gt; MODE   EIGENVALUE\nimode&amp;gt;    1  2.05448e-05\nimode&amp;gt;    2  5.46551e-05\nimode&amp;gt;    3  1.57342e-04\nimode&amp;gt;    4  3.81292e-04\nimode&amp;gt;    5  6.05538e-04\nimode&amp;gt;    6  1.41292e-03\nimode&amp;gt;    7  2.48869e-03\nimode&amp;gt;    8  3.14694e-03\nimode&amp;gt;    9  4.44243e-03\nimode&amp;gt;   10  5.40564e-03\nimode&amp;gt;\nimode&amp;gt;\nimode&amp;gt; SAVED FILES:\nimode&amp;gt; Log file:                                                imods_evecs.log\nimode&amp;gt; Model PDB:                                         imods_evecs_model.pdb\nimode&amp;gt; ICS eigenvectors:                                    imods_evecs_ic.evec\nimode&amp;gt;\nimode&amp;gt; Bye!\n\nINFO     /tmp/biobb/unitests_43/imod_imode/imod_imode_log.out:file_utils.py:391 Removed: [&amp;#x27;b5c71add-8b45-456b-8c8e-d08a115fadc9&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_43\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imove.py::TestImodImove::test_imod_imove&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_imod_imove.py::TestImodImove::test_imod_imove&#34;, &#34;duration&#34;: &#34;378 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_flexdyn/test/unitests/test_flexdyn/test_imod_imove.py::TestImodImove::test_imod_imove&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;378 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 -----------------------------\n2024-05-24 09:47:16,787 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.imod_imove Version: 4.1.0\n2024-05-24 09:47:16,787 [MainThread  ] [INFO ]  Creating 12da7015-b447-4398-88ea-3f52b5f724db temporary folder\n2024-05-24 09:47:16,788 [MainThread  ] [INFO ]  cd 12da7015-b447-4398-88ea-3f52b5f724db ; imove structure_cleaned.pdb imod_imode_evecs.dat imod_imove_output.pdb 1 -c 11\n\n2024-05-24 09:47:16,810 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-24 09:47:16,810 [MainThread  ] [INFO ]  imove&amp;gt;\nimove&amp;gt; Welcome to the Internal Coordinates Motion Tool v1.14\nimove&amp;gt;\nimove&amp;gt; Input PDB-file structure_cleaned.pdb\nimove&amp;gt; Multi-PDB output file imod_imove_output.pdb\nimove&amp;gt; Number of frames to be generated 11\nimove&amp;gt; Normal Mode choosen 1\nimove&amp;gt; Reading PDB file structure_cleaned.pdb\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimove&amp;gt; Formatting residues names\nimove&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimove&amp;gt; Ptraj info: imod_imode_evecs.dat  vectors=20  components=168\nimove&amp;gt; Maximum internal coordinate amplitude: 761.802917\nimove&amp;gt; Selected model number of residues: 85\nimove&amp;gt; Number of Dihedral angles: 168\nimove&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimove&amp;gt; Predicted number of ICs (Eckart): 168\nimove&amp;gt; Number of ICs predicted by seg_props(): 168\nimove&amp;gt; Moving analiticaly (moving internal coordinates)\nimove&amp;gt; Added frame    -5 to Multi-PDB\nimove&amp;gt; Added frame    -4 to Multi-PDB\nimove&amp;gt; Added frame    -3 to Multi-PDB\nimove&amp;gt; Added frame    -2 to Multi-PDB\nimove&amp;gt; Added frame    -1 to Multi-PDB\nimove&amp;gt; Added frame     0 to Multi-PDB &amp;lt;-- 1st model (structure_cleaned.pdb)\nimove&amp;gt; Added frame     1 to Multi-PDB\nimove&amp;gt; Added frame     2 to Multi-PDB\nimove&amp;gt; Added frame     3 to Multi-PDB\nimove&amp;gt; Added frame     4 to Multi-PDB\nimove&amp;gt; Added frame     5 to Multi-PDB\nimove&amp;gt;\nimove&amp;gt; Success!\nimove&amp;gt; Written movie: imod_imove_output.pdb (11 frames)\nimove&amp;gt; Bye!\n\n2024-05-24 09:47:16,811 [MainThread  ] [INFO ]  Removed: [&amp;#x27;12da7015-b447-4398-88ea-3f52b5f724db&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_43/imod_imove/imod_imove_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_43/imod_imove/imod_imove_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/reference/flexdyn/imod_imove_output.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 716\n     Atoms ALIGNED in PDB_B: 716\n     RMS: 3.73364302621313e-05\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_43/imod_imove/imod_imove_log.out:file_utils.py:391 Executing biobb_flexdyn.flexdyn.imod_imove Version: 4.1.0\nINFO     /tmp/biobb/unitests_43/imod_imove/imod_imove_log.out:file_utils.py:391 Creating 12da7015-b447-4398-88ea-3f52b5f724db temporary folder\nINFO     /tmp/biobb/unitests_43/imod_imove/imod_imove_log.out:cmd_wrapper.py:33 cd 12da7015-b447-4398-88ea-3f52b5f724db ; imove structure_cleaned.pdb imod_imode_evecs.dat imod_imove_output.pdb 1 -c 11\n\nINFO     /tmp/biobb/unitests_43/imod_imove/imod_imove_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_43/imod_imove/imod_imove_log.out:cmd_wrapper.py:52 imove&amp;gt;\nimove&amp;gt; Welcome to the Internal Coordinates Motion Tool v1.14\nimove&amp;gt;\nimove&amp;gt; Input PDB-file structure_cleaned.pdb\nimove&amp;gt; Multi-PDB output file imod_imove_output.pdb\nimove&amp;gt; Number of frames to be generated 11\nimove&amp;gt; Normal Mode choosen 1\nimove&amp;gt; Reading PDB file structure_cleaned.pdb\nmolinf&amp;gt;\nmolinf&amp;gt; Mol Chains   Segments    Atoms\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt;  1   1-&amp;gt;A\nmolinf&amp;gt;             1    85 aa    716\nmolinf&amp;gt;\nmolinf&amp;gt; --- ------ -----------  -------\nmolinf&amp;gt; SUMMARY:\nmolinf&amp;gt; Number of Molecules ..... 1\nmolinf&amp;gt; Number of Chain ......... 1\nmolinf&amp;gt; Number of Segments ...... 1\nmolinf&amp;gt; Number of Groups ........ 85\nmolinf&amp;gt; Number of Atoms ......... 716\nmolinf&amp;gt; Number of Hetero Mol .... 0\nmolinf&amp;gt; Number of Hetero Atoms... 0\nmolinf&amp;gt;\nimove&amp;gt; Formatting residues names\nimove&amp;gt; Coarse-Graining model: Full-Atom (no coarse-graining)\nimove&amp;gt; Ptraj info: imod_imode_evecs.dat  vectors=20  components=168\nimove&amp;gt; Maximum internal coordinate amplitude: 761.802917\nimove&amp;gt; Selected model number of residues: 85\nimove&amp;gt; Number of Dihedral angles: 168\nimove&amp;gt; Rotational/Translational ICs (Non-Eckart): 6\nimove&amp;gt; Predicted number of ICs (Eckart): 168\nimove&amp;gt; Number of ICs predicted by seg_props(): 168\nimove&amp;gt; Moving analiticaly (moving internal coordinates)\nimove&amp;gt; Added frame    -5 to Multi-PDB\nimove&amp;gt; Added frame    -4 to Multi-PDB\nimove&amp;gt; Added frame    -3 to Multi-PDB\nimove&amp;gt; Added frame    -2 to Multi-PDB\nimove&amp;gt; Added frame    -1 to Multi-PDB\nimove&amp;gt; Added frame     0 to Multi-PDB &amp;lt;-- 1st model (structure_cleaned.pdb)\nimove&amp;gt; Added frame     1 to Multi-PDB\nimove&amp;gt; Added frame     2 to Multi-PDB\nimove&amp;gt; Added frame     3 to Multi-PDB\nimove&amp;gt; Added frame     4 to Multi-PDB\nimove&amp;gt; Added frame     5 to Multi-PDB\nimove&amp;gt;\nimove&amp;gt; Success!\nimove&amp;gt; Written movie: imod_imove_output.pdb (11 frames)\nimove&amp;gt; Bye!\n\nINFO     /tmp/biobb/unitests_43/imod_imove/imod_imove_log.out:file_utils.py:391 Removed: [&amp;#x27;12da7015-b447-4398-88ea-3f52b5f724db&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_43\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_nolb.py::TestNolb_nma::test_nolb_nma&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_nolb.py::TestNolb_nma::test_nolb_nma&#34;, &#34;duration&#34;: &#34;427 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_flexdyn/test/unitests/test_flexdyn/test_nolb.py::TestNolb_nma::test_nolb_nma&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;427 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 -----------------------------\n2024-05-24 09:47:17,167 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.nolb_nma Version: 4.1.0\n2024-05-24 09:47:17,167 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_43/nolb_nma/d9f4ea02-a24b-4633-a5d4-5a3929f6f89b\n2024-05-24 09:47:17,167 [MainThread  ] [INFO ]  NOLB d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/structure.pdb -o /tmp/biobb/unitests_43/nolb_nma/d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/nolb_ensemble -m -s 20 -c 5.0 --rmsd 1.0 --dist 1 --nSteps 5000 --tol 0.001\n\n2024-05-24 09:47:17,576 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-24 09:47:17,576 [MainThread  ] [INFO ]  *******************************************************************\n*-----------------------------------------------------------------*\n*-----------NOLB : a Non-Linear rigid block NMA method------------*\n*----------Authors: Alexandre Hoffmann &amp;amp; Sergei Grudinin----------*\n*-Copyright (c): Nano-D team, Inria/CNRS Grenoble, France, 2019.--*\n*--------------- e-mail: sergei.grudinin@inria.fr ----------------*\n*---- http://team.inria.fr/nano-d/software/nolb-normal-modes/ ----*\n*-----------------------------------------------------------------*\n*******************************************************************\nHostname......................................................... : biobb-runners\nRun at........................................................... : Fri May 24 09:47:17 2024\nCommand-line arguments........................................... : NOLB d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/structure.pdb -o /tmp/biobb/unitests_43/nolb_nma/d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/nolb_ensemble -m -s 20 -c 5.0 --rmsd 1.0 --dist 1 --nSteps 5000 --tol 0.001 \n=====================Reading input PDB file======================\nInput PDB file................................................... : d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/structure.pdb\nNumber of chains read............................................ : 2\nNumber of atoms read............................................. : 716\nFound............................................................ : 724 covalent bonds\n................................................................. : 966 angles\n======================Constructing Hessian=======================\nNumber of disconnected atoms..................................... : 0\nNumber of interactions........................................... : 16156\nInteraction cutoff distance...................................... : 5 A\nMemory required for the Hessian matrix........................... : 3.32803 Mb\nAll-atom Hessian size : ......................................... : 2148 x 2148\n============================Doing NMA============================\nMemory required for the RTB projection matrix.................... : 0.196655 Mb\nReduced Hessian size : .......................................... : 510 x 510\nNumber of computed modes......................................... : 10 \nNull-space size.................................................. : 1 \nLowest mode frequency............................................ : 7.08086e-05 \nHighest mode frequency........................................... : 0.0017141 \nFrequencies :\n            [ 1]................................................. : 7.08086e-05 \n            [ 2]................................................. : 9.22104e-05 \n            [ 3]................................................. : 0.000160579 \n            [ 4]................................................. : 0.000271988 \n            [ 5]................................................. : 0.000359596 \n            [ 6]................................................. : 0.000917588 \n            [ 7]................................................. : 0.00102481 \n            [ 8]................................................. : 0.00123429 \n            [ 9]................................................. : 0.0013176 \n            [10]................................................. : 0.0017141 \n===================Writing output Decoy files====================\nNumber of files.................................................. : 20\nOutput RMSD...................................................... : 1 A\nUsing outputfilename............................................. : /tmp/biobb/unitests_43/nolb_nma/d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/nolb_ensemble_nlb_decoys.pdb\nCurrent energy................................................... : 0.000802458\nN minimization steps............................................. : 17\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.838698\nCurrent energy................................................... : 0.000492936\nN minimization steps............................................. : 36\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.660651\nCurrent energy................................................... : 0.000204576\nN minimization steps............................................. : 18\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.138729\nCurrent energy................................................... : 0.000755071\nN minimization steps............................................. : 28\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.304596\nCurrent energy................................................... : 0.000423189\nN minimization steps............................................. : 24\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.289287\nCurrent energy................................................... : 0.000490861\nN minimization steps............................................. : 26\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.348679\nCurrent energy................................................... : 0.000536261\nN minimization steps............................................. : 33\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.373157\nCurrent energy................................................... : 0.000600031\nN minimization steps............................................. : 49\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.724211\nCurrent energy................................................... : 0.000574138\nN minimization steps............................................. : 34\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.361212\nCurrent energy................................................... : 0.000721136\nN minimization steps............................................. : 69\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.924134\nCurrent energy................................................... : 0.00116361\nN minimization steps............................................. : 50\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.834636\nCurrent energy................................................... : 0.000324975\nN minimization steps............................................. : 17\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.127239\nCurrent energy................................................... : 0.000960058\nN minimization steps............................................. : 52\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.618944\nCurrent energy................................................... : 0.000619613\nN minimization steps............................................. : 65\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.55831\nCurrent energy................................................... : 0.000841583\nN minimization steps............................................. : 56\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.569489\nCurrent energy................................................... : 0.000284024\nN minimization steps............................................. : 25\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.23718\nCurrent energy................................................... : 0.000582824\nN minimization steps............................................. : 21\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.154705\nCurrent energy................................................... : 0.000723304\nN minimization steps............................................. : 66\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.793648\nCurrent energy................................................... : 0.00122979\nN minimization steps............................................. : 57\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.887673\nCurrent energy................................................... : 0.000270424\nN minimization steps............................................. : 18\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.0829017\n=================================================================\n=========================== Timing : ============================\n=================================================================\nParsing arguments................................................ : 0.000228639 s\nReading input PDB file........................................... : 0.00189294 s\nConstructing Hessian............................................. : 0.0121292 s\nDoing NMA........................................................ : 0.0512874 s\nWriting output Decoy files....................................... : 0.33892 s\n.................................................................\nTotal time : .................................................... : 0.404458 s\n=================================================================\n\nMain Reference: Alexandre Hoffmann &amp;amp; Sergei Grudinin. NOLB : Nonlinear rigid block normal mode analysis method. Journal of Chemical Theory and Computation, 2017, 13 (5), pp.2123-2134. DOI: 10.1021/acs.jctc.7b00197.\n\nReference for clustering and decoy generation: Emilie Neveu, Petr Popov, Alexandre Hoffmann, Angelo Migliosi, Xavier Besseron, Gregoire Danoy, Pascal Bouvry, Sergei Grudinin. RapidRMSD: Rapid determination of RMSDs corresponding to motions of flexible molecules. Bioinformatics, Oxford University Press (OUP), 2018. DOI: 10.1093/bioinformatics/bty160.\n\n\n2024-05-24 09:47:17,578 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_43/nolb_nma/d9f4ea02-a24b-4633-a5d4-5a3929f6f89b&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_43/nolb_nma/nolb_output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_43/nolb_nma/nolb_nma_log.out:file_utils.py:391 Executing biobb_flexdyn.flexdyn.nolb_nma Version: 4.1.0\nINFO     /tmp/biobb/unitests_43/nolb_nma/nolb_nma_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_43/nolb_nma/d9f4ea02-a24b-4633-a5d4-5a3929f6f89b\nINFO     /tmp/biobb/unitests_43/nolb_nma/nolb_nma_log.out:cmd_wrapper.py:33 NOLB d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/structure.pdb -o /tmp/biobb/unitests_43/nolb_nma/d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/nolb_ensemble -m -s 20 -c 5.0 --rmsd 1.0 --dist 1 --nSteps 5000 --tol 0.001\n\nINFO     /tmp/biobb/unitests_43/nolb_nma/nolb_nma_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_43/nolb_nma/nolb_nma_log.out:cmd_wrapper.py:52 *******************************************************************\n*-----------------------------------------------------------------*\n*-----------NOLB : a Non-Linear rigid block NMA method------------*\n*----------Authors: Alexandre Hoffmann &amp;amp; Sergei Grudinin----------*\n*-Copyright (c): Nano-D team, Inria/CNRS Grenoble, France, 2019.--*\n*--------------- e-mail: sergei.grudinin@inria.fr ----------------*\n*---- http://team.inria.fr/nano-d/software/nolb-normal-modes/ ----*\n*-----------------------------------------------------------------*\n*******************************************************************\nHostname......................................................... : biobb-runners\nRun at........................................................... : Fri May 24 09:47:17 2024\nCommand-line arguments........................................... : NOLB d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/structure.pdb -o /tmp/biobb/unitests_43/nolb_nma/d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/nolb_ensemble -m -s 20 -c 5.0 --rmsd 1.0 --dist 1 --nSteps 5000 --tol 0.001 \n=====================Reading input PDB file======================\nInput PDB file................................................... : d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/structure.pdb\nNumber of chains read............................................ : 2\nNumber of atoms read............................................. : 716\nFound............................................................ : 724 covalent bonds\n................................................................. : 966 angles\n======================Constructing Hessian=======================\nNumber of disconnected atoms..................................... : 0\nNumber of interactions........................................... : 16156\nInteraction cutoff distance...................................... : 5 A\nMemory required for the Hessian matrix........................... : 3.32803 Mb\nAll-atom Hessian size : ......................................... : 2148 x 2148\n============================Doing NMA============================\nMemory required for the RTB projection matrix.................... : 0.196655 Mb\nReduced Hessian size : .......................................... : 510 x 510\nNumber of computed modes......................................... : 10 \nNull-space size.................................................. : 1 \nLowest mode frequency............................................ : 7.08086e-05 \nHighest mode frequency........................................... : 0.0017141 \nFrequencies :\n            [ 1]................................................. : 7.08086e-05 \n            [ 2]................................................. : 9.22104e-05 \n            [ 3]................................................. : 0.000160579 \n            [ 4]................................................. : 0.000271988 \n            [ 5]................................................. : 0.000359596 \n            [ 6]................................................. : 0.000917588 \n            [ 7]................................................. : 0.00102481 \n            [ 8]................................................. : 0.00123429 \n            [ 9]................................................. : 0.0013176 \n            [10]................................................. : 0.0017141 \n===================Writing output Decoy files====================\nNumber of files.................................................. : 20\nOutput RMSD...................................................... : 1 A\nUsing outputfilename............................................. : /tmp/biobb/unitests_43/nolb_nma/d9f4ea02-a24b-4633-a5d4-5a3929f6f89b/nolb_ensemble_nlb_decoys.pdb\nCurrent energy................................................... : 0.000802458\nN minimization steps............................................. : 17\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.838698\nCurrent energy................................................... : 0.000492936\nN minimization steps............................................. : 36\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.660651\nCurrent energy................................................... : 0.000204576\nN minimization steps............................................. : 18\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.138729\nCurrent energy................................................... : 0.000755071\nN minimization steps............................................. : 28\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.304596\nCurrent energy................................................... : 0.000423189\nN minimization steps............................................. : 24\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.289287\nCurrent energy................................................... : 0.000490861\nN minimization steps............................................. : 26\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.348679\nCurrent energy................................................... : 0.000536261\nN minimization steps............................................. : 33\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.373157\nCurrent energy................................................... : 0.000600031\nN minimization steps............................................. : 49\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.724211\nCurrent energy................................................... : 0.000574138\nN minimization steps............................................. : 34\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.361212\nCurrent energy................................................... : 0.000721136\nN minimization steps............................................. : 69\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.924134\nCurrent energy................................................... : 0.00116361\nN minimization steps............................................. : 50\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.834636\nCurrent energy................................................... : 0.000324975\nN minimization steps............................................. : 17\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.127239\nCurrent energy................................................... : 0.000960058\nN minimization steps............................................. : 52\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.618944\nCurrent energy................................................... : 0.000619613\nN minimization steps............................................. : 65\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.55831\nCurrent energy................................................... : 0.000841583\nN minimization steps............................................. : 56\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.569489\nCurrent energy................................................... : 0.000284024\nN minimization steps............................................. : 25\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.23718\nCurrent energy................................................... : 0.000582824\nN minimization steps............................................. : 21\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.154705\nCurrent energy................................................... : 0.000723304\nN minimization steps............................................. : 66\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.793648\nCurrent energy................................................... : 0.00122979\nN minimization steps............................................. : 57\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.887673\nCurrent energy................................................... : 0.000270424\nN minimization steps............................................. : 18\nCurrent Gradient norm............................................ : 0.001\nDisplacement .................................................... : 0\nRMSD after minimization.......................................... : 0.0829017\n=================================================================\n=========================== Timing : ============================\n=================================================================\nParsing arguments................................................ : 0.000228639 s\nReading input PDB file........................................... : 0.00189294 s\nConstructing Hessian............................................. : 0.0121292 s\nDoing NMA........................................................ : 0.0512874 s\nWriting output Decoy files....................................... : 0.33892 s\n.................................................................\nTotal time : .................................................... : 0.404458 s\n=================================================================\n\nMain Reference: Alexandre Hoffmann &amp;amp; Sergei Grudinin. NOLB : Nonlinear rigid block normal mode analysis method. Journal of Chemical Theory and Computation, 2017, 13 (5), pp.2123-2134. DOI: 10.1021/acs.jctc.7b00197.\n\nReference for clustering and decoy generation: Emilie Neveu, Petr Popov, Alexandre Hoffmann, Angelo Migliosi, Xavier Besseron, Gregoire Danoy, Pascal Bouvry, Sergei Grudinin. RapidRMSD: Rapid determination of RMSDs corresponding to motions of flexible molecules. Bioinformatics, Oxford University Press (OUP), 2018. DOI: 10.1093/bioinformatics/bty160.\n\n\nINFO     /tmp/biobb/unitests_43/nolb_nma/nolb_nma_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_43/nolb_nma/d9f4ea02-a24b-4633-a5d4-5a3929f6f89b&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_43\n&#34;}], &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_prody_anm.py::TestProdyANM::test_prody_anm&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_flexdyn/test/unitests/test_flexdyn/test_prody_anm.py::TestProdyANM::test_prody_anm&#34;, &#34;duration&#34;: &#34;245 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_flexdyn/test/unitests/test_flexdyn/test_prody_anm.py::TestProdyANM::test_prody_anm&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;245 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 -----------------------------\n2024-05-24 09:47:17,596 [MainThread  ] [INFO ]  Executing biobb_flexdyn.flexdyn.prody_anm Version: 4.1.0\n2024-05-24 09:47:17,596 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_43/prody_anm/e06dacd0-f09a-47bd-83e3-319b105109ed\n2024-05-24 09:47:17,675 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_43/prody_anm/e06dacd0-f09a-47bd-83e3-319b105109ed&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_43/prody_anm/prody_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_43/prody_anm/prody_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/reference/flexdyn/prody_output.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 85\n     Atoms ALIGNED in PDB_B: 85\n     RMS: 8.764934491121054e-15\n     RMS_CUTOFF: 1\n\n----------------------------- Captured stderr call -----------------------------\n@&amp;gt; 775 atoms and 1 coordinate set(s) were parsed in 0.01s.\n@&amp;gt; Hessian was built in 0.01s.\n@&amp;gt; 20 modes were calculated in 0.02s.\n@&amp;gt; Parameter: rmsd = 4.00 A\n@&amp;gt; Parameter: n_confs = 20\n@&amp;gt; Modes are scaled by 2.0041663692903064.\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_43/prody_anm/prody_anm_log.out:file_utils.py:391 Executing biobb_flexdyn.flexdyn.prody_anm Version: 4.1.0\nINFO     /tmp/biobb/unitests_43/prody_anm/prody_anm_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_flexdyn/biobb_flexdyn/biobb_flexdyn/test/data/flexdyn/structure.pdb to /tmp/biobb/unitests_43/prody_anm/e06dacd0-f09a-47bd-83e3-319b105109ed\nDEBUG    .prody:logger.py:135 775 atoms and 1 coordinate set(s) were parsed in 0.01s.\nDEBUG    .prody:logger.py:135 Hessian was built in 0.01s.\nDEBUG    .prody:logger.py:135 20 modes were calculated in 0.02s.\nINFO     .prody:logger.py:123 Parameter: rmsd = 4.00 A\nINFO     .prody:logger.py:123 Parameter: n_confs = 20\nINFO     .prody:logger.py:123 Modes are scaled by 2.0041663692903064.\nINFO     /tmp/biobb/unitests_43/prody_anm/prody_anm_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_43/prody_anm/e06dacd0-f09a-47bd-83e3-319b105109ed&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_43\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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