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I don’t think the two things are related, but - when running under Mac OS the refinement tests of Rosetta (3.9 = 2018.09.60072) with PHENIX 1.14-3260 - I am also getting a (different) RuntimeError. The same test suite worked just fine with 1.13, so maybe there’s
some general Rosetta compatibility issue with 1.14?
<div class="">Best, Luca
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 6 Oct 2018, at 15:12, Simone Pellegrino <<a href="mailto:simonpelle81@gmail.com" class="">simonpelle81@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
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<div class="">Dear all,</div>
<div class=""><br class="">
</div>
<div class="">I encounter a problem running the rosetta.run_tests after having compiled rosetta for interfacing with phenix. I have the following error:</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">DEBUG dumping error message<br class="">
ERROR: Rosetta exited with status 139<br class="">
stderr output:<br class="">
Segmentation fault (core dumped)<br class="">
Traceback (most recent call last):<br class="">
File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 307, in <module><br class="">
run(sys.argv[1:], create_dir=True)<br class="">
File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run<br class="">
debug=params.output.debug)<br class="">
File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__<br class="">
self.run_jobs()<br class="">
File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 387, in run_jobs<br class="">
check_result(result)<br class="">
File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 378, in check_result<br class="">
raise RuntimeError("Aborted due to error in job %d." % result.job_id)<br class="">
RuntimeError: Aborted due to error in job 1.<br class="">
<br class="">
</div>
<div class="">Could you please help me in solving this issue?</div>
<div class="">Many thanks in advance</div>
<div class="">Best regards</div>
<div class="">Simone<br class="">
</div>
<div class=""><br class="">
-- <br class="">
<div dir="ltr" class="gmail_signature">Dr. Simone Pellegrino<br class="">
I.G.B.M.C.<br class="">
1, Rue Laurent Fries<br class="">
67404 Illkirch Cedex<br class="">
France</div>
</div>
</div>
</div>
</div>
_______________________________________________<br class="">
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Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" class="">phenixbb-leave@phenix-online.org</a></div>
</blockquote>
<br class="">
</div>
<div>//</div>
<div><br class="">
</div>
<div>
<div>OSX> rosetta.run_tests</div>
<div>Running Rosetta refinement tests</div>
<div>/usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.pdb</div>
<div>/usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz</div>
<div>phenix.rosetta_refine /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.pdb /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz number_of_models=2</div>
<div><br class="">
</div>
<div>============================== Collecting inputs ==============================</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div> ----------Processing X-ray data----------</div>
<div><br class="">
</div>
<div>F-obs:</div>
<div> /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X</div>
<div>Miller array info: /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X</div>
<div>Observation type: xray.amplitude</div>
<div>Type of data: double, size=495</div>
<div>Type of sigmas: double, size=495</div>
<div>Number of Miller indices: 495</div>
<div>Anomalous flag: False</div>
<div>Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)</div>
<div>Space group: P 1 21 1 (No. 4)</div>
<div>Systematic absences: 0</div>
<div>Centric reflections: 199</div>
<div>Resolution range: 22.4416 1.80066</div>
<div>Completeness in resolution range: 0.895118</div>
<div>Completeness with d_max=infinity: 0.895118</div>
<div>Wavelength: 1.0000</div>
<div><br class="">
</div>
<div>Number of F-obs in resolution range: 495</div>
<div>Number of F-obs<0 (these reflections will be rejected): 0</div>
<div>Number of F-obs=0 (these reflections will be used in refinement): 0</div>
<div>Refinement resolution range: d_max = 22.4416</div>
<div> d_min = 1.8007</div>
<div><br class="">
</div>
<div>R-free flags:</div>
<div> /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags</div>
<div>Miller array info: /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags</div>
<div>Observation type: None</div>
<div>Type of data: int, size=495</div>
<div>Type of sigmas: None</div>
<div>Number of Miller indices: 495</div>
<div>Anomalous flag: False</div>
<div>Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)</div>
<div>Space group: P 1 21 1 (No. 4)</div>
<div>Systematic absences: 0</div>
<div>Centric reflections: 199</div>
<div>Resolution range: 22.4416 1.80066</div>
<div>Completeness in resolution range: 0.895118</div>
<div>Completeness with d_max=infinity: 0.895118</div>
<div>Wavelength: 1.0000</div>
<div><br class="">
</div>
<div>Test (R-free flags) flag value: 1</div>
<div><br class="">
</div>
<div>Number of work/free reflections by resolution:</div>
<div> work free %free</div>
<div> bin 1: 22.4433 - 3.8734 [61/70] 59 2 3.3%</div>
<div> bin 2: 3.8734 - 3.0770 [53/58] 49 4 7.5%</div>
<div> bin 3: 3.0770 - 2.6887 [49/55] 46 3 6.1%</div>
<div> bin 4: 2.6887 - 2.4432 [37/40] 35 2 5.4%</div>
<div> bin 5: 2.4432 - 2.2683 [62/66] 60 2 3.2%</div>
<div> bin 6: 2.2683 - 2.1347 [51/56] 49 2 3.9%</div>
<div> bin 7: 2.1347 - 2.0278 [50/55] 46 4 8.0%</div>
<div> bin 8: 2.0278 - 1.9396 [49/56] 49 0 0.0%</div>
<div> bin 9: 1.9396 - 1.8650 [43/50] 42 1 2.3%</div>
<div> bin 10: 1.8650 - 1.8007 [40/47] 40 0 0.0%</div>
<div> overall 475 20 4.0%</div>
<div><br class="">
</div>
<div> ----------Processing PDB file(s)----------</div>
<div><br class="">
</div>
<div> Monomer Library directory:</div>
<div> "/usr/local/phenix/phenix-1.14-3260/modules/chem_data/mon_lib"</div>
<div> Total number of atoms: 66</div>
<div> Number of models: 1</div>
<div> Model: ""</div>
<div> Number of chains: 2</div>
<div> Chain: "A"</div>
<div> Number of atoms: 59</div>
<div> Number of conformers: 1</div>
<div> Conformer: ""</div>
<div> Number of residues, atoms: 7, 59</div>
<div> Classifications: {'peptide': 7}</div>
<div> Modifications used: {'COO': 1}</div>
<div> Link IDs: {'TRANS': 6}</div>
<div> Chain: " "</div>
<div> Number of atoms: 7</div>
<div> Number of conformers: 1</div>
<div> Conformer: ""</div>
<div> Number of residues, atoms: 7, 7</div>
<div> Classifications: {'water': 7}</div>
<div> Link IDs: {None: 6}</div>
<div> Time building chain proxies: 0.06, per 1000 atoms: 0.91</div>
<div> Number of scatterers: 66</div>
<div> At special positions: 0</div>
<div> Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)</div>
<div> Space group: P 1 21 1 (No. 4)</div>
<div> Number of sites at special positions: 0</div>
<div> Number of scattering types: 3</div>
<div> Type Number sf(0)</div>
<div> O 21 8.00</div>
<div> N 12 7.00</div>
<div> C 33 6.00</div>
<div> sf(0) = scattering factor at diffraction angle 0.</div>
<div><br class="">
</div>
<div> Number of disulfides: simple=0, symmetry=0</div>
<div> Custom bonds:</div>
<div> Warning: Ignoring bond with distance_ideal = None:</div>
<div> atom_selection_1 = None</div>
<div> atom_selection_2 = None</div>
<div> Total number of custom bonds: 0</div>
<div> Custom angles:</div>
<div> Warning: Ignoring angle with angle_ideal = None:</div>
<div> atom_selection_1 = None</div>
<div> atom_selection_2 = None</div>
<div> atom_selection_3 = None</div>
<div> Total number of custom angles: 0</div>
<div> Custom dihedrals:</div>
<div> Warning: Ignoring dihedral with angle_ideal = None:</div>
<div> atom_selection_1 = None</div>
<div> atom_selection_2 = None</div>
<div> atom_selection_3 = None</div>
<div> atom_selection_4 = None</div>
<div> Total number of custom dihedrals: 0</div>
<div> Custom planarities:</div>
<div> Warning: Ignoring planarity with with sigma <= 0:</div>
<div> atom_selection = None</div>
<div>None</div>
<div> Total number of custom planarities: 0</div>
<div> Custom parallelities:</div>
<div>Warning: Ignoring parallelity with empty atom selection.</div>
<div> Total number of custom parallelities: 0</div>
<div><br class="">
</div>
<div> Automatic linking</div>
<div> Parameters for automatic linking</div>
<div> Linking & cutoffs</div>
<div> Metal : False - 3.50</div>
<div> Amimo acid : False - 1.90</div>
<div> Carbohydrate : True - 1.99</div>
<div> Ligands : True - 1.99</div>
<div> Small molecules : False - 1.98</div>
<div> Amino acid - RNA/DNA : False</div>
<div><br class="">
</div>
<div> Number of custom bonds: simple=0, symmetry=0</div>
<div> Time building additional restraints: 0.01</div>
<div> Conformation dependent library (CDL) restraints added in 3.8 milliseconds</div>
<div><br class="">
</div>
<div> Adding C-beta torsion restraints...</div>
<div> Number of C-beta restraints generated: 12</div>
<div><br class="">
</div>
<div> Time building geometry restraints manager: 0.03 seconds</div>
<div><br class="">
</div>
<div> NOTE: a complete listing of the restraints can be obtained by requesting</div>
<div> output of .geo file.</div>
<div><br class="">
</div>
<div> Histogram of bond lengths:</div>
<div> 1.23 - 1.29: 13</div>
<div> 1.29 - 1.36: 11</div>
<div> 1.36 - 1.42: 7</div>
<div> 1.42 - 1.49: 6</div>
<div> 1.49 - 1.55: 22</div>
<div> Bond restraints: 59</div>
<div> Sorted by residual:</div>
<div> bond pdb=" N GLY A 1 "</div>
<div> pdb=" CA GLY A 1 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 1.451 1.507 -0.056 1.60e-02 3.91e+03 1.23e+01</div>
<div> bond pdb=" CA GLN A 4 "</div>
<div> pdb=" C GLN A 4 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 1.522 1.553 -0.030 1.18e-02 7.18e+03 6.53e+00</div>
<div> bond pdb=" N GLN A 4 "</div>
<div> pdb=" CA GLN A 4 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 1.460 1.485 -0.025 1.17e-02 7.31e+03 4.40e+00</div>
<div> bond pdb=" CA ASN A 2 "</div>
<div> pdb=" C ASN A 2 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 1.524 1.498 0.025 1.26e-02 6.30e+03 4.00e+00</div>
<div> bond pdb=" CA ASN A 6 "</div>
<div> pdb=" C ASN A 6 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 1.526 1.504 0.022 1.28e-02 6.10e+03 2.85e+00</div>
<div> ... (remaining 54 not shown)</div>
<div><br class="">
</div>
<div> Histogram of bond angle deviations from ideal:</div>
<div> 107.05 - 110.59: 8</div>
<div> 110.59 - 114.13: 19</div>
<div> 114.13 - 117.67: 11</div>
<div> 117.67 - 121.21: 23</div>
<div> 121.21 - 124.75: 18</div>
<div> Bond angle restraints: 79</div>
<div> Sorted by residual:</div>
<div> angle pdb=" N ASN A 3 "</div>
<div> pdb=" CA ASN A 3 "</div>
<div> pdb=" C ASN A 3 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 108.90 113.48 -4.58 1.63e+00 3.76e-01 7.90e+00</div>
<div> angle pdb=" N GLN A 4 "</div>
<div> pdb=" CA GLN A 4 "</div>
<div> pdb=" C GLN A 4 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 108.02 111.93 -3.91 1.78e+00 3.16e-01 4.84e+00</div>
<div> angle pdb=" CA GLN A 4 "</div>
<div> pdb=" C GLN A 4 "</div>
<div> pdb=" O GLN A 4 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 120.33 122.27 -1.94 1.08e+00 8.57e-01 3.23e+00</div>
<div> angle pdb=" CA GLN A 5 "</div>
<div> pdb=" C GLN A 5 "</div>
<div> pdb=" O GLN A 5 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 120.38 122.31 -1.93 1.09e+00 8.42e-01 3.13e+00</div>
<div> angle pdb=" C GLN A 4 "</div>
<div> pdb=" N GLN A 5 "</div>
<div> pdb=" CA GLN A 5 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 123.00 120.57 2.43 1.38e+00 5.25e-01 3.09e+00</div>
<div> ... (remaining 74 not shown)</div>
<div><br class="">
</div>
<div> Histogram of dihedral angle deviations from ideal:</div>
<div> 0.04 - 14.51: 26</div>
<div> 14.51 - 28.98: 5</div>
<div> 28.98 - 43.45: 1</div>
<div> 43.45 - 57.92: 1</div>
<div> 57.92 - 72.39: 1</div>
<div> Dihedral angle restraints: 34</div>
<div> sinusoidal: 15</div>
<div> harmonic: 19</div>
<div> Sorted by residual:</div>
<div> dihedral pdb=" CA ASN A 3 "</div>
<div> pdb=" C ASN A 3 "</div>
<div> pdb=" N GLN A 4 "</div>
<div> pdb=" CA GLN A 4 "</div>
<div> ideal model delta harmonic sigma weight residual</div>
<div> 180.00 166.21 13.79 0 5.00e+00 4.00e-02 7.60e+00</div>
<div> dihedral pdb=" CB GLN A 5 "</div>
<div> pdb=" CG GLN A 5 "</div>
<div> pdb=" CD GLN A 5 "</div>
<div> pdb=" OE1 GLN A 5 "</div>
<div> ideal model delta sinusoidal sigma weight residual</div>
<div> 0.00 -72.39 72.39 2 3.00e+01 1.11e-03 4.85e+00</div>
<div> dihedral pdb=" CB GLN A 4 "</div>
<div> pdb=" CG GLN A 4 "</div>
<div> pdb=" CD GLN A 4 "</div>
<div> pdb=" OE1 GLN A 4 "</div>
<div> ideal model delta sinusoidal sigma weight residual</div>
<div> 0.00 54.08 -54.08 2 3.00e+01 1.11e-03 3.50e+00</div>
<div> ... (remaining 31 not shown)</div>
<div><br class="">
</div>
<div> Histogram of chiral volume deviations from ideal:</div>
<div> 0.000 - 0.024: 1</div>
<div> 0.024 - 0.047: 1</div>
<div> 0.047 - 0.071: 1</div>
<div> 0.071 - 0.094: 1</div>
<div> 0.094 - 0.118: 2</div>
<div> Chirality restraints: 6</div>
<div> Sorted by residual:</div>
<div> chirality pdb=" CA GLN A 5 "</div>
<div> pdb=" N GLN A 5 "</div>
<div> pdb=" C GLN A 5 "</div>
<div> pdb=" CB GLN A 5 "</div>
<div> both_signs ideal model delta sigma weight residual</div>
<div> False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01</div>
<div> chirality pdb=" CA ASN A 6 "</div>
<div> pdb=" N ASN A 6 "</div>
<div> pdb=" C ASN A 6 "</div>
<div> pdb=" CB ASN A 6 "</div>
<div> both_signs ideal model delta sigma weight residual</div>
<div> False 2.51 2.62 -0.11 2.00e-01 2.50e+01 2.86e-01</div>
<div> chirality pdb=" CA ASN A 2 "</div>
<div> pdb=" N ASN A 2 "</div>
<div> pdb=" C ASN A 2 "</div>
<div> pdb=" CB ASN A 2 "</div>
<div> both_signs ideal model delta sigma weight residual</div>
<div> False 2.51 2.43 0.08 2.00e-01 2.50e+01 1.80e-01</div>
<div> ... (remaining 3 not shown)</div>
<div><br class="">
</div>
<div> Planarity restraints: 13</div>
<div> Sorted by residual:</div>
<div> delta sigma weight rms_deltas residual</div>
<div> plane pdb=" CB TYR A 7 " -0.006 2.00e-02 2.50e+03 9.66e-03 1.87e+00</div>
<div> pdb=" CG TYR A 7 " 0.022 2.00e-02 2.50e+03</div>
<div> pdb=" CD1 TYR A 7 " -0.004 2.00e-02 2.50e+03</div>
<div> pdb=" CD2 TYR A 7 " -0.008 2.00e-02 2.50e+03</div>
<div> pdb=" CE1 TYR A 7 " -0.001 2.00e-02 2.50e+03</div>
<div> pdb=" CE2 TYR A 7 " 0.002 2.00e-02 2.50e+03</div>
<div> pdb=" CZ TYR A 7 " -0.011 2.00e-02 2.50e+03</div>
<div> pdb=" OH TYR A 7 " 0.006 2.00e-02 2.50e+03</div>
<div> delta sigma weight rms_deltas residual</div>
<div> plane pdb=" CB ASN A 2 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00</div>
<div> pdb=" CG ASN A 2 " -0.021 2.00e-02 2.50e+03</div>
<div> pdb=" OD1 ASN A 2 " 0.008 2.00e-02 2.50e+03</div>
<div> pdb=" ND2 ASN A 2 " 0.007 2.00e-02 2.50e+03</div>
<div> delta sigma weight rms_deltas residual</div>
<div> plane pdb=" CA GLN A 4 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00</div>
<div> pdb=" C GLN A 4 " -0.019 2.00e-02 2.50e+03</div>
<div> pdb=" O GLN A 4 " 0.007 2.00e-02 2.50e+03</div>
<div> pdb=" N GLN A 5 " 0.006 2.00e-02 2.50e+03</div>
<div> ... (remaining 10 not shown)</div>
<div><br class="">
</div>
<div> Histogram of nonbonded interaction distances:</div>
<div> 2.53 - 3.00: 50</div>
<div> 3.00 - 3.48: 107</div>
<div> 3.48 - 3.95: 243</div>
<div> 3.95 - 4.42: 255</div>
<div> 4.42 - 4.90: 523</div>
<div> Nonbonded interactions: 1178</div>
<div> Sorted by model distance:</div>
<div> nonbonded pdb=" OH TYR A 7 "</div>
<div> pdb=" O HOH 11 "</div>
<div> model vdw sym.op.</div>
<div> 2.525 2.440 -x+1,y-1/2,-z+1</div>
<div> nonbonded pdb=" O HOH 11 "</div>
<div> pdb=" OH TYR A 7 "</div>
<div> model vdw sym.op.</div>
<div> 2.525 2.440 -x+1,y+1/2,-z+1</div>
<div> nonbonded pdb=" O HOH 14 "</div>
<div> pdb=" O HOH 13 "</div>
<div> model vdw sym.op.</div>
<div> 2.634 2.440 x,y-1,z</div>
<div> nonbonded pdb=" O HOH 13 "</div>
<div> pdb=" O HOH 14 "</div>
<div> model vdw sym.op.</div>
<div> 2.634 2.440 x,y+1,z</div>
<div> nonbonded pdb=" N GLY A 1 "</div>
<div> pdb=" O GLY A 1 "</div>
<div> model vdw</div>
<div> 2.665 2.496</div>
<div> ... (remaining 1173 not shown)</div>
<div><br class="">
</div>
<div> NOTE: a complete listing of the restraints can be obtained by requesting</div>
<div> output of .geo file.</div>
<div><br class="">
</div>
<div>============================== Scattering factors =============================</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div> ----------X-ray scattering dictionary----------</div>
<div><br class="">
</div>
<div>Number of scattering types: 3</div>
<div> Type Number sf(0) Gaussians</div>
<div> O 21 7.97 2</div>
<div> N 12 6.97 2</div>
<div> C 33 5.97 2</div>
<div> sf(0) = scattering factor at diffraction angle 0.</div>
<div><br class="">
</div>
<div>Number of scatterers: 66</div>
<div>At special positions: 0</div>
<div>Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)</div>
<div>Space group: P 1 21 1 (No. 4)</div>
<div><br class="">
</div>
<div> ----------F(model) initialization----------</div>
<div><br class="">
</div>
<div>Twinning will be detected automatically.</div>
<div> start: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.: 495</div>
<div> re-set all scales: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.: 495</div>
<div> remove outliers: r(all,work,free)=0.2103 0.2117 0.1924 n_refl.: 493</div>
<div>bulk-solvent and scaling: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.: 493</div>
<div> remove outliers: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.: 493</div>
<div>|--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06 % free)--------------|</div>
<div>| |</div>
<div>| r_work= 0.1758 r_free= 0.1728 coordinate error (max.-lik. estimate): 0.00 A |</div>
<div>| |</div>
<div>| normalized target function (ml) (work): 2.637727 |</div>
<div>| target function (ml) not normalized (work): 1247.644901 |</div>
<div>| target function (ml) not normalized (free): 60.766973 |</div>
<div>|-----------------------------------------------------------------------------|</div>
<div><br class="">
</div>
<div>End of input processing</div>
<div><br class="">
</div>
<div>======================= ROSETTA/PHENIX X-ray refinement =======================</div>
<div><br class="">
</div>
<div>Output directory:</div>
<div> /usr/local/rosetta/rosetta-2018.09.60072/test/rosetta_1</div>
<div><br class="">
</div>
<div> ----------Setting up input files for Rosetta----------</div>
<div><br class="">
</div>
<div>/usr/local/rosetta/rosetta-2018.09.60072/main/source</div>
<div>|-starting model--------------------------------------------------------------|</div>
<div>| target_work(ml) = 2.63773 r_work = 0.1758 r_free = 0.1728 |</div>
<div>|-----------------------------------------------------------------------------|</div>
<div><br class="">
</div>
<div> Validation statistics (starting model):</div>
<div> Ramachandran outliers = 0.00 %</div>
<div> favored = 100.00 %</div>
<div> Rotamer outliers = 0.00 %</div>
<div> C-beta deviations = 0</div>
<div> Clashscore = 0.00</div>
<div> RMS(bonds) = 0.0000</div>
<div> RMS(angles) = 0.00</div>
<div> MolProbity score = 0.50</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div>Rosetta command-line arguments:</div>
<div> -parser:protocol /usr/local/rosetta/rosetta-2018.09.60072/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml</div>
<div> -s 1yjp_rosetta_in.pdb</div>
<div> -mtzfile 1yjp_rosetta_data.mtz</div>
<div> -run:preserve_header</div>
<div> -crystal_refine</div>
<div> -parser:script_vars symmdef=1yjp_rosetta.symm</div>
<div> -parser:script_vars bfactstrat=individual</div>
<div> -parser:script_vars map_type=Auto</div>
<div> -nstruct 1</div>
<div><br class="">
</div>
<div>Generating 2 models on 1 processors...</div>
<div><br class="">
</div>
<div> 1: r_work = 0.4326 r_free = 0.4380 energy = -19.44 rmsd = 26.004 ***</div>
<div> 2: r_work = 0.3910 r_free = 0.5014 energy = 34.57 rmsd = 12.233</div>
<div><br class="">
</div>
<div>|-after ROSETTA---------------------------------------------------------------|</div>
<div>| target_work(ml) = 3.3273 r_work = 0.4326 r_free = 0.4380 |</div>
<div>|-----------------------------------------------------------------------------|</div>
<div><br class="">
</div>
<div> Validation statistics after ROSETTA:</div>
<div> Ramachandran outliers = 0.00 %</div>
<div> favored = 100.00 %</div>
<div> Rotamer outliers = 0.00 %</div>
<div> C-beta deviations = 1</div>
<div> Clashscore = 18.69</div>
<div> RMS(bonds) = 0.0000</div>
<div> RMS(angles) = 0.00</div>
<div> MolProbity score = 1.77</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div> ----------Running phenix.refine (with null strategy)----------</div>
<div><br class="">
</div>
<div>start r_work=0.4915 r_free=0.4690</div>
<div>1_bss r_work=0.3789 r_free=0.4327</div>
<div>end r_work=0.3789 r_free=0.4327</div>
<div> Ramachandran outliers = 0.00 %</div>
<div> favored = 100.00 %</div>
<div> Rotamer outliers = 0.00 %</div>
<div> C-beta deviations = 1</div>
<div> Clashscore = 19.05</div>
<div> RMS(bonds) = 0.0000</div>
<div> RMS(angles) = 0.00</div>
<div> MolProbity score = 1.78</div>
<div><br class="">
</div>
<div> ----------Final results----------</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div>Refined model: 1yjp_rosetta_phenix_001.pdb</div>
<div>Final maps: 1yjp_rosetta_phenix_001.mtz</div>
<div><br class="">
</div>
<div>Elapsed time: 669.9s</div>
<div><br class="">
</div>
<div>Citation:</div>
<div><br class="">
</div>
<div>DiMaio F., Echols N., Headd J.J., Terwilliger T.C., Adams P.D., and Baker D.</div>
<div>(2013). Improved low-resolution crystallographic refinement with Phenix and</div>
<div>Rosetta. Nat Methods 10, 1102-4.</div>
<div><br class="">
</div>
<div>phenix.rosetta_refine /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.pdb /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz number_of_models=2 nproc=2</div>
<div><br class="">
</div>
<div>============================== Collecting inputs ==============================</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div> ----------Processing X-ray data----------</div>
<div><br class="">
</div>
<div>F-obs:</div>
<div> /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X</div>
<div>Miller array info: /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X</div>
<div>Observation type: xray.amplitude</div>
<div>Type of data: double, size=495</div>
<div>Type of sigmas: double, size=495</div>
<div>Number of Miller indices: 495</div>
<div>Anomalous flag: False</div>
<div>Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)</div>
<div>Space group: P 1 21 1 (No. 4)</div>
<div>Systematic absences: 0</div>
<div>Centric reflections: 199</div>
<div>Resolution range: 22.4416 1.80066</div>
<div>Completeness in resolution range: 0.895118</div>
<div>Completeness with d_max=infinity: 0.895118</div>
<div>Wavelength: 1.0000</div>
<div><br class="">
</div>
<div>Number of F-obs in resolution range: 495</div>
<div>Number of F-obs<0 (these reflections will be rejected): 0</div>
<div>Number of F-obs=0 (these reflections will be used in refinement): 0</div>
<div>Refinement resolution range: d_max = 22.4416</div>
<div> d_min = 1.8007</div>
<div><br class="">
</div>
<div>R-free flags:</div>
<div> /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags</div>
<div>Miller array info: /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags</div>
<div>Observation type: None</div>
<div>Type of data: int, size=495</div>
<div>Type of sigmas: None</div>
<div>Number of Miller indices: 495</div>
<div>Anomalous flag: False</div>
<div>Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)</div>
<div>Space group: P 1 21 1 (No. 4)</div>
<div>Systematic absences: 0</div>
<div>Centric reflections: 199</div>
<div>Resolution range: 22.4416 1.80066</div>
<div>Completeness in resolution range: 0.895118</div>
<div>Completeness with d_max=infinity: 0.895118</div>
<div>Wavelength: 1.0000</div>
<div><br class="">
</div>
<div>Test (R-free flags) flag value: 1</div>
<div><br class="">
</div>
<div>Number of work/free reflections by resolution:</div>
<div> work free %free</div>
<div> bin 1: 22.4433 - 3.8734 [61/70] 59 2 3.3%</div>
<div> bin 2: 3.8734 - 3.0770 [53/58] 49 4 7.5%</div>
<div> bin 3: 3.0770 - 2.6887 [49/55] 46 3 6.1%</div>
<div> bin 4: 2.6887 - 2.4432 [37/40] 35 2 5.4%</div>
<div> bin 5: 2.4432 - 2.2683 [62/66] 60 2 3.2%</div>
<div> bin 6: 2.2683 - 2.1347 [51/56] 49 2 3.9%</div>
<div> bin 7: 2.1347 - 2.0278 [50/55] 46 4 8.0%</div>
<div> bin 8: 2.0278 - 1.9396 [49/56] 49 0 0.0%</div>
<div> bin 9: 1.9396 - 1.8650 [43/50] 42 1 2.3%</div>
<div> bin 10: 1.8650 - 1.8007 [40/47] 40 0 0.0%</div>
<div> overall 475 20 4.0%</div>
<div><br class="">
</div>
<div> ----------Processing PDB file(s)----------</div>
<div><br class="">
</div>
<div> Monomer Library directory:</div>
<div> "/usr/local/phenix/phenix-1.14-3260/modules/chem_data/mon_lib"</div>
<div> Total number of atoms: 66</div>
<div> Number of models: 1</div>
<div> Model: ""</div>
<div> Number of chains: 2</div>
<div> Chain: "A"</div>
<div> Number of atoms: 59</div>
<div> Number of conformers: 1</div>
<div> Conformer: ""</div>
<div> Number of residues, atoms: 7, 59</div>
<div> Classifications: {'peptide': 7}</div>
<div> Modifications used: {'COO': 1}</div>
<div> Link IDs: {'TRANS': 6}</div>
<div> Chain: " "</div>
<div> Number of atoms: 7</div>
<div> Number of conformers: 1</div>
<div> Conformer: ""</div>
<div> Number of residues, atoms: 7, 7</div>
<div> Classifications: {'water': 7}</div>
<div> Link IDs: {None: 6}</div>
<div> Time building chain proxies: 0.06, per 1000 atoms: 0.91</div>
<div> Number of scatterers: 66</div>
<div> At special positions: 0</div>
<div> Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)</div>
<div> Space group: P 1 21 1 (No. 4)</div>
<div> Number of sites at special positions: 0</div>
<div> Number of scattering types: 3</div>
<div> Type Number sf(0)</div>
<div> O 21 8.00</div>
<div> N 12 7.00</div>
<div> C 33 6.00</div>
<div> sf(0) = scattering factor at diffraction angle 0.</div>
<div><br class="">
</div>
<div> Number of disulfides: simple=0, symmetry=0</div>
<div> Custom bonds:</div>
<div> Warning: Ignoring bond with distance_ideal = None:</div>
<div> atom_selection_1 = None</div>
<div> atom_selection_2 = None</div>
<div> Total number of custom bonds: 0</div>
<div> Custom angles:</div>
<div> Warning: Ignoring angle with angle_ideal = None:</div>
<div> atom_selection_1 = None</div>
<div> atom_selection_2 = None</div>
<div> atom_selection_3 = None</div>
<div> Total number of custom angles: 0</div>
<div> Custom dihedrals:</div>
<div> Warning: Ignoring dihedral with angle_ideal = None:</div>
<div> atom_selection_1 = None</div>
<div> atom_selection_2 = None</div>
<div> atom_selection_3 = None</div>
<div> atom_selection_4 = None</div>
<div> Total number of custom dihedrals: 0</div>
<div> Custom planarities:</div>
<div> Warning: Ignoring planarity with with sigma <= 0:</div>
<div> atom_selection = None</div>
<div>None</div>
<div> Total number of custom planarities: 0</div>
<div> Custom parallelities:</div>
<div>Warning: Ignoring parallelity with empty atom selection.</div>
<div> Total number of custom parallelities: 0</div>
<div><br class="">
</div>
<div> Automatic linking</div>
<div> Parameters for automatic linking</div>
<div> Linking & cutoffs</div>
<div> Metal : False - 3.50</div>
<div> Amimo acid : False - 1.90</div>
<div> Carbohydrate : True - 1.99</div>
<div> Ligands : True - 1.99</div>
<div> Small molecules : False - 1.98</div>
<div> Amino acid - RNA/DNA : False</div>
<div><br class="">
</div>
<div> Number of custom bonds: simple=0, symmetry=0</div>
<div> Time building additional restraints: 0.01</div>
<div> Conformation dependent library (CDL) restraints added in 2.9 milliseconds</div>
<div><br class="">
</div>
<div> Adding C-beta torsion restraints...</div>
<div> Number of C-beta restraints generated: 12</div>
<div><br class="">
</div>
<div> Time building geometry restraints manager: 0.01 seconds</div>
<div><br class="">
</div>
<div> NOTE: a complete listing of the restraints can be obtained by requesting</div>
<div> output of .geo file.</div>
<div><br class="">
</div>
<div> Histogram of bond lengths:</div>
<div> 1.23 - 1.29: 13</div>
<div> 1.29 - 1.36: 11</div>
<div> 1.36 - 1.42: 7</div>
<div> 1.42 - 1.49: 6</div>
<div> 1.49 - 1.55: 22</div>
<div> Bond restraints: 59</div>
<div> Sorted by residual:</div>
<div> bond pdb=" N GLY A 1 "</div>
<div> pdb=" CA GLY A 1 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 1.451 1.507 -0.056 1.60e-02 3.91e+03 1.23e+01</div>
<div> bond pdb=" CA GLN A 4 "</div>
<div> pdb=" C GLN A 4 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 1.522 1.553 -0.030 1.18e-02 7.18e+03 6.53e+00</div>
<div> bond pdb=" N GLN A 4 "</div>
<div> pdb=" CA GLN A 4 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 1.460 1.485 -0.025 1.17e-02 7.31e+03 4.40e+00</div>
<div> bond pdb=" CA ASN A 2 "</div>
<div> pdb=" C ASN A 2 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 1.524 1.498 0.025 1.26e-02 6.30e+03 4.00e+00</div>
<div> bond pdb=" CA ASN A 6 "</div>
<div> pdb=" C ASN A 6 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 1.526 1.504 0.022 1.28e-02 6.10e+03 2.85e+00</div>
<div> ... (remaining 54 not shown)</div>
<div><br class="">
</div>
<div> Histogram of bond angle deviations from ideal:</div>
<div> 107.05 - 110.59: 8</div>
<div> 110.59 - 114.13: 19</div>
<div> 114.13 - 117.67: 11</div>
<div> 117.67 - 121.21: 23</div>
<div> 121.21 - 124.75: 18</div>
<div> Bond angle restraints: 79</div>
<div> Sorted by residual:</div>
<div> angle pdb=" N ASN A 3 "</div>
<div> pdb=" CA ASN A 3 "</div>
<div> pdb=" C ASN A 3 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 108.90 113.48 -4.58 1.63e+00 3.76e-01 7.90e+00</div>
<div> angle pdb=" N GLN A 4 "</div>
<div> pdb=" CA GLN A 4 "</div>
<div> pdb=" C GLN A 4 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 108.02 111.93 -3.91 1.78e+00 3.16e-01 4.84e+00</div>
<div> angle pdb=" CA GLN A 4 "</div>
<div> pdb=" C GLN A 4 "</div>
<div> pdb=" O GLN A 4 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 120.33 122.27 -1.94 1.08e+00 8.57e-01 3.23e+00</div>
<div> angle pdb=" CA GLN A 5 "</div>
<div> pdb=" C GLN A 5 "</div>
<div> pdb=" O GLN A 5 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 120.38 122.31 -1.93 1.09e+00 8.42e-01 3.13e+00</div>
<div> angle pdb=" C GLN A 4 "</div>
<div> pdb=" N GLN A 5 "</div>
<div> pdb=" CA GLN A 5 "</div>
<div> ideal model delta sigma weight residual</div>
<div> 123.00 120.57 2.43 1.38e+00 5.25e-01 3.09e+00</div>
<div> ... (remaining 74 not shown)</div>
<div><br class="">
</div>
<div> Histogram of dihedral angle deviations from ideal:</div>
<div> 0.04 - 14.51: 26</div>
<div> 14.51 - 28.98: 5</div>
<div> 28.98 - 43.45: 1</div>
<div> 43.45 - 57.92: 1</div>
<div> 57.92 - 72.39: 1</div>
<div> Dihedral angle restraints: 34</div>
<div> sinusoidal: 15</div>
<div> harmonic: 19</div>
<div> Sorted by residual:</div>
<div> dihedral pdb=" CA ASN A 3 "</div>
<div> pdb=" C ASN A 3 "</div>
<div> pdb=" N GLN A 4 "</div>
<div> pdb=" CA GLN A 4 "</div>
<div> ideal model delta harmonic sigma weight residual</div>
<div> 180.00 166.21 13.79 0 5.00e+00 4.00e-02 7.60e+00</div>
<div> dihedral pdb=" CB GLN A 5 "</div>
<div> pdb=" CG GLN A 5 "</div>
<div> pdb=" CD GLN A 5 "</div>
<div> pdb=" OE1 GLN A 5 "</div>
<div> ideal model delta sinusoidal sigma weight residual</div>
<div> 0.00 -72.39 72.39 2 3.00e+01 1.11e-03 4.85e+00</div>
<div> dihedral pdb=" CB GLN A 4 "</div>
<div> pdb=" CG GLN A 4 "</div>
<div> pdb=" CD GLN A 4 "</div>
<div> pdb=" OE1 GLN A 4 "</div>
<div> ideal model delta sinusoidal sigma weight residual</div>
<div> 0.00 54.08 -54.08 2 3.00e+01 1.11e-03 3.50e+00</div>
<div> ... (remaining 31 not shown)</div>
<div><br class="">
</div>
<div> Histogram of chiral volume deviations from ideal:</div>
<div> 0.000 - 0.024: 1</div>
<div> 0.024 - 0.047: 1</div>
<div> 0.047 - 0.071: 1</div>
<div> 0.071 - 0.094: 1</div>
<div> 0.094 - 0.118: 2</div>
<div> Chirality restraints: 6</div>
<div> Sorted by residual:</div>
<div> chirality pdb=" CA GLN A 5 "</div>
<div> pdb=" N GLN A 5 "</div>
<div> pdb=" C GLN A 5 "</div>
<div> pdb=" CB GLN A 5 "</div>
<div> both_signs ideal model delta sigma weight residual</div>
<div> False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01</div>
<div> chirality pdb=" CA ASN A 6 "</div>
<div> pdb=" N ASN A 6 "</div>
<div> pdb=" C ASN A 6 "</div>
<div> pdb=" CB ASN A 6 "</div>
<div> both_signs ideal model delta sigma weight residual</div>
<div> False 2.51 2.62 -0.11 2.00e-01 2.50e+01 2.86e-01</div>
<div> chirality pdb=" CA ASN A 2 "</div>
<div> pdb=" N ASN A 2 "</div>
<div> pdb=" C ASN A 2 "</div>
<div> pdb=" CB ASN A 2 "</div>
<div> both_signs ideal model delta sigma weight residual</div>
<div> False 2.51 2.43 0.08 2.00e-01 2.50e+01 1.80e-01</div>
<div> ... (remaining 3 not shown)</div>
<div><br class="">
</div>
<div> Planarity restraints: 13</div>
<div> Sorted by residual:</div>
<div> delta sigma weight rms_deltas residual</div>
<div> plane pdb=" CB TYR A 7 " -0.006 2.00e-02 2.50e+03 9.66e-03 1.87e+00</div>
<div> pdb=" CG TYR A 7 " 0.022 2.00e-02 2.50e+03</div>
<div> pdb=" CD1 TYR A 7 " -0.004 2.00e-02 2.50e+03</div>
<div> pdb=" CD2 TYR A 7 " -0.008 2.00e-02 2.50e+03</div>
<div> pdb=" CE1 TYR A 7 " -0.001 2.00e-02 2.50e+03</div>
<div> pdb=" CE2 TYR A 7 " 0.002 2.00e-02 2.50e+03</div>
<div> pdb=" CZ TYR A 7 " -0.011 2.00e-02 2.50e+03</div>
<div> pdb=" OH TYR A 7 " 0.006 2.00e-02 2.50e+03</div>
<div> delta sigma weight rms_deltas residual</div>
<div> plane pdb=" CB ASN A 2 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00</div>
<div> pdb=" CG ASN A 2 " -0.021 2.00e-02 2.50e+03</div>
<div> pdb=" OD1 ASN A 2 " 0.008 2.00e-02 2.50e+03</div>
<div> pdb=" ND2 ASN A 2 " 0.007 2.00e-02 2.50e+03</div>
<div> delta sigma weight rms_deltas residual</div>
<div> plane pdb=" CA GLN A 4 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00</div>
<div> pdb=" C GLN A 4 " -0.019 2.00e-02 2.50e+03</div>
<div> pdb=" O GLN A 4 " 0.007 2.00e-02 2.50e+03</div>
<div> pdb=" N GLN A 5 " 0.006 2.00e-02 2.50e+03</div>
<div> ... (remaining 10 not shown)</div>
<div><br class="">
</div>
<div> Histogram of nonbonded interaction distances:</div>
<div> 2.53 - 3.00: 50</div>
<div> 3.00 - 3.48: 107</div>
<div> 3.48 - 3.95: 243</div>
<div> 3.95 - 4.42: 255</div>
<div> 4.42 - 4.90: 523</div>
<div> Nonbonded interactions: 1178</div>
<div> Sorted by model distance:</div>
<div> nonbonded pdb=" OH TYR A 7 "</div>
<div> pdb=" O HOH 11 "</div>
<div> model vdw sym.op.</div>
<div> 2.525 2.440 -x+1,y-1/2,-z+1</div>
<div> nonbonded pdb=" O HOH 11 "</div>
<div> pdb=" OH TYR A 7 "</div>
<div> model vdw sym.op.</div>
<div> 2.525 2.440 -x+1,y+1/2,-z+1</div>
<div> nonbonded pdb=" O HOH 14 "</div>
<div> pdb=" O HOH 13 "</div>
<div> model vdw sym.op.</div>
<div> 2.634 2.440 x,y-1,z</div>
<div> nonbonded pdb=" O HOH 13 "</div>
<div> pdb=" O HOH 14 "</div>
<div> model vdw sym.op.</div>
<div> 2.634 2.440 x,y+1,z</div>
<div> nonbonded pdb=" N GLY A 1 "</div>
<div> pdb=" O GLY A 1 "</div>
<div> model vdw</div>
<div> 2.665 2.496</div>
<div> ... (remaining 1173 not shown)</div>
<div><br class="">
</div>
<div> NOTE: a complete listing of the restraints can be obtained by requesting</div>
<div> output of .geo file.</div>
<div><br class="">
</div>
<div>============================== Scattering factors =============================</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div> ----------X-ray scattering dictionary----------</div>
<div><br class="">
</div>
<div>Number of scattering types: 3</div>
<div> Type Number sf(0) Gaussians</div>
<div> O 21 7.97 2</div>
<div> N 12 6.97 2</div>
<div> C 33 5.97 2</div>
<div> sf(0) = scattering factor at diffraction angle 0.</div>
<div><br class="">
</div>
<div>Number of scatterers: 66</div>
<div>At special positions: 0</div>
<div>Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)</div>
<div>Space group: P 1 21 1 (No. 4)</div>
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</div>
<div> ----------F(model) initialization----------</div>
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</div>
<div>Twinning will be detected automatically.</div>
<div> start: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.: 495</div>
<div> re-set all scales: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.: 495</div>
<div> remove outliers: r(all,work,free)=0.2103 0.2117 0.1924 n_refl.: 493</div>
<div>bulk-solvent and scaling: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.: 493</div>
<div> remove outliers: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.: 493</div>
<div>|--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06 % free)--------------|</div>
<div>| |</div>
<div>| r_work= 0.1758 r_free= 0.1728 coordinate error (max.-lik. estimate): 0.00 A |</div>
<div>| |</div>
<div>| normalized target function (ml) (work): 2.637727 |</div>
<div>| target function (ml) not normalized (work): 1247.644901 |</div>
<div>| target function (ml) not normalized (free): 60.766973 |</div>
<div>|-----------------------------------------------------------------------------|</div>
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<div>End of input processing</div>
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</div>
<div>======================= ROSETTA/PHENIX X-ray refinement =======================</div>
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</div>
<div>Output directory:</div>
<div> /usr/local/rosetta/rosetta-2018.09.60072/test/rosetta_2</div>
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<div> ----------Setting up input files for Rosetta----------</div>
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<div>/usr/local/rosetta/rosetta-2018.09.60072/main/source</div>
<div>|-starting model--------------------------------------------------------------|</div>
<div>| target_work(ml) = 2.63773 r_work = 0.1758 r_free = 0.1728 |</div>
<div>|-----------------------------------------------------------------------------|</div>
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<div> Validation statistics (starting model):</div>
<div> Ramachandran outliers = 0.00 %</div>
<div> favored = 100.00 %</div>
<div> Rotamer outliers = 0.00 %</div>
<div> C-beta deviations = 0</div>
<div> Clashscore = 0.00</div>
<div> RMS(bonds) = 0.0000</div>
<div> RMS(angles) = 0.00</div>
<div> MolProbity score = 0.50</div>
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<div>Rosetta command-line arguments:</div>
<div> -parser:protocol /usr/local/rosetta/rosetta-2018.09.60072/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml</div>
<div> -s 1yjp_rosetta_in.pdb</div>
<div> -mtzfile 1yjp_rosetta_data.mtz</div>
<div> -run:preserve_header</div>
<div> -crystal_refine</div>
<div> -parser:script_vars symmdef=1yjp_rosetta.symm</div>
<div> -parser:script_vars bfactstrat=individual</div>
<div> -parser:script_vars map_type=Auto</div>
<div> -nstruct 1</div>
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<div>Generating 2 models on 2 processors...</div>
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<div>Traceback (most recent call last):</div>
<div> File "/usr/local/phenix/phenix-1.14-3260/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 307, in <module></div>
<div>DEBUG dumping error message</div>
<div>ERROR: Rosetta exited with status -9</div>
<div>stderr output:</div>
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<div> run(sys.argv[1:], create_dir=True)</div>
<div> File "/usr/local/phenix/phenix-1.14-3260/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run</div>
<div> debug=params.output.debug)</div>
<div> File "/usr/local/phenix/phenix-1.14-3260/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__</div>
<div> self.run_jobs()</div>
<div> File "/usr/local/phenix/phenix-1.14-3260/modules/phenix/phenix/rosetta/refine.py", line 396, in run_jobs</div>
<div> check_result(result)</div>
<div> File "/usr/local/phenix/phenix-1.14-3260/modules/phenix/phenix/rosetta/refine.py", line 382, in check_result</div>
<div> raise RuntimeError("File '%s' not found." % result.file_name)</div>
<div>RuntimeError: File 'None' not found.</div>
<div>OSX></div>
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