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2025-04-11 02:15:25,249 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:15:25,249 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-11 02:15:25,249 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-11 02:15:25,249 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:15:25,249 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:15:25,277 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/6_relaxed.pdb
2025-04-11 02:15:25,279 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:15:25,281 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 916 atoms.
2025-04-11 02:15:25,281 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:15:25,285 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:15:25,306 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:15:25,307 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:15:25,308 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:15:25,308 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:15:25,318 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:15:25,318 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:15:25,329 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:15:25,472 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:15:25,473 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:15:25,473 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:15:25,476 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 02:22:06,544 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:22:06,544 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-11 02:22:06,544 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-11 02:22:06,544 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:22:06,544 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:22:06,580 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/6_relaxed.pdb
2025-04-11 02:22:06,585 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:22:06,588 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 916 atoms.
2025-04-11 02:22:06,588 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:22:06,589 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:22:06,590 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:22:06,590 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:22:06,600 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:22:06,601 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:22:06,601 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:22:06,601 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:22:06,610 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:22:06,610 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:22:06,624 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:22:06,749 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:22:06,750 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:22:06,750 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:22:06,753 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 08:40:15,514 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 08:40:15,515 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-11 08:40:15,515 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-11 08:40:15,515 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 08:40:15,516 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 08:40:15,586 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/6_relaxed.pdb
2025-04-11 08:40:15,594 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 08:40:15,618 INFO:main.py:408:setup_molecule:Created biomolecule object with 73 residues and 1092 atoms.
2025-04-11 08:40:15,618 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 08:40:15,621 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-11 08:40:15,622 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-04-11 08:40:15,622 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-04-11 08:40:15,622 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-04-11 08:40:15,622 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-04-11 08:40:15,622 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 97 and LEU A 98!
2025-04-11 08:40:15,622 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 98 and TYR A 99!
2025-04-11 08:40:15,622 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-11 08:40:15,622 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 140 and GLY A 142!
2025-04-11 08:40:15,622 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 145 and GLN A 146!
2025-04-11 08:40:15,623 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 146 and LYS A 147!
2025-04-11 08:40:15,623 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-11 08:40:15,623 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-11 08:40:15,623 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-11 08:40:15,623 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 173 and ALA A 174!
2025-04-11 08:40:15,623 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 174 and ILE A 175!
2025-04-11 08:40:15,623 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-04-11 08:40:15,623 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-04-11 08:40:15,623 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 189 and ALA A 190!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 190 and CYS A 191!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 191 and GLN A 192!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 192 and GLY A 193!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and GLY A 211!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 212 and VAL A 213!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 213 and SER A 214!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 214 and TRP A 215!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 215 and LYS A 216!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 216 and GLU A 217!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 217 and MET A 218!
2025-04-11 08:40:15,624 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between MET A 218 and CYS A 220!
2025-04-11 08:40:15,625 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 220 and ALA A 221!
2025-04-11 08:40:15,625 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-04-11 08:40:15,625 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 225 and GLY A 226!
2025-04-11 08:40:15,625 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 226 and ILE A 227!
2025-04-11 08:40:15,625 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 08:40:15,634 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 08:40:15,636 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 08:40:15,636 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 08:40:15,636 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 08:40:15,661 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 08:40:15,662 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 08:40:16,667 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 57
2025-04-11 08:40:17,344 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 145
2025-04-11 08:40:20,353 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 199
2025-04-11 08:40:20,368 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 08:40:26,607 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 08:40:26,653 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 08:40:26,654 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 08:40:26,740 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 09:18:43,150 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:18:43,150 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 09:18:43,150 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 09:18:43,150 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 09:18:43,152 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 09:18:43,203 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/6_relaxed.pdb
2025-04-15 09:18:43,209 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:18:43,226 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 09:18:43,227 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:18:43,234 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:18:43,234 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:18:43,234 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:18:43,234 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:18:43,234 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:18:43,235 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:18:43,248 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:18:43,251 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:18:43,251 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:18:43,252 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:18:43,281 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:18:43,282 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:18:43,311 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:18:43,537 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:18:43,539 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:18:43,540 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:18:43,549 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 09:31:40,793 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:31:40,793 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 09:31:40,793 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 09:31:40,793 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 09:31:40,794 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 09:31:40,836 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/6_relaxed.pdb
2025-04-15 09:31:40,840 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:31:40,854 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 09:31:40,854 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:31:40,856 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:31:40,856 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:31:40,856 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:31:40,856 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:31:40,856 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:31:40,857 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:31:40,862 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:31:40,864 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:31:40,864 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:31:40,864 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:31:40,879 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:31:40,880 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:31:40,904 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:31:41,110 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:31:41,111 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:31:41,111 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:31:41,116 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:06:00,688 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:06:00,689 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 13:06:00,689 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 13:06:00,689 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:06:00,689 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:06:00,753 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/6_relaxed.pdb
2025-04-15 13:06:00,758 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:06:00,766 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 13:06:00,766 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:06:00,769 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:06:00,770 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:06:00,770 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:06:00,770 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:06:00,770 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:06:00,770 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:06:00,798 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:06:00,800 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:06:00,800 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:06:00,801 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:06:00,828 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:06:00,829 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:06:00,856 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:06:01,026 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:06:01,027 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:06:01,027 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:06:01,033 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:25:34,174 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:25:34,174 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 13:25:34,175 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 13:25:34,175 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:25:34,175 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:25:34,202 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/6_relaxed.pdb
2025-04-15 13:25:34,206 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:25:34,214 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 13:25:34,214 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:25:34,216 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:25:34,217 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:25:34,217 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:25:34,217 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:25:34,217 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:25:34,217 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:25:34,229 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:25:34,229 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:25:34,230 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:25:34,230 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:25:34,240 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:25:34,241 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:25:34,251 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:25:34,334 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:25:34,335 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:25:34,335 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:25:34,338 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 17:10:55,785 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 17:10:55,786 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 17:10:55,786 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 17:10:55,786 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 17:10:55,787 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 17:10:55,828 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/6_relaxed.pdb
2025-04-15 17:10:55,832 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 17:10:55,849 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 17:10:55,850 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 17:10:55,853 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 17:10:55,854 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 17:10:55,854 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 17:10:55,854 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 17:10:55,854 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 17:10:55,854 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 17:10:55,860 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 17:10:55,861 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 17:10:55,861 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 17:10:55,862 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 17:10:55,873 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 17:10:55,873 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 17:10:55,890 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 17:10:56,099 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 17:10:56,101 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 17:10:56,102 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 17:10:56,110 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 18:18:20,761 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 18:18:20,761 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 18:18:20,761 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 18:18:20,761 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 18:18:20,762 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 18:18:20,820 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/6_relaxed.pdb
2025-04-15 18:18:20,828 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 18:18:20,853 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 18:18:20,853 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 18:18:20,857 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 18:18:20,857 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 18:18:20,857 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 18:18:20,857 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 18:18:20,857 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 18:18:20,858 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 18:18:20,864 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 18:18:20,865 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 18:18:20,865 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 18:18:20,866 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 18:18:20,886 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 18:18:20,887 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 18:18:20,912 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 18:18:21,235 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 18:18:21,236 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 18:18:21,237 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 18:18:21,246 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 21:59:50,283 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 21:59:50,284 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 21:59:50,284 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 21:59:50,284 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 21:59:50,285 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 21:59:50,328 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/6_relaxed.pdb
2025-04-15 21:59:50,335 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 21:59:50,352 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 21:59:50,353 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 21:59:50,354 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 21:59:50,354 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 21:59:50,354 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 21:59:50,354 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 21:59:50,354 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 21:59:50,355 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 21:59:50,359 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 21:59:50,359 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 21:59:50,360 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 21:59:50,360 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 21:59:50,376 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 21:59:50,377 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 21:59:50,389 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 21:59:50,521 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 21:59:50,522 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 21:59:50,522 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 21:59:50,526 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 22:09:42,790 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 22:09:42,790 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 22:09:42,790 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 22:09:42,790 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 22:09:42,790 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 22:09:42,825 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/6_relaxed.pdb
2025-04-15 22:09:42,828 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 22:09:42,840 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 22:09:42,840 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 22:09:42,845 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 22:09:42,845 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 22:09:42,845 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 22:09:42,845 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 22:09:42,845 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 22:09:42,846 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 22:09:42,854 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 22:09:42,855 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 22:09:42,855 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 22:09:42,856 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 22:09:42,867 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 22:09:42,868 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 22:09:42,885 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 22:09:43,076 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 22:09:43,077 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 22:09:43,077 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 22:09:43,080 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-05-05 10:19:46,578 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-05-05 10:19:46,579 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-05-05 10:19:46,579 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-05-05 10:19:46,579 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-05-05 10:19:46,580 INFO:main.py:763:main_driver:Loading topology files.
2025-05-05 10:19:46,641 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/6_relaxed.pdb
2025-05-05 10:19:46,646 INFO:main.py:770:main_driver:Setting up molecule.
2025-05-05 10:19:46,670 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-05-05 10:19:46,670 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-05-05 10:19:46,674 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-05-05 10:19:46,674 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-05-05 10:19:46,674 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-05-05 10:19:46,674 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-05-05 10:19:46,674 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-05-05 10:19:46,675 INFO:main.py:604:non_trivial:Loading forcefield.
2025-05-05 10:19:46,682 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-05-05 10:19:46,685 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-05-05 10:19:46,685 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-05-05 10:19:46,686 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-05-05 10:19:46,712 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-05-05 10:19:46,713 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-05-05 10:19:46,735 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-05-05 10:19:47,003 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-05-05 10:19:47,005 INFO:main.py:713:non_trivial:Regenerating headers.
2025-05-05 10:19:47,006 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-05-05 10:19:47,013 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.