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2025-04-11 02:15:25,260 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:15:25,260 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 02:15:25,260 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 02:15:25,260 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:15:25,261 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:15:25,287 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/7_relaxed.pdb
2025-04-11 02:15:25,289 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:15:25,292 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 908 atoms.
2025-04-11 02:15:25,292 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:15:25,293 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:15:25,293 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:15:25,293 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:15:25,310 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:15:25,311 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:15:25,311 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:15:25,311 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:15:25,321 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:15:25,321 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 02:15:25,405 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:15:25,406 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:15:25,406 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:15:25,410 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 02:22:06,520 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:22:06,521 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 02:22:06,521 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 02:22:06,521 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:22:06,521 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:22:06,548 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/7_relaxed.pdb
2025-04-11 02:22:06,550 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:22:06,553 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 908 atoms.
2025-04-11 02:22:06,553 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:22:06,555 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:22:06,555 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:22:06,556 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:22:06,568 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:22:06,569 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:22:06,569 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:22:06,569 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:22:06,577 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:22:06,577 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:22:06,585 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:22:06,653 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:22:06,654 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:22:06,654 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:22:06,657 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 08:40:15,589 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/7_relaxed.pdb
2025-04-11 08:40:15,593 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 08:40:15,617 INFO:main.py:408:setup_molecule:Created biomolecule object with 73 residues and 1073 atoms.
2025-04-11 08:40:15,617 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 08:40:15,620 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-11 08:40:15,621 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-11 08:40:15,621 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-11 08:40:15,621 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-11 08:40:15,621 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-11 08:40:15,622 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 08:40:15,631 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 08:40:15,633 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 08:40:15,633 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 08:40:15,634 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 08:40:15,663 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 08:40:15,664 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 08:40:15,694 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 08:40:15,915 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 08:40:15,917 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 08:40:15,917 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 08:40:15,926 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 09:18:43,151 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 09:18:43,151 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 09:18:43,151 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 09:18:43,209 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/7_relaxed.pdb
2025-04-15 09:18:43,216 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:18:43,238 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 09:18:43,238 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:18:43,242 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:18:43,242 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:18:43,243 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:18:43,243 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:18:43,243 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:18:43,243 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:18:43,254 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:18:43,257 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:18:43,257 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:18:43,258 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:18:43,285 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:18:43,286 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:18:43,313 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:18:43,578 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:18:43,579 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:18:43,580 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:18:43,586 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 09:31:40,784 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:31:40,785 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 09:31:40,785 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 09:31:40,785 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 09:31:40,786 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 09:31:40,852 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/7_relaxed.pdb
2025-04-15 09:31:40,860 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:31:40,882 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 09:31:40,882 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:31:40,886 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:31:40,887 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:31:40,887 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:31:40,887 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:31:40,887 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:31:40,887 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:31:40,897 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:31:40,899 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:31:40,899 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:31:40,900 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:31:40,925 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:31:40,926 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:31:40,946 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:31:41,177 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:31:41,178 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:31:41,178 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:31:41,184 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 13:06:00,756 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/7_relaxed.pdb
2025-04-15 13:06:00,763 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:06:00,770 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 13:06:00,770 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:06:00,772 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:06:00,773 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:06:00,773 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:06:00,773 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:06:00,773 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:06:00,773 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:06:00,801 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:06:00,803 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:06:00,803 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:06:00,803 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:06:00,829 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:06:00,830 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 13:06:01,086 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:06:01,087 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:06:01,088 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:06:01,097 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:25:34,193 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:25:34,194 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 13:25:34,194 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 13:25:34,194 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:25:34,194 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:25:34,238 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/7_relaxed.pdb
2025-04-15 13:25:34,245 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:25:34,253 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 13:25:34,253 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:25:34,255 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:25:34,256 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:25:34,256 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:25:34,256 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:25:34,256 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:25:34,257 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:25:34,267 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:25:34,268 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:25:34,268 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:25:34,268 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:25:34,278 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:25:34,279 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:25:34,289 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:25:34,467 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:25:34,468 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:25:34,468 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:25:34,474 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 17:10:55,787 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 17:10:55,787 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 17:10:55,787 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 17:10:55,833 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/7_relaxed.pdb
2025-04-15 17:10:55,837 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 17:10:55,866 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 17:10:55,866 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 17:10:55,867 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 17:10:55,867 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 17:10:55,867 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 17:10:55,867 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 17:10:55,868 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 17:10:55,868 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 17:10:55,872 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 17:10:55,873 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 17:10:55,873 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 17:10:55,873 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 17:10:55,891 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 17:10:55,892 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 17:10:55,912 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 17:10:56,033 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 17:10:56,034 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 17:10:56,034 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 17:10:56,038 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 18:18:20,765 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 18:18:20,766 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 18:18:20,766 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 18:18:20,766 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 18:18:20,766 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 18:18:20,813 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/7_relaxed.pdb
2025-04-15 18:18:20,817 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 18:18:20,830 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 18:18:20,830 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 18:18:20,833 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 18:18:20,833 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 18:18:20,834 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 18:18:20,834 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 18:18:20,834 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 18:18:20,834 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 18:18:20,844 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 18:18:20,846 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 18:18:20,846 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 18:18:20,847 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 18:18:20,877 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 18:18:20,878 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 18:18:20,907 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 18:18:21,061 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 18:18:21,062 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 18:18:21,062 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 18:18:21,068 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 21:59:50,281 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 21:59:50,282 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 21:59:50,282 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 21:59:50,282 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 21:59:50,282 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 21:59:50,326 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/7_relaxed.pdb
2025-04-15 21:59:50,329 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 21:59:50,344 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 21:59:50,344 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 21:59:50,345 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 21:59:50,346 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 21:59:50,346 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 21:59:50,346 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 21:59:50,346 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 21:59:50,346 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 21:59:50,350 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 21:59:50,352 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 21:59:50,352 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 21:59:50,353 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 21:59:50,372 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 21:59:50,373 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 21:59:50,385 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 21:59:50,498 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 21:59:50,499 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 21:59:50,499 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 21:59:50,503 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 22:09:42,811 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 22:09:42,812 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 22:09:42,812 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 22:09:42,812 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 22:09:42,813 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 22:09:42,854 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/7_relaxed.pdb
2025-04-15 22:09:42,856 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 22:09:42,867 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 22:09:42,867 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 22:09:42,868 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 22:09:42,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 22:09:42,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 22:09:42,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 22:09:42,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 22:09:42,869 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 22:09:42,873 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 22:09:42,873 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 22:09:42,873 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 22:09:42,874 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 22:09:42,885 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 22:09:42,885 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 22:09:42,896 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 22:09:43,084 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 22:09:43,085 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 22:09:43,085 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 22:09:43,089 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-05-05 10:19:46,577 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-05-05 10:19:46,578 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 10:19:46,578 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 10:19:46,578 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-05-05 10:19:46,579 INFO:main.py:763:main_driver:Loading topology files.
2025-05-05 10:19:46,636 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/7_relaxed.pdb
2025-05-05 10:19:46,643 INFO:main.py:770:main_driver:Setting up molecule.
2025-05-05 10:19:46,665 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1066 atoms.
2025-05-05 10:19:46,665 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-05-05 10:19:46,672 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-05-05 10:19:46,672 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-05-05 10:19:46,672 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-05-05 10:19:46,672 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-05-05 10:19:46,673 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-05-05 10:19:46,673 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 10:19:46,684 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 10:19:46,685 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-05-05 10:19:46,715 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-05-05 10:19:46,716 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-05-05 10:19:46,742 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-05-05 10:19:46,943 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-05-05 10:19:46,945 INFO:main.py:713:non_trivial:Regenerating headers.
2025-05-05 10:19:46,946 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-05-05 10:19:46,953 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.