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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 02:15:25,250 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 02:15:25,250 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 02:15:25,250 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:15:25,250 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:15:25,293 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/2_relaxed.pdb
2025-04-11 02:15:25,295 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:15:25,298 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 914 atoms.
2025-04-11 02:15:25,298 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:15:25,299 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 375 and TYR A 383!
2025-04-11 02:15:25,299 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 383 and TYR A 415!
2025-04-11 02:15:25,299 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:15:25,299 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 473 and GLN A 474!
2025-04-11 02:15:25,299 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 474 and HIS A 475!
2025-04-11 02:15:25,299 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 475 and ARG A 476!
2025-04-11 02:15:25,299 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 477 and THR A 478!
2025-04-11 02:15:25,299 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 479 and GLU A 481!
2025-04-11 02:15:25,300 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 487 and LEU A 489!
2025-04-11 02:15:25,300 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 490 and PRO A 495!
2025-04-11 02:15:25,300 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 496 and VAL A 497!
2025-04-11 02:15:25,300 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 497 and ARG A 498!
2025-04-11 02:15:25,300 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 500 and ARG A 501!
2025-04-11 02:15:25,300 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 501 and SER A 502!
2025-04-11 02:15:25,300 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 502 and ALA A 504!
2025-04-11 02:15:25,300 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:15:25,300 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 528 and ALA A 529!
2025-04-11 02:15:25,300 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:15:25,311 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:15:25,312 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:15:25,312 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:15:25,312 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:15:25,320 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 02:15:25,381 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:15:25,382 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:15:25,382 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:15:25,385 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 02:22:06,524 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:22:06,524 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 02:22:06,524 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 02:22:06,524 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:22:06,525 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:22:06,551 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/2_relaxed.pdb
2025-04-11 02:22:06,553 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:22:06,556 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 914 atoms.
2025-04-11 02:22:06,556 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:22:06,557 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 375 and TYR A 383!
2025-04-11 02:22:06,557 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 383 and TYR A 415!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 473 and GLN A 474!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 474 and HIS A 475!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 475 and ARG A 476!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 477 and THR A 478!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 479 and GLU A 481!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 487 and LEU A 489!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 490 and PRO A 495!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 496 and VAL A 497!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 497 and ARG A 498!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 500 and ARG A 501!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 501 and SER A 502!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 502 and ALA A 504!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:22:06,558 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 528 and ALA A 529!
2025-04-11 02:22:06,558 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:22:06,570 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:22:06,571 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:22:06,571 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:22:06,571 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:22:06,579 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:22:06,580 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:22:06,588 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:22:06,636 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:22:06,637 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:22:06,637 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:22:06,640 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 08:40:15,517 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 08:40:15,517 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 08:40:15,517 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 08:40:15,518 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 08:40:15,518 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/2p16/2_relaxed.pdb
2025-04-11 08:40:15,592 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 08:40:15,615 INFO:main.py:408:setup_molecule:Created biomolecule object with 73 residues and 1070 atoms.
2025-04-11 08:40:15,615 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 08:40:15,618 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-11 08:40:15,619 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-11 08:40:15,619 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-11 08:40:15,619 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-11 08:40:15,619 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-11 08:40:15,620 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 08:40:15,629 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 08:40:15,631 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 08:40:15,631 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 08:40:15,631 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 08:40:15,658 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 08:40:15,659 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 08:40:15,686 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 08:40:15,933 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 08:40:15,934 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 08:40:15,935 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 08:40:15,943 WARNING:main.py:311:print_pqr:Ignoring 391 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 09:18:43,211 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/2_relaxed.pdb
2025-04-15 09:18:43,219 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:18:43,243 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 09:18:43,243 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:18:43,245 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:18:43,246 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:18:43,246 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:18:43,246 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:18:43,246 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:18:43,246 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:18:43,256 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 09:18:43,274 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:18:43,274 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:18:43,293 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:18:43,540 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:18:43,542 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:18:43,542 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:18:43,551 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 09:31:40,792 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:31:40,792 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 09:31:40,792 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 09:31:40,792 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 09:31:40,792 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 09:31:40,856 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/2_relaxed.pdb
2025-04-15 09:31:40,862 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:31:40,885 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 09:31:40,885 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:31:40,889 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:31:40,889 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:31:40,889 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:31:40,889 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:31:40,889 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:31:40,890 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:31:40,899 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:31:40,901 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:31:40,902 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:31:40,902 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:31:40,920 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:31:40,921 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:31:40,950 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:31:41,193 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:31:41,195 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:31:41,195 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:31:41,202 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 13:06:00,688 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 13:06:00,688 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 13:06:00,688 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 13:06:00,751 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/2_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 1060 atoms.
2025-04-15 13:06:00,766 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:06:00,770 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:06:00,771 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:06:00,771 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:06:00,771 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:06:00,771 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:06:00,771 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:06:00,795 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:06:00,797 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:06:00,797 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:06:00,798 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:06:00,819 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:06:00,819 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:06:00,845 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:06:01,101 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:06:01,102 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:06:01,103 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:06:01,109 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:25:34,157 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:25:34,157 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 13:25:34,157 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 13:25:34,157 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:25:34,157 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:25:34,190 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/2_relaxed.pdb
2025-04-15 13:25:34,195 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:25:34,201 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 13:25:34,201 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:25:34,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:25:34,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:25:34,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:25:34,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:25:34,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:25:34,203 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:25:34,219 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:25:34,220 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:25:34,220 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:25:34,220 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:25:34,238 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:25:34,239 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:25:34,249 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:25:34,406 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:25:34,407 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:25:34,407 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:25:34,410 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 17:10:55,823 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/2_relaxed.pdb
2025-04-15 17:10:55,827 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 17:10:55,851 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 17:10:55,851 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 17:10:55,853 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 17:10:55,853 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 17:10:55,874 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 17:10:55,874 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 17:10:55,886 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 17:10:56,087 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 17:10:56,088 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 17:10:56,089 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 17:10:56,094 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 18:18:20,832 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/2_relaxed.pdb
2025-04-15 18:18:20,836 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 18:18:20,855 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 18:18:20,855 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 18:18:20,858 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 18:18:20,858 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 18:18:20,868 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 18:18:20,870 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 18:18:20,870 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 18:18:20,871 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 18:18:20,901 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 18:18:20,902 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 18:18:20,932 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 18:18:21,215 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 18:18:21,217 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 18:18:21,217 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 18:18:21,222 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 21:59:50,280 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 21:59:50,280 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 21:59:50,280 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 21:59:50,281 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 21:59:50,281 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 21:59:50,321 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/2_relaxed.pdb
2025-04-15 21:59:50,324 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 21:59:50,341 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 21:59:50,342 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 21:59:50,344 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 21:59:50,344 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 21:59:50,344 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 21:59:50,344 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 21:59:50,344 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 21:59:50,344 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 21:59:50,348 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 21:59:50,349 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 21:59:50,349 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 21:59:50,349 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 21:59:50,361 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 21:59:50,362 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 21:59:50,376 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 21:59:50,508 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 21:59:50,509 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 21:59:50,509 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 21:59:50,513 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 22:09:42,791 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 22:09:42,791 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 22:09:42,791 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 22:09:42,792 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 22:09:42,838 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/2_relaxed.pdb
2025-04-15 22:09:42,841 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 22:09:42,854 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 22:09:42,854 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 22:09:42,856 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 22:09:42,856 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 22:09:42,857 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 22:09:42,857 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 22:09:42,857 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 22:09:42,858 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 22:09:42,864 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 22:09:42,865 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 22:09:42,865 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 22:09:42,865 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 22:09:42,876 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 22:09:42,877 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 22:09:42,887 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 22:09:43,027 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 22:09:43,028 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 22:09:43,028 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 22:09:43,031 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 10:19:46,645 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/2_relaxed.pdb
2025-05-05 10:19:46,654 INFO:main.py:770:main_driver:Setting up molecule.
2025-05-05 10:19:46,682 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1056 atoms.
2025-05-05 10:19:46,683 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-05-05 10:19:46,686 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-05-05 10:19:46,686 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-05-05 10:19:46,686 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-05-05 10:19:46,686 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-05-05 10:19:46,687 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-05-05 10:19:46,687 INFO:main.py:604:non_trivial:Loading forcefield.
2025-05-05 10:19:46,693 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-05-05 10:19:46,694 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-05-05 10:19:46,694 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-05-05 10:19:46,695 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-05-05 10:19:46,725 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-05-05 10:19:46,726 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-05-05 10:19:46,751 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-05-05 10:19:46,995 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-05-05 10:19:46,998 INFO:main.py:713:non_trivial:Regenerating headers.
2025-05-05 10:19:46,998 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-05-05 10:19:47,007 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.