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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 02:15:25,276 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/3_relaxed.pdb
2025-04-11 02:15:25,278 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:15:25,280 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 908 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 GLY A 375 and TYR A 383!
2025-04-11 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 383 and TYR A 415!
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 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 473 and GLY A 474!
2025-04-11 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 474 and HIS A 475!
2025-04-11 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 475 and ASN A 476!
2025-04-11 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASN A 476 and PRO A 477!
2025-04-11 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 477 and THR A 478!
2025-04-11 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 479 and GLU A 481!
2025-04-11 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 487 and LEU A 489!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 490 and PRO A 495!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 496 and PHE A 497!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 497 and ARG A 498!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 500 and GLU A 501!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 501 and SER A 502!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 502 and ALA A 504!
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 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 528 and ALA A 529!
2025-04-11 02:15:25,285 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:15:25,299 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:15:25,300 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:15:25,300 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:15:25,300 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:15:25,311 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:15:25,312 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:15:25,324 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:15:25,389 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:15:25,390 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:15:25,390 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:15:25,395 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 02:22:06,522 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:22:06,523 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 02:22:06,523 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 02:22:06,523 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:22:06,523 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:22:06,549 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/3_relaxed.pdb
2025-04-11 02:22:06,552 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 908 atoms.
2025-04-11 02:22:06,556 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:22:06,559 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 375 and TYR A 383!
2025-04-11 02:22:06,559 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 383 and TYR A 415!
2025-04-11 02:22:06,559 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:22:06,559 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 473 and GLY A 474!
2025-04-11 02:22:06,560 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 474 and HIS A 475!
2025-04-11 02:22:06,560 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 475 and ASN A 476!
2025-04-11 02:22:06,560 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASN A 476 and PRO A 477!
2025-04-11 02:22:06,560 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 477 and THR A 478!
2025-04-11 02:22:06,560 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 479 and GLU A 481!
2025-04-11 02:22:06,560 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 487 and LEU A 489!
2025-04-11 02:22:06,560 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 490 and PRO A 495!
2025-04-11 02:22:06,560 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 496 and PHE A 497!
2025-04-11 02:22:06,560 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 497 and ARG A 498!
2025-04-11 02:22:06,561 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 500 and GLU A 501!
2025-04-11 02:22:06,561 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 501 and SER A 502!
2025-04-11 02:22:06,561 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 502 and ALA A 504!
2025-04-11 02:22:06,561 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:22:06,561 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 528 and ALA A 529!
2025-04-11 02:22:06,561 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:22:06,578 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:22:06,578 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:22:06,578 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:22:06,578 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:22:06,587 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:22:06,587 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:22:06,595 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:22:06,648 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:22:06,649 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:22:06,649 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:22:06,651 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 08:40:15,515 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 08:40:15,585 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/3_relaxed.pdb
2025-04-11 08:40:15,591 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 1090 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 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 GLN A 151 and LEU A 158!
2025-04-11 08:40:15,622 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-11 08:40:15,622 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 08:40:15,632 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 08:40:15,634 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 08:40:15,634 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 08:40:15,635 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 08:40:15,663 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 08:40:15,685 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 08:40:15,943 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 08:40:15,946 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 08:40:15,946 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 08:40:15,954 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 09:18:43,225 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/3_relaxed.pdb
2025-04-15 09:18:43,232 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:18:43,254 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1061 atoms.
2025-04-15 09:18:43,255 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:18:43,258 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:18:43,258 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:18:43,258 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:18:43,258 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:18:43,259 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:18:43,259 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:18:43,266 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:18:43,267 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:18:43,267 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:18:43,268 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:18:43,295 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:18:43,296 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:18:43,321 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:18:43,470 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:18:43,471 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:18:43,472 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:18:43,480 WARNING:main.py:311:print_pqr:Ignoring 391 header lines in output.
2025-04-15 09:31:40,790 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:31:40,790 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 09:31:40,790 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 09:31:40,790 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 09:31:40,790 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 09:31:40,842 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/3_relaxed.pdb
2025-04-15 09:31:40,850 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:31:40,869 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1061 atoms.
2025-04-15 09:31:40,870 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:31:40,873 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:31:40,873 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:31:40,874 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:31:40,874 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:31:40,874 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:31:40,874 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:31:40,885 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:31:40,887 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:31:40,887 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:31:40,888 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:31:40,909 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:31:40,910 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:31:40,933 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:31:41,078 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:31:41,079 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:31:41,079 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:31:41,089 WARNING:main.py:311:print_pqr:Ignoring 391 header lines in output.
2025-04-15 13:06:00,689 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 13:06:00,690 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:06:00,755 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/3_relaxed.pdb
2025-04-15 13:06:00,762 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:06:00,769 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1061 atoms.
2025-04-15 13:06:00,769 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 13:06:00,772 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:06:00,772 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:06:00,772 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:06:00,772 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 13:06:00,800 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:06:00,802 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:06:00,802 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 13:06:00,825 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:06:00,826 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:06:00,849 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:06:01,046 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:06:01,048 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:06:01,048 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:06:01,057 WARNING:main.py:311:print_pqr:Ignoring 391 header lines in output.
2025-04-15 13:25:34,171 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:25:34,171 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 13:25:34,171 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 13:25:34,171 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:25:34,171 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:25:34,197 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/3_relaxed.pdb
2025-04-15 13:25:34,200 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:25:34,203 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1061 atoms.
2025-04-15 13:25:34,204 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:25:34,205 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:25:34,205 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:25:34,205 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:25:34,205 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:25:34,205 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:25:34,205 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:25:34,220 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:25:34,221 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:25:34,221 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:25:34,221 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:25:34,232 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:25:34,232 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:25:34,242 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:25:34,301 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:25:34,302 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:25:34,302 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:25:34,305 WARNING:main.py:311:print_pqr:Ignoring 391 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 17:10:55,836 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/3_relaxed.pdb
2025-04-15 17:10:55,841 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 17:10:55,858 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1061 atoms.
2025-04-15 17:10:55,858 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 17:10:55,860 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 17:10:55,860 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 17:10:55,860 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 17:10:55,860 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 17:10:55,860 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 17:10:55,861 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 17:10:55,866 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 17:10:55,868 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 17:10:55,868 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 17:10:55,868 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 17:10:55,896 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 17:10:55,897 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 17:10:56,026 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 17:10:56,028 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 17:10:56,029 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 17:10:56,035 WARNING:main.py:311:print_pqr:Ignoring 391 header lines in output.
2025-04-15 18:18:20,776 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 18:18:20,777 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 18:18:20,777 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 18:18:20,777 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 18:18:20,777 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 18:18:20,836 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/3_relaxed.pdb
2025-04-15 18:18:20,843 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 18:18:20,866 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1061 atoms.
2025-04-15 18:18:20,866 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 18:18:20,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 18:18:20,870 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 18:18:20,870 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 18:18:20,870 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 18:18:20,870 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 18:18:20,871 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 18:18:20,878 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 18:18:20,879 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 18:18:20,879 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 18:18:20,879 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 18:18:20,906 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 18:18:20,907 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 18:18:20,924 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 18:18:21,096 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 18:18:21,098 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 18:18:21,099 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 18:18:21,108 WARNING:main.py:311:print_pqr:Ignoring 391 header lines in output.
2025-04-15 21:59:50,288 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 21:59:50,289 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 21:59:50,289 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 21:59:50,289 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 21:59:50,289 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/3_relaxed.pdb
2025-04-15 21:59:50,324 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 21:59:50,342 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1061 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 21:59:50,365 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 21:59:50,366 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 21:59:50,378 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 21:59:50,449 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 21:59:50,450 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 21:59:50,450 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 21:59:50,454 WARNING:main.py:311:print_pqr:Ignoring 391 header lines in output.
2025-04-15 22:09:42,799 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 22:09:42,800 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 22:09:42,800 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 22:09:42,800 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 22:09:42,801 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 22:09:42,829 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/3_relaxed.pdb
2025-04-15 22:09:42,831 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 22:09:42,846 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1061 atoms.
2025-04-15 22:09:42,846 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 22:09:42,848 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 22:09:42,848 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 22:09:42,848 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 22:09:42,848 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 22:09:42,848 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 22:09:42,848 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 22:09:42,856 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 22:09:42,856 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 22:09:42,874 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 22:09:42,875 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 22:09:42,886 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 22:09:42,993 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 22:09:42,995 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 22:09:42,995 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 22:09:43,000 WARNING:main.py:311:print_pqr:Ignoring 391 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 10:19:46,651 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/3_relaxed.pdb
2025-05-05 10:19:46,657 INFO:main.py:770:main_driver:Setting up molecule.
2025-05-05 10:19:46,681 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1064 atoms.
2025-05-05 10:19:46,682 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-05-05 10:19:46,684 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-05-05 10:19:46,684 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-05-05 10:19:46,685 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-05-05 10:19:46,685 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-05-05 10:19:46,685 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-05-05 10:19:46,685 INFO:main.py:604:non_trivial:Loading forcefield.
2025-05-05 10:19:46,692 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-05-05 10:19:46,693 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-05-05 10:19:46,693 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-05-05 10:19:46,694 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-05-05 10:19:46,722 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-05-05 10:19:46,723 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-05-05 10:19:46,749 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-05-05 10:19:46,896 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-05-05 10:19:46,897 INFO:main.py:713:non_trivial:Regenerating headers.
2025-05-05 10:19:46,898 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-05-05 10:19:46,905 WARNING:main.py:311:print_pqr:Ignoring 391 header lines in output.