2025-04-11 02:15:25,248 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:15:25,248 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 02:15:25,248 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 02:15:25,248 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:15:25,249 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:15:25,277 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/5_relaxed.pdb
2025-04-11 02:15:25,279 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:15:25,282 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 911 atoms.
2025-04-11 02:15:25,282 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 375 and TYR A 383!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 383 and TYR A 415!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 473 and THR A 474!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 474 and HIS A 475!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 475 and MET A 476!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between MET A 476 and VAL A 477!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 477 and THR A 478!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 479 and GLU A 481!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 487 and LEU A 489!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 490 and PRO A 495!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 496 and HIS A 497!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 497 and ARG A 498!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 500 and ILE A 501!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 501 and SER A 502!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 502 and ALA A 504!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:15:25,283 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 528 and ALA A 529!
2025-04-11 02:15:25,283 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 02:15:25,301 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:15:25,301 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:15:25,301 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:15:25,317 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:15:25,318 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:15:25,326 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:15:25,396 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:15:25,397 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:15:25,397 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:15:25,400 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 02:22:06,517 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:22:06,517 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 02:22:06,517 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 02:22:06,517 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:22:06,517 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:22:06,543 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/5_relaxed.pdb
2025-04-11 02:22:06,546 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:22:06,548 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 911 atoms.
2025-04-11 02:22:06,549 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:22:06,550 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:22:06,550 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:22:06,550 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:22:06,562 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:22:06,562 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:22:06,563 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:22:06,563 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:22:06,572 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:22:06,572 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:22:06,580 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:22:06,637 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:22:06,638 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:22:06,638 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:22:06,641 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 08:40:15,518 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 08:40:15,519 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 08:40:15,519 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 08:40:15,519 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 08:40:15,520 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 08:40:15,579 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/5_relaxed.pdb
2025-04-11 08:40:15,586 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 08:40:15,614 INFO:main.py:408:setup_molecule:Created biomolecule object with 73 residues and 1069 atoms.
2025-04-11 08:40:15,614 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 08:40:15,618 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-11 08:40:15,618 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 08:40:15,619 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 08:40:15,627 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 08:40:15,629 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 08:40:15,629 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 08:40:15,630 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 08:40:15,655 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 08:40:15,657 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 08:40:15,674 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 08:40:15,988 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 08:40:15,990 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 08:40:15,991 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 08:40:15,998 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 09:18:43,213 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/5_relaxed.pdb
2025-04-15 09:18:43,218 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:18:43,241 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 09:18:43,242 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:18:43,244 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:18:43,245 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:18:43,245 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:18:43,245 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:18:43,245 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:18:43,245 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:18:43,252 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:18:43,254 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:18:43,254 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:18:43,255 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:18:43,278 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:18:43,279 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:18:43,303 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:18:43,555 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:18:43,557 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:18:43,558 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:18:43,566 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 09:31:40,814 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:31:40,814 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 09:31:40,814 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 09:31:40,814 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 09:31:40,814 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 09:31:40,878 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/5_relaxed.pdb
2025-04-15 09:31:40,884 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:31:40,903 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 09:31:40,903 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:31:40,906 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:31:40,906 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:31:40,907 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:31:40,907 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:31:40,907 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:31:40,907 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:31:40,916 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:31:40,918 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:31:40,918 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:31:40,919 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:31:40,943 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:31:40,943 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:31:40,959 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:31:41,192 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:31:41,194 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:31:41,194 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:31:41,203 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 13:06:00,759 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/5_relaxed.pdb
2025-04-15 13:06:00,766 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:06:00,774 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 13:06:00,774 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:06:00,777 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:06:00,778 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:06:00,778 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:06:00,778 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:06:00,778 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:06:00,778 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:06:00,803 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:06:00,804 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:06:00,804 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:06:00,804 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 13:06:00,820 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:06:00,843 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:06:01,140 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:06:01,141 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:06:01,141 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:06:01,146 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:25:34,179 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:25:34,179 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 13:25:34,179 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 13:25:34,179 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:25:34,179 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:25:34,221 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/5_relaxed.pdb
2025-04-15 13:25:34,224 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:25:34,228 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 13:25:34,228 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:25:34,229 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:25:34,230 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:25:34,230 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:25:34,230 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:25:34,230 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:25:34,230 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:25:34,241 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:25:34,242 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:25:34,242 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:25:34,242 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:25:34,252 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:25:34,252 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:25:34,262 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:25:34,402 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:25:34,403 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:25:34,403 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:25:34,407 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 17:10:55,786 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 17:10:55,829 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/5_relaxed.pdb
2025-04-15 17:10:55,832 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 17:10:55,855 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 17:10:55,855 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 17:10:55,859 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 17:10:55,859 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 17:10:55,859 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 17:10:55,859 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 17:10:55,860 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 17:10:55,868 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 17:10:55,869 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 17:10:55,869 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 17:10:55,870 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 17:10:55,895 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 17:10:55,896 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 17:10:55,909 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 17:10:56,054 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 17:10:56,056 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 17:10:56,056 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 17:10:56,063 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 18:18:20,767 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/5_relaxed.pdb
2025-04-15 18:18:20,836 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 18:18:20,859 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 18:18:20,859 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 18:18:20,862 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 18:18:20,862 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 18:18:20,862 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 18:18:20,862 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 18:18:20,862 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 18:18:20,862 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 18:18:20,869 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 18:18:20,870 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 18:18:20,896 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 18:18:20,897 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 18:18:20,927 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 18:18:21,144 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 18:18:21,146 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 18:18:21,147 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 18:18:21,157 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 21:59:50,284 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 21:59:50,284 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 21:59:50,284 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 21:59:50,284 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 21:59:50,284 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 21:59:50,316 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/5_relaxed.pdb
2025-04-15 21:59:50,318 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 21:59:50,335 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 21:59:50,335 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 21:59:50,336 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 21:59:50,336 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 21:59:50,337 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 21:59:50,337 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 21:59:50,337 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 21:59:50,337 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 21:59:50,347 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 21:59:50,374 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 21:59:50,501 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 21:59:50,502 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 21:59:50,502 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 21:59:50,506 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 22:09:42,789 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 22:09:42,789 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 22:09:42,789 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 22:09:42,790 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 22:09:42,790 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 22:09:42,828 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/5_relaxed.pdb
2025-04-15 22:09:42,831 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 22:09:42,844 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 22:09:42,845 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 22:09:42,846 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 22:09:42,846 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 22:09:42,846 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 22:09:42,846 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 22:09:42,846 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 22:09:42,846 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 22:09:42,852 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 22:09:42,854 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 22:09:42,854 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 22:09:42,855 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 22:09:42,871 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 22:09:42,872 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 22:09:42,890 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 22:09:43,031 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 22:09:43,032 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 22:09:43,032 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 22:09:43,036 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-05-05 10:19:46,578 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-05-05 10:19:46,579 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-05-05 10:19:46,579 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-05-05 10:19:46,579 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-05-05 10:19:46,580 INFO:main.py:763:main_driver:Loading topology files.
2025-05-05 10:19:46,657 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/5_relaxed.pdb
2025-05-05 10:19:46,663 INFO:main.py:770:main_driver:Setting up molecule.
2025-05-05 10:19:46,683 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1065 atoms.
2025-05-05 10:19:46,684 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-05-05 10:19:46,687 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-05-05 10:19:46,688 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-05-05 10:19:46,688 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-05-05 10:19:46,688 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-05-05 10:19:46,688 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-05-05 10:19:46,689 INFO:main.py:604:non_trivial:Loading forcefield.
2025-05-05 10:19:46,696 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-05-05 10:19:46,697 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-05-05 10:19:46,697 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-05-05 10:19:46,697 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 10:19:46,717 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-05-05 10:19:46,740 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-05-05 10:19:46,962 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-05-05 10:19:46,965 INFO:main.py:713:non_trivial:Regenerating headers.
2025-05-05 10:19:46,966 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-05-05 10:19:46,973 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.