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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 02:15:25,278 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/0_relaxed.pdb
2025-04-11 02:15:25,280 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:15:25,283 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 918 atoms.
2025-04-11 02:15:25,283 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:15:25,284 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:15:25,284 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:15:25,308 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:15:25,308 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:15:25,308 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:15:25,308 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:15:25,317 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 02:15:25,339 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:15:25,420 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:15:25,421 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:15:25,421 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:15:25,424 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 02:22:06,491 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:22:06,491 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 02:22:06,491 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 02:22:06,491 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:22:06,492 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:22:06,539 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/0_relaxed.pdb
2025-04-11 02:22:06,542 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:22:06,544 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 918 atoms.
2025-04-11 02:22:06,544 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:22:06,546 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:22:06,546 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:22:06,546 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:22:06,556 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:22:06,556 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:22:06,556 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:22:06,556 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:22:06,565 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:22:06,566 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:22:06,575 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:22:06,660 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:22:06,661 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:22:06,661 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:22:06,664 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 08:40:15,516 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 08:40:15,516 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 08:40:15,516 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 08:40:15,517 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 08:40:15,573 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/0_relaxed.pdb
2025-04-11 08:40:15,577 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 08:40:15,594 INFO:main.py:408:setup_molecule:Created biomolecule object with 73 residues and 1081 atoms.
2025-04-11 08:40:15,594 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 08:40:15,601 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-11 08:40:15,601 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-11 08:40:15,601 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-11 08:40:15,602 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-11 08:40:15,602 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-11 08:40:15,602 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 08:40:15,615 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 08:40:15,618 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 08:40:15,618 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 08:40:15,619 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 08:40:15,640 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 08:40:15,641 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 08:40:15,663 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 08:40:15,900 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 08:40:15,901 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 08:40:15,902 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 08:40:15,907 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 09:18:43,212 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/0_relaxed.pdb
2025-04-15 09:18:43,218 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 1070 atoms.
2025-04-15 09:18:43,244 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:18:43,247 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:18:43,248 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:18:43,248 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:18:43,248 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:18:43,248 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:18:43,248 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:18:43,259 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:18:43,261 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:18:43,261 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:18:43,262 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:18:43,288 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:18:43,289 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:18:43,313 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:18:43,522 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:18:43,524 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:18:43,524 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:18:43,533 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 09:31:40,789 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:31:40,789 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 09:31:40,789 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 09:31:40,789 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 09:31:40,851 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/0_relaxed.pdb
2025-04-15 09:31:40,859 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:31:40,880 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 09:31:40,880 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:31:40,883 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:31:40,884 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:31:40,884 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:31:40,884 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:31:40,884 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:31:40,884 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:31:40,892 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:31:40,894 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:31:40,894 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:31:40,895 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:31:40,913 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:31:40,914 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 09:31:41,182 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:31:41,184 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:31:41,184 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:31:41,192 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:06:00,694 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:06:00,694 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 13:06:00,695 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 13:06:00,695 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:06:00,695 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:06:00,752 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/0_relaxed.pdb
2025-04-15 13:06:00,760 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:06:00,765 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 13:06:00,765 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 13:06:00,800 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:06:00,801 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 13:06:00,830 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:06:00,831 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:06:00,857 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:06:01,039 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:06:01,041 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:06:01,041 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:06:01,049 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:25:34,174 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:25:34,174 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 13:25:34,174 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 13:25:34,174 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:25:34,175 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:25:34,224 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/0_relaxed.pdb
2025-04-15 13:25:34,228 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:25:34,232 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 13:25:34,232 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:25:34,233 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:25:34,234 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:25:34,234 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:25:34,234 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:25:34,234 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:25:34,234 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:25:34,245 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:25:34,245 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:25:34,245 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:25:34,246 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:25:34,262 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:25:34,263 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:25:34,288 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:25:34,424 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:25:34,424 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:25:34,425 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:25:34,433 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 17:10:55,785 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 17:10:55,787 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 17:10:55,787 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 17:10:55,787 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 17:10:55,787 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 17:10:55,833 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/0_relaxed.pdb
2025-04-15 17:10:55,836 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 17:10:55,857 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 17:10:55,857 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 17:10:55,861 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 17:10:55,861 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 17:10:55,861 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 17:10:55,861 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 17:10:55,862 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 17:10:55,871 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 17:10:55,873 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 17:10:55,873 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 17:10:55,874 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 17:10:55,908 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 17:10:56,001 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 17:10:56,002 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 17:10:56,002 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 17:10:56,007 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 18:18:20,762 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 18:18:20,763 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 18:18:20,763 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 18:18:20,763 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 18:18:20,763 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 18:18:20,824 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/0_relaxed.pdb
2025-04-15 18:18:20,828 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 18:18:20,850 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 18:18:20,851 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 18:18:20,855 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 18:18:20,855 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 18:18:20,856 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 18:18:20,856 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 18:18:20,856 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 18:18:20,856 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 18:18:20,867 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 18:18:20,901 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 18:18:20,927 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 18:18:21,122 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 18:18:21,124 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 18:18:21,124 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 18:18:21,132 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 21:59:50,282 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 21:59:50,283 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 21:59:50,283 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 21:59:50,283 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 21:59:50,283 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 21:59:50,315 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/0_relaxed.pdb
2025-04-15 21:59:50,318 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 21:59:50,329 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 21:59:50,329 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 21:59:50,334 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 21:59:50,334 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 21:59:50,334 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 21:59:50,334 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 21:59:50,335 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 21:59:50,336 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 21:59:50,342 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 21:59:50,343 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 21:59:50,343 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 21:59:50,343 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 21:59:50,362 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 21:59:50,363 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 21:59:50,375 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 21:59:50,550 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 21:59:50,553 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 21:59:50,554 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 21:59:50,558 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 22:09:42,807 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 22:09:42,808 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 22:09:42,808 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 22:09:42,808 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 22:09:42,809 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 22:09:42,839 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/0_relaxed.pdb
2025-04-15 22:09:42,844 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 22:09:42,863 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1070 atoms.
2025-04-15 22:09:42,863 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 22:09:42,864 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 22:09:42,864 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 22:09:42,865 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 22:09:42,865 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 22:09:42,865 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 22:09:42,865 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 22:09:42,869 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 22:09:42,869 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 22:09:42,869 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 22:09:42,870 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 22:09:42,894 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 22:09:42,895 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 22:09:42,916 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 22:09:43,077 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 22:09:43,079 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 22:09:43,080 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 22:09:43,088 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 10:19:46,645 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/0_relaxed.pdb
2025-05-05 10:19:46,653 INFO:main.py:770:main_driver:Setting up molecule.
2025-05-05 10:19:46,680 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1061 atoms.
2025-05-05 10:19:46,681 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 10:19:46,685 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 10:19:46,686 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 10:19:46,694 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 10:19:46,751 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-05-05 10:19:46,942 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-05-05 10:19:46,943 INFO:main.py:713:non_trivial:Regenerating headers.
2025-05-05 10:19:46,943 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-05-05 10:19:46,952 WARNING:main.py:311:print_pqr:Ignoring 391 header lines in output.