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2025-04-11 02:15:25,254 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:15:25,254 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 02:15:25,254 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 02:15:25,254 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:15:25,254 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:15:25,279 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/4_relaxed.pdb
2025-04-11 02:15:25,282 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:15:25,284 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 906 atoms.
2025-04-11 02:15:25,284 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 375 and TYR A 383!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 383 and TYR A 415!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 473 and LYS A 474!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 474 and HIS A 475!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 475 and GLY A 476!
2025-04-11 02:15:25,285 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 476 and THR A 477!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 477 and THR A 478!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 479 and GLU A 481!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 487 and LEU A 489!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 490 and PRO A 495!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 496 and GLY A 497!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 497 and ARG A 498!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 500 and PHE A 501!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 501 and SER A 502!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 502 and ALA A 504!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:15:25,286 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 528 and ALA A 529!
2025-04-11 02:15:25,286 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:15:25,300 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 02:15:25,313 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:15:25,314 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:15:25,335 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:15:25,405 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:15:25,406 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:15:25,406 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:15:25,409 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 02:22:06,529 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:22:06,529 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 02:22:06,529 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 02:22:06,529 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:22:06,530 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:22:06,592 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/4_relaxed.pdb
2025-04-11 02:22:06,598 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:22:06,605 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 906 atoms.
2025-04-11 02:22:06,605 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:22:06,606 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:22:06,606 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:22:06,606 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:22:06,616 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:22:06,616 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:22:06,616 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:22:06,616 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:22:06,624 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:22:06,625 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:22:06,639 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:22:06,737 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:22:06,738 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:22:06,738 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:22:06,741 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 08:40:15,516 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/2p16/4_relaxed.pdb
2025-04-11 08:40:15,580 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 08:40:15,606 INFO:main.py:408:setup_molecule:Created biomolecule object with 73 residues and 1068 atoms.
2025-04-11 08:40:15,606 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 08:40:15,610 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-11 08:40:15,610 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-04-11 08:40:15,610 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-04-11 08:40:15,610 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-04-11 08:40:15,610 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-04-11 08:40:15,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 96 and GLU A 97!
2025-04-11 08:40:15,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 97 and THR A 98!
2025-04-11 08:40:15,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 98 and TYR A 99!
2025-04-11 08:40:15,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-11 08:40:15,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 140 and GLY A 142!
2025-04-11 08:40:15,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 145 and GLU A 146!
2025-04-11 08:40:15,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 146 and LYS A 147!
2025-04-11 08:40:15,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-11 08:40:15,611 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-11 08:40:15,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-11 08:40:15,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 173 and PHE A 174!
2025-04-11 08:40:15,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 174 and ILE A 175!
2025-04-11 08:40:15,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-04-11 08:40:15,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-04-11 08:40:15,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 189 and ALA A 190!
2025-04-11 08:40:15,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 190 and SER A 191!
2025-04-11 08:40:15,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 191 and HIS A 192!
2025-04-11 08:40:15,612 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 192 and GLY A 193!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and GLY A 211!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 212 and VAL A 213!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 213 and SER A 214!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 214 and LYS A 215!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 215 and GLY A 216!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 216 and GLU A 217!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 217 and GLY A 218!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 218 and SER A 220!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 220 and ALA A 221!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 225 and GLY A 226!
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 226 and ILE A 227!
2025-04-11 08:40:15,613 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 08:40:15,621 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 08:40:15,623 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 08:40:15,623 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 08:40:15,624 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 08:40:15,647 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 08:40:15,648 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 08:40:16,655 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 57
2025-04-11 08:40:17,342 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 145
2025-04-11 08:40:19,296 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 192
2025-04-11 08:40:28,161 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 199
2025-04-11 08:40:28,170 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 08:40:30,086 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 08:40:30,111 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 08:40:30,130 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 08:40:30,169 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 09:18:43,219 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/4_relaxed.pdb
2025-04-15 09:18:43,225 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:18:43,250 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 09:18:43,250 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:18:43,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:18:43,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:18:43,255 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:18:43,255 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:18:43,255 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:18:43,255 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 09:18:43,268 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 09:18:43,297 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:18:43,298 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:18:43,323 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:18:43,516 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:18:43,518 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:18:43,519 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:18:43,524 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 09:31:40,800 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:31:40,801 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 09:31:40,801 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 09:31:40,801 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 09:31:40,801 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 09:31:40,866 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/4_relaxed.pdb
2025-04-15 09:31:40,870 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:31:40,890 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 09:31:40,890 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:31:40,893 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:31:40,894 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:31:40,894 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:31:40,894 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:31:40,894 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:31:40,894 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:31:40,903 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:31:40,905 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:31:40,905 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:31:40,905 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:31:40,926 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:31:40,927 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:31:40,941 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:31:41,177 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:31:41,179 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:31:41,179 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:31:41,184 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:06:00,688 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:06:00,689 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 13:06:00,689 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 13:06:00,689 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:06:00,689 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:06:00,754 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/4_relaxed.pdb
2025-04-15 13:06:00,760 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:06:00,767 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 13:06:00,768 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 13:06:00,799 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 13:06:00,801 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:06:00,802 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:06:00,826 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:06:00,827 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:06:00,846 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:06:01,118 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:06:01,120 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:06:01,121 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:06:01,129 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:25:34,165 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:25:34,165 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 13:25:34,165 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 13:25:34,165 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:25:34,166 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:25:34,196 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/4_relaxed.pdb
2025-04-15 13:25:34,199 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:25:34,202 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 13:25:34,202 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:25:34,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:25:34,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:25:34,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:25:34,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:25:34,203 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:25:34,204 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:25:34,219 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:25:34,220 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:25:34,220 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:25:34,220 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:25:34,231 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:25:34,231 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:25:34,241 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:25:34,350 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:25:34,350 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:25:34,351 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:25:34,354 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 17:10:55,828 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/4_relaxed.pdb
2025-04-15 17:10:55,834 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 17:10:55,852 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 17:10:55,853 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 17:10:55,854 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 17:10:55,855 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 17:10:55,855 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 17:10:55,855 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 17:10:55,855 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 17:10:55,855 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 17:10:55,860 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 17:10:55,861 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 17:10:55,861 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 17:10:55,862 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 17:10:55,873 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 17:10:55,874 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 17:10:55,886 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 17:10:56,119 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 17:10:56,120 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 17:10:56,120 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 17:10:56,124 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 18:18:20,760 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 18:18:20,761 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 18:18:20,761 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 18:18:20,761 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 18:18:20,761 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 18:18:20,826 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/4_relaxed.pdb
2025-04-15 18:18:20,833 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 18:18:20,855 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 18:18:20,855 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 18:18:20,858 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 18:18:20,858 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 18:18:20,858 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 18:18:20,858 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 18:18:20,858 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 18:18:20,858 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 18:18:20,868 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 18:18:20,871 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 18:18:20,871 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 18:18:20,871 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 18:18:20,902 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 18:18:20,903 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 18:18:20,934 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 18:18:21,127 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 18:18:21,129 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 18:18:21,130 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 18:18:21,140 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 21:59:50,292 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 21:59:50,293 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 21:59:50,293 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 21:59:50,293 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 21:59:50,293 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 21:59:50,337 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/4_relaxed.pdb
2025-04-15 21:59:50,340 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 21:59:50,353 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 21:59:50,354 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 21:59:50,355 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 21:59:50,355 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 21:59:50,355 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 21:59:50,355 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 21:59:50,355 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 21:59:50,355 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 21:59:50,359 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 21:59:50,360 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 21:59:50,360 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 21:59:50,361 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 21:59:50,380 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 21:59:50,381 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 21:59:50,410 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 21:59:50,519 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 21:59:50,520 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 21:59:50,520 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 21:59:50,524 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 22:09:42,823 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 22:09:42,824 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 22:09:42,824 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 22:09:42,824 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 22:09:42,824 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 22:09:42,868 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/4_relaxed.pdb
2025-04-15 22:09:42,871 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 22:09:42,881 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1060 atoms.
2025-04-15 22:09:42,881 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 22:09:42,883 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 22:09:42,883 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 22:09:42,883 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 22:09:42,883 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 22:09:42,883 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 22:09:42,883 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 22:09:42,887 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 22:09:42,888 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 22:09:42,888 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 22:09:42,888 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 22:09:42,902 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 22:09:42,903 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 22:09:42,921 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 22:09:43,080 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 22:09:43,081 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 22:09:43,081 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 10:19:46,577 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 10:19:46,647 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/4_relaxed.pdb
2025-05-05 10:19:46,654 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 1073 atoms.
2025-05-05 10:19:46,681 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-05-05 10:19:46,685 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 10:19:46,686 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-05-05 10:19:46,686 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 10:19:46,694 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-05-05 10:19:46,696 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-05-05 10:19:46,696 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 10:19:46,720 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-05-05 10:19:46,721 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-05-05 10:19:46,745 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-05-05 10:19:46,945 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-05-05 10:19:46,947 INFO:main.py:713:non_trivial:Regenerating headers.
2025-05-05 10:19:46,948 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-05-05 10:19:46,956 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.