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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 02:15:25,296 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/1_relaxed.pdb
2025-04-11 02:15:25,301 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:15:25,305 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 918 atoms.
2025-04-11 02:15:25,306 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:15:25,307 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:15:25,307 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:15:25,307 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:15:25,318 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:15:25,319 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:15:25,319 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:15:25,319 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:15:25,327 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:15:25,328 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 02:15:25,399 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:15:25,400 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:15:25,400 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:15:25,403 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 02:22:06,537 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:22:06,537 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 02:22:06,537 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 02:22:06,537 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:22:06,538 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:22:06,580 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/1_relaxed.pdb
2025-04-11 02:22:06,582 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:22:06,585 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 918 atoms.
2025-04-11 02:22:06,585 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:22:06,587 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:22:06,588 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:22:06,588 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:22:06,599 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:22:06,600 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 02:22:06,600 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:22:06,600 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:22:06,612 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:22:06,612 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:22:06,621 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:22:06,677 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:22:06,678 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:22:06,678 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:22:06,681 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 08:40:15,520 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 08:40:15,520 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 08:40:15,520 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 08:40:15,520 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 08:40:15,521 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 08:40:15,584 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/1_relaxed.pdb
2025-04-11 08:40:15,588 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 08:40:15,610 INFO:main.py:408:setup_molecule:Created biomolecule object with 73 residues and 1083 atoms.
2025-04-11 08:40:15,610 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 08:40:15,613 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-11 08:40:15,614 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-04-11 08:40:15,614 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-04-11 08:40:15,614 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-04-11 08:40:15,614 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-04-11 08:40:15,614 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 96 and LYS A 97!
2025-04-11 08:40:15,614 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 97 and ALA A 98!
2025-04-11 08:40:15,614 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 98 and TYR A 99!
2025-04-11 08:40:15,615 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-11 08:40:15,615 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 140 and GLY A 142!
2025-04-11 08:40:15,615 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 145 and TRP A 146!
2025-04-11 08:40:15,615 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 146 and LYS A 147!
2025-04-11 08:40:15,615 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-11 08:40:15,615 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-11 08:40:15,615 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-11 08:40:15,615 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 173 and ILE A 174!
2025-04-11 08:40:15,615 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 174 and ILE A 175!
2025-04-11 08:40:15,615 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-04-11 08:40:15,616 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-04-11 08:40:15,616 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 189 and ASP A 190!
2025-04-11 08:40:15,616 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 190 and CYS A 191!
2025-04-11 08:40:15,616 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 191 and GLN A 192!
2025-04-11 08:40:15,616 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 192 and GLY A 193!
2025-04-11 08:40:15,616 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and GLY A 211!
2025-04-11 08:40:15,616 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 212 and VAL A 213!
2025-04-11 08:40:15,616 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 213 and SER A 214!
2025-04-11 08:40:15,616 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 214 and TRP A 215!
2025-04-11 08:40:15,617 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 215 and GLY A 216!
2025-04-11 08:40:15,617 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 216 and GLU A 217!
2025-04-11 08:40:15,617 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 217 and GLY A 218!
2025-04-11 08:40:15,617 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 218 and CYS A 220!
2025-04-11 08:40:15,617 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 220 and ALA A 221!
2025-04-11 08:40:15,617 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-04-11 08:40:15,617 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 225 and GLY A 226!
2025-04-11 08:40:15,617 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 226 and ILE A 227!
2025-04-11 08:40:15,617 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 08:40:15,625 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 08:40:15,626 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-11 08:40:15,626 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 08:40:15,626 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 08:40:15,650 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 08:40:15,651 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 08:40:16,734 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 57
2025-04-11 08:40:17,458 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 145
2025-04-11 08:40:20,041 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 199
2025-04-11 08:40:20,048 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 08:40:21,516 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 08:40:21,559 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 08:40:21,560 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 08:40:21,608 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 09:18:43,150 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 09:18:43,150 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 09:18:43,150 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 09:18:43,223 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/1_relaxed.pdb
2025-04-15 09:18:43,228 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:18:43,251 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1063 atoms.
2025-04-15 09:18:43,251 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:18:43,253 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 09:18:43,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:18:43,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:18:43,254 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 09:18:43,265 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:18:43,266 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:18:43,266 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:18:43,267 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:18:43,285 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:18:43,286 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:18:43,312 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:18:43,502 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:18:43,504 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:18:43,505 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:18:43,513 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 09:31:40,785 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:31:40,785 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 09:31:40,785 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 09:31:40,785 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 09:31:40,786 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 09:31:40,845 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/1_relaxed.pdb
2025-04-15 09:31:40,849 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:31:40,865 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1063 atoms.
2025-04-15 09:31:40,865 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:31:40,868 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:31:40,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:31:40,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:31:40,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:31:40,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:31:40,869 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:31:40,876 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:31:40,877 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 09:31:40,877 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:31:40,878 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:31:40,899 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:31:40,900 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:31:40,920 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:31:41,166 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:31:41,168 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:31:41,168 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:31:41,177 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:06:00,687 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:06:00,688 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 13:06:00,688 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 13:06:00,688 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:06:00,689 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:06:00,754 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/1_relaxed.pdb
2025-04-15 13:06:00,761 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:06:00,768 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1063 atoms.
2025-04-15 13:06:00,769 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:06:00,770 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:06:00,770 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:06:00,770 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 13:06:00,796 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:06:00,797 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:06:00,797 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:06:00,798 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:06:00,823 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:06:00,824 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 13:06:01,021 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:06:01,023 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:06:01,023 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:06:01,032 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:25:34,169 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:25:34,169 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 13:25:34,169 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 13:25:34,169 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:25:34,169 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/1_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 1063 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 13:25:34,221 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:25:34,223 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 13:25:34,223 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:25:34,224 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:25:34,249 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:25:34,250 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:25:34,272 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:25:34,379 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:25:34,380 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:25:34,380 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:25:34,384 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 17:10:55,786 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 17:10:55,786 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 17:10:55,786 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 17:10:55,787 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 17:10:55,832 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/1_relaxed.pdb
2025-04-15 17:10:55,838 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 17:10:55,861 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1063 atoms.
2025-04-15 17:10:55,861 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 17:10:55,864 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 17:10:55,864 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 17:10:55,864 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 17:10:55,864 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 17:10:55,865 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 17:10:55,865 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 17:10:55,872 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 17:10:55,874 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 17:10:55,874 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 17:10:55,899 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 17:10:55,899 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 17:10:55,919 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 17:10:56,143 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 17:10:56,144 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 17:10:56,144 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 17:10:56,148 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 18:18:20,761 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 18:18:20,762 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 18:18:20,762 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 18:18:20,762 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 18:18:20,762 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 18:18:20,831 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/1_relaxed.pdb
2025-04-15 18:18:20,839 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 18:18:20,864 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1063 atoms.
2025-04-15 18:18:20,864 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 18:18:20,868 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 18:18:20,868 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 18:18:20,868 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 18:18:20,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 18:18:20,869 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 18:18:20,869 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 18:18:20,879 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 18:18:20,880 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 18:18:20,881 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 18:18:20,881 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 18:18:20,904 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 18:18:20,906 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 18:18:20,925 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 18:18:21,130 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 18:18:21,132 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 18:18:21,132 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 18:18:21,141 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 21:59:50,281 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 21:59:50,281 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 21:59:50,281 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 21:59:50,281 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 21:59:50,282 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 21:59:50,329 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/1_relaxed.pdb
2025-04-15 21:59:50,333 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 1063 atoms.
2025-04-15 21:59:50,354 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 21:59:50,356 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 21:59:50,357 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 21:59:50,357 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 21:59:50,357 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 21:59:50,357 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 21:59:50,358 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 21:59:50,367 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 21:59:50,369 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 21:59:50,369 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 21:59:50,369 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 21:59:50,388 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 21:59:50,389 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 21:59:50,401 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 21:59:50,517 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 21:59:50,518 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 21:59:50,519 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 22:09:42,792 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 22:09:42,792 INFO:main.py:242:print_splash_screen:Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
2025-04-15 22:09:42,792 INFO:main.py:242:print_splash_screen:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
2025-04-15 22:09:42,792 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 22:09:42,792 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 22:09:42,831 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/1_relaxed.pdb
2025-04-15 22:09:42,834 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 22:09:42,860 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 1063 atoms.
2025-04-15 22:09:42,860 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 22:09:42,863 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 22:09:42,863 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 22:09:42,863 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 22:09:42,863 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 22:09:42,863 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 22:09:42,864 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 22:09:42,873 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 22:09:42,875 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-04-15 22:09:42,875 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 22:09:42,876 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 22:09:42,900 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 22:09:42,901 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 22:09:42,928 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 22:09:43,019 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 22:09:43,020 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 22:09:43,020 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 22:09:43,025 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/1_relaxed.pdb
2025-05-05 10:19:46,651 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 1063 atoms.
2025-05-05 10:19:46,680 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-05-05 10:19:46,684 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-05-05 10:19:46,684 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-05-05 10:19:46,684 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-05-05 10:19:46,684 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-05-05 10:19:46,684 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-05-05 10:19:46,685 INFO:main.py:604:non_trivial:Loading forcefield.
2025-05-05 10:19:46,692 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-05-05 10:19:46,694 INFO:main.py:459:is_repairable:This biomolecule is clean.  No repair needed.
2025-05-05 10:19:46,695 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-05-05 10:19:46,695 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-05-05 10:19:46,717 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 10:19:46,736 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-05-05 10:19:46,907 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-05-05 10:19:46,909 INFO:main.py:713:non_trivial:Regenerating headers.
2025-05-05 10:19:46,909 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-05-05 10:19:46,919 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.