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Pocket-Gen
File size: 74,868 Bytes 
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2025-04-11 02:24:56,222 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 02:24:56,223 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 02:24:56,223 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 02:24:56,223 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 02:24:56,223 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 02:24:56,250 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/2p16_pocket.pdb
2025-04-11 02:24:56,251 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 02:24:56,253 INFO:main.py:408:setup_molecule:Created biomolecule object with 56 residues and 460 atoms.
2025-04-11 02:24:56,253 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 02:24:56,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 375 and TYR A 383!
2025-04-11 02:24:56,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 383 and TYR A 415!
2025-04-11 02:24:56,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 427 and ASP A 470!
2025-04-11 02:24:56,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 479 and GLU A 481!
2025-04-11 02:24:56,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 487 and LEU A 489!
2025-04-11 02:24:56,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 490 and PRO A 495!
2025-04-11 02:24:56,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 502 and ALA A 504!
2025-04-11 02:24:56,254 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 504 and TYR A 524!
2025-04-11 02:24:56,254 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 02:24:56,265 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 02:24:56,266 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue LYS A 533
2025-04-11 02:24:56,266 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue LYS A 533
2025-04-11 02:24:56,266 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
2025-04-11 02:24:56,266 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue LYS A 533
2025-04-11 02:24:56,266 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue LYS A 533 at coordinates 44.965, 90.149, 5.616
2025-04-11 02:24:56,267 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 02:24:56,267 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 02:24:56,272 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 02:24:56,304 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 02:24:56,335 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 02:24:56,386 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 02:24:56,387 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 02:24:56,387 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 02:24:56,390 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-11 08:45:48,075 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-11 08:45:48,077 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 08:45:48,077 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 08:45:48,077 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-11 08:45:48,078 INFO:main.py:763:main_driver:Loading topology files.
2025-04-11 08:45:48,119 INFO:main.py:765:main_driver:Loading molecule: ./generate/2p16/2p16_pocket.pdb
2025-04-11 08:45:48,121 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-11 08:45:48,124 INFO:main.py:408:setup_molecule:Created biomolecule object with 73 residues and 556 atoms.
2025-04-11 08:45:48,124 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-11 08:45:48,125 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-11 08:45:48,125 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-04-11 08:45:48,125 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-04-11 08:45:48,126 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-04-11 08:45:48,126 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-04-11 08:45:48,126 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-11 08:45:48,126 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 140 and GLY A 142!
2025-04-11 08:45:48,126 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-11 08:45:48,126 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-11 08:45:48,126 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-11 08:45:48,126 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-04-11 08:45:48,127 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-04-11 08:45:48,127 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and GLY A 211!
2025-04-11 08:45:48,127 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-04-11 08:45:48,127 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-11 08:45:48,139 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-11 08:45:48,141 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-11 08:45:48,141 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-11 08:45:48,141 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
2025-04-11 08:45:48,142 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-11 08:45:48,142 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue THR A 229 at coordinates 22.281, 41.961, 60.699
2025-04-11 08:45:48,142 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-11 08:45:48,142 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-11 08:45:48,152 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-11 08:45:48,210 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-11 08:45:48,275 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-11 08:45:48,466 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-11 08:45:48,468 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-11 08:45:48,468 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-11 08:45:48,472 WARNING:main.py:311:print_pqr:Ignoring 391 header lines in output.
2025-04-15 09:24:52,344 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:24:52,345 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 09:24:52,346 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 09:24:52,346 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 09:24:52,346 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 09:24:52,384 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/pocket.pdb
2025-04-15 09:24:52,386 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:24:52,389 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 548 atoms.
2025-04-15 09:24:52,389 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:24:52,390 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:24:52,390 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-04-15 09:24:52,390 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-04-15 09:24:52,390 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 96 and PRO A 97!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 97 and THR A 98!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 98 and TYR A 99!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 139 and GLY A 142!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 145 and ARG A 146!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 146 and LYS A 147!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:24:52,391 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 173 and PHE A 174!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 174 and ILE A 175!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 189 and ASP A 190!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 190 and CYS A 191!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 191 and GLN A 192!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 192 and GLY A 193!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and ILE A 212!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 212 and TRP A 213!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 213 and SER A 214!
2025-04-15 09:24:52,392 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 214 and ALA A 215!
2025-04-15 09:24:52,393 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 215 and GLY A 216!
2025-04-15 09:24:52,393 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 216 and GLU A 217!
2025-04-15 09:24:52,393 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 217 and ALA A 218!
2025-04-15 09:24:52,393 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 218 and GLY A 220!
2025-04-15 09:24:52,393 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 220 and ALA A 221!
2025-04-15 09:24:52,393 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-04-15 09:24:52,393 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 225 and GLY A 226!
2025-04-15 09:24:52,393 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 226 and ILE A 227!
2025-04-15 09:24:52,393 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:24:52,411 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:24:52,412 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 09:24:52,413 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 09:24:52,413 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
2025-04-15 09:24:52,413 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 09:24:52,413 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue THR A 229 at coordinates 22.281, 41.961, 60.699
2025-04-15 09:24:52,413 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:24:52,414 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:24:52,424 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:24:52,475 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:24:53,171 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 57
2025-04-15 09:24:53,218 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 95
2025-04-15 09:24:53,234 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump LYS A 96
2025-04-15 09:24:53,235 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PRO A 97
2025-04-15 09:24:53,606 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 98
2025-04-15 09:24:53,657 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 144
2025-04-15 09:24:54,117 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 145
2025-04-15 09:24:55,634 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ARG A 146
2025-04-15 09:24:56,632 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PHE A 174
2025-04-15 09:24:56,709 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 177
2025-04-15 09:24:56,781 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ASP A 190
2025-04-15 09:24:56,812 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump CYS A 191
2025-04-15 09:24:57,422 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLN A 192
2025-04-15 09:24:58,021 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 199
2025-04-15 09:24:59,445 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump TRP A 213
2025-04-15 09:24:59,446 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 215
2025-04-15 09:24:59,447 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 218
2025-04-15 09:24:59,448 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLY A 220
2025-04-15 09:24:59,508 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 229
2025-04-15 09:24:59,508 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:24:59,691 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:24:59,692 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:24:59,692 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:24:59,696 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 09:37:39,583 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 09:37:39,583 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 09:37:39,583 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 09:37:39,583 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 09:37:39,583 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 09:37:39,624 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/pocket.pdb
2025-04-15 09:37:39,626 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 09:37:39,629 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 548 atoms.
2025-04-15 09:37:39,629 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 96 and PRO A 97!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 97 and THR A 98!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 98 and TYR A 99!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 139 and GLY A 142!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 145 and ARG A 146!
2025-04-15 09:37:39,630 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 146 and LYS A 147!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 173 and PHE A 174!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 174 and ILE A 175!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 189 and ASP A 190!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 190 and CYS A 191!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 191 and GLN A 192!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 192 and GLY A 193!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and ILE A 212!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 212 and TRP A 213!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 213 and SER A 214!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 214 and ALA A 215!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 215 and GLY A 216!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 216 and GLU A 217!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 217 and ALA A 218!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 218 and GLY A 220!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 220 and ALA A 221!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 225 and GLY A 226!
2025-04-15 09:37:39,631 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 226 and ILE A 227!
2025-04-15 09:37:39,631 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 09:37:39,645 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 09:37:39,646 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 09:37:39,646 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 09:37:39,646 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
2025-04-15 09:37:39,647 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 09:37:39,647 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue THR A 229 at coordinates 22.281, 41.961, 60.699
2025-04-15 09:37:39,647 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 09:37:39,647 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 09:37:39,657 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 09:37:39,709 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 09:37:40,490 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 57
2025-04-15 09:37:40,537 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 95
2025-04-15 09:37:40,552 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump LYS A 96
2025-04-15 09:37:40,553 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PRO A 97
2025-04-15 09:37:40,904 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 98
2025-04-15 09:37:40,965 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 144
2025-04-15 09:37:41,510 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 145
2025-04-15 09:37:42,941 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ARG A 146
2025-04-15 09:37:43,846 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PHE A 174
2025-04-15 09:37:43,892 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 177
2025-04-15 09:37:43,935 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ASP A 190
2025-04-15 09:37:43,966 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump CYS A 191
2025-04-15 09:37:44,543 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLN A 192
2025-04-15 09:37:45,198 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 199
2025-04-15 09:37:46,755 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump TRP A 213
2025-04-15 09:37:46,756 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 215
2025-04-15 09:37:46,757 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 218
2025-04-15 09:37:46,758 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLY A 220
2025-04-15 09:37:46,823 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 229
2025-04-15 09:37:46,824 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 09:37:46,984 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 09:37:46,985 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 09:37:46,985 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 09:37:46,990 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:12:02,490 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:12:02,491 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).
2025-04-15 13:12:02,491 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).
2025-04-15 13:12:02,491 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:12:02,491 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:12:02,528 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/pocket.pdb
2025-04-15 13:12:02,530 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:12:02,532 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 548 atoms.
2025-04-15 13:12:02,533 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:12:02,534 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:12:02,534 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-04-15 13:12:02,534 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-04-15 13:12:02,534 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-04-15 13:12:02,534 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-04-15 13:12:02,534 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 96 and PRO A 97!
2025-04-15 13:12:02,534 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 97 and THR A 98!
2025-04-15 13:12:02,535 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 98 and TYR A 99!
2025-04-15 13:12:02,535 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:12:02,535 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 139 and GLY A 142!
2025-04-15 13:12:02,535 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 145 and ARG A 146!
2025-04-15 13:12:02,535 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 146 and LYS A 147!
2025-04-15 13:12:02,535 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:12:02,535 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:12:02,535 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:12:02,536 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 173 and PHE A 174!
2025-04-15 13:12:02,536 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 174 and ILE A 175!
2025-04-15 13:12:02,536 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-04-15 13:12:02,536 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-04-15 13:12:02,536 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 189 and ASP A 190!
2025-04-15 13:12:02,536 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 190 and CYS A 191!
2025-04-15 13:12:02,536 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 191 and GLN A 192!
2025-04-15 13:12:02,536 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 192 and GLY A 193!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and ILE A 212!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 212 and TRP A 213!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 213 and SER A 214!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 214 and ALA A 215!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 215 and GLY A 216!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 216 and GLU A 217!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 217 and ALA A 218!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 218 and GLY A 220!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 220 and ALA A 221!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 225 and GLY A 226!
2025-04-15 13:12:02,537 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 226 and ILE A 227!
2025-04-15 13:12:02,537 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:12:02,550 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:12:02,551 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 13:12:02,551 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 13:12:02,551 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
2025-04-15 13:12:02,551 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 13:12:02,552 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue THR A 229 at coordinates 22.281, 41.961, 60.699
2025-04-15 13:12:02,552 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:12:02,552 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:12:02,562 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:12:02,608 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:12:03,428 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 57
2025-04-15 13:12:03,472 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 95
2025-04-15 13:12:03,486 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump LYS A 96
2025-04-15 13:12:03,487 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PRO A 97
2025-04-15 13:12:03,841 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 98
2025-04-15 13:12:03,896 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 144
2025-04-15 13:12:04,389 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 145
2025-04-15 13:12:06,001 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ARG A 146
2025-04-15 13:12:07,166 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PHE A 174
2025-04-15 13:12:07,212 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 177
2025-04-15 13:12:07,264 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ASP A 190
2025-04-15 13:12:07,297 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump CYS A 191
2025-04-15 13:12:07,867 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLN A 192
2025-04-15 13:12:08,479 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 199
2025-04-15 13:12:10,128 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump TRP A 213
2025-04-15 13:12:10,129 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 215
2025-04-15 13:12:10,131 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 218
2025-04-15 13:12:10,131 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLY A 220
2025-04-15 13:12:10,192 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 229
2025-04-15 13:12:10,192 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:12:10,381 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:12:10,382 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:12:10,382 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:12:10,386 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 13:30:14,616 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 13:30:14,616 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 13:30:14,616 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 13:30:14,616 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 13:30:14,617 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 13:30:14,645 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/pocket.pdb
2025-04-15 13:30:14,646 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 13:30:14,648 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 548 atoms.
2025-04-15 13:30:14,648 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 13:30:14,649 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 96 and PRO A 97!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 97 and THR A 98!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 98 and TYR A 99!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 139 and GLY A 142!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 145 and ARG A 146!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 146 and LYS A 147!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 173 and PHE A 174!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 174 and ILE A 175!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-04-15 13:30:14,650 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 189 and ASP A 190!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 190 and CYS A 191!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 191 and GLN A 192!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 192 and GLY A 193!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and ILE A 212!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 212 and TRP A 213!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 213 and SER A 214!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 214 and ALA A 215!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 215 and GLY A 216!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 216 and GLU A 217!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 217 and ALA A 218!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 218 and GLY A 220!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 220 and ALA A 221!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 225 and GLY A 226!
2025-04-15 13:30:14,651 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 226 and ILE A 227!
2025-04-15 13:30:14,651 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 13:30:14,664 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 13:30:14,665 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 13:30:14,665 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 13:30:14,665 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
2025-04-15 13:30:14,665 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 13:30:14,665 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue THR A 229 at coordinates 22.281, 41.961, 60.699
2025-04-15 13:30:14,665 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 13:30:14,666 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 13:30:14,673 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 13:30:14,706 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 13:30:15,230 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 57
2025-04-15 13:30:15,262 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 95
2025-04-15 13:30:15,273 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump LYS A 96
2025-04-15 13:30:15,274 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PRO A 97
2025-04-15 13:30:15,520 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 98
2025-04-15 13:30:15,558 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 144
2025-04-15 13:30:15,912 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 145
2025-04-15 13:30:16,892 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ARG A 146
2025-04-15 13:30:17,509 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PHE A 174
2025-04-15 13:30:17,539 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 177
2025-04-15 13:30:17,567 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ASP A 190
2025-04-15 13:30:17,589 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump CYS A 191
2025-04-15 13:30:17,980 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLN A 192
2025-04-15 13:30:18,398 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 199
2025-04-15 13:30:19,429 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump TRP A 213
2025-04-15 13:30:19,430 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 215
2025-04-15 13:30:19,431 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 218
2025-04-15 13:30:19,431 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLY A 220
2025-04-15 13:30:19,470 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 229
2025-04-15 13:30:19,471 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 13:30:19,579 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 13:30:19,580 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 13:30:19,580 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 13:30:19,583 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 18:24:09,592 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 18:24:09,595 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 18:24:09,595 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 18:24:09,595 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 18:24:09,595 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 18:24:09,622 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/pocket.pdb
2025-04-15 18:24:09,624 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 18:24:09,625 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 548 atoms.
2025-04-15 18:24:09,626 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 18:24:09,626 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 18:24:09,626 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 96 and PRO A 97!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 97 and THR A 98!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 98 and TYR A 99!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 139 and GLY A 142!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 145 and ARG A 146!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 146 and LYS A 147!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 173 and PHE A 174!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 174 and ILE A 175!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 189 and ASP A 190!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 190 and CYS A 191!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 191 and GLN A 192!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 192 and GLY A 193!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and ILE A 212!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 212 and TRP A 213!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 213 and SER A 214!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 214 and ALA A 215!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 215 and GLY A 216!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 216 and GLU A 217!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 217 and ALA A 218!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 218 and GLY A 220!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 220 and ALA A 221!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 225 and GLY A 226!
2025-04-15 18:24:09,627 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 226 and ILE A 227!
2025-04-15 18:24:09,627 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 18:24:09,638 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 18:24:09,638 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 18:24:09,639 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 18:24:09,639 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
2025-04-15 18:24:09,639 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 18:24:09,639 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue THR A 229 at coordinates 22.281, 41.961, 60.699
2025-04-15 18:24:09,639 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 18:24:09,639 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 18:24:09,647 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 18:24:09,682 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 18:24:10,234 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 57
2025-04-15 18:24:10,267 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 95
2025-04-15 18:24:10,278 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump LYS A 96
2025-04-15 18:24:10,279 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PRO A 97
2025-04-15 18:24:10,544 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 98
2025-04-15 18:24:10,588 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 144
2025-04-15 18:24:10,968 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 145
2025-04-15 18:24:12,029 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ARG A 146
2025-04-15 18:24:12,705 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PHE A 174
2025-04-15 18:24:12,739 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 177
2025-04-15 18:24:12,770 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ASP A 190
2025-04-15 18:24:12,793 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump CYS A 191
2025-04-15 18:24:13,254 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLN A 192
2025-04-15 18:24:13,718 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 199
2025-04-15 18:24:14,843 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump TRP A 213
2025-04-15 18:24:14,844 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 215
2025-04-15 18:24:14,845 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 218
2025-04-15 18:24:14,845 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLY A 220
2025-04-15 18:24:14,889 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 229
2025-04-15 18:24:14,889 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 18:24:15,010 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 18:24:15,011 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 18:24:15,011 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 18:24:15,014 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-04-15 22:14:38,094 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-04-15 22:14:38,094 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 22:14:38,094 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 22:14:38,094 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-04-15 22:14:38,095 INFO:main.py:763:main_driver:Loading topology files.
2025-04-15 22:14:38,123 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/pocket.pdb
2025-04-15 22:14:38,125 INFO:main.py:770:main_driver:Setting up molecule.
2025-04-15 22:14:38,127 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 548 atoms.
2025-04-15 22:14:38,127 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 96 and PRO A 97!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 97 and THR A 98!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 98 and TYR A 99!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 139 and GLY A 142!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 145 and ARG A 146!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 146 and LYS A 147!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 173 and PHE A 174!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 174 and ILE A 175!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 189 and ASP A 190!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 190 and CYS A 191!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 191 and GLN A 192!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 192 and GLY A 193!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and ILE A 212!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 212 and TRP A 213!
2025-04-15 22:14:38,128 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 213 and SER A 214!
2025-04-15 22:14:38,129 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 214 and ALA A 215!
2025-04-15 22:14:38,129 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 215 and GLY A 216!
2025-04-15 22:14:38,129 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 216 and GLU A 217!
2025-04-15 22:14:38,129 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 217 and ALA A 218!
2025-04-15 22:14:38,129 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 218 and GLY A 220!
2025-04-15 22:14:38,129 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 220 and ALA A 221!
2025-04-15 22:14:38,129 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-04-15 22:14:38,129 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 225 and GLY A 226!
2025-04-15 22:14:38,129 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 226 and ILE A 227!
2025-04-15 22:14:38,129 INFO:main.py:604:non_trivial:Loading forcefield.
2025-04-15 22:14:38,142 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-04-15 22:14:38,143 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 22:14:38,143 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 22:14:38,143 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
2025-04-15 22:14:38,143 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-04-15 22:14:38,143 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue THR A 229 at coordinates 22.281, 41.961, 60.699
2025-04-15 22:14:38,144 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-04-15 22:14:38,144 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-04-15 22:14:38,151 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-04-15 22:14:38,188 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-04-15 22:14:38,741 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 57
2025-04-15 22:14:38,774 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 95
2025-04-15 22:14:38,785 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump LYS A 96
2025-04-15 22:14:38,786 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PRO A 97
2025-04-15 22:14:39,043 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 98
2025-04-15 22:14:39,084 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 144
2025-04-15 22:14:39,459 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 145
2025-04-15 22:14:40,497 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ARG A 146
2025-04-15 22:14:41,170 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PHE A 174
2025-04-15 22:14:41,206 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 177
2025-04-15 22:14:41,240 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ASP A 190
2025-04-15 22:14:41,265 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump CYS A 191
2025-04-15 22:14:41,676 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLN A 192
2025-04-15 22:14:42,119 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 199
2025-04-15 22:14:43,670 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump TRP A 213
2025-04-15 22:14:43,671 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 215
2025-04-15 22:14:43,672 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 218
2025-04-15 22:14:43,672 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLY A 220
2025-04-15 22:14:43,716 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 229
2025-04-15 22:14:43,716 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-04-15 22:14:43,850 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-04-15 22:14:43,851 INFO:main.py:713:non_trivial:Regenerating headers.
2025-04-15 22:14:43,851 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-04-15 22:14:43,855 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.
2025-05-05 10:26:03,729 INFO:main.py:240:print_splash_screen:PDB2PQR v3.6.1: biomolecular structure conversion software.
2025-05-05 10:26:03,729 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 10:26:03,729 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 10:26:03,730 INFO:main.py:759:main_driver:Checking and transforming input arguments.
2025-05-05 10:26:03,730 INFO:main.py:763:main_driver:Loading topology files.
2025-05-05 10:26:03,783 INFO:main.py:765:main_driver:Loading molecule: ./generate/upload/protein_pocket.pdb
2025-05-05 10:26:03,785 INFO:main.py:770:main_driver:Setting up molecule.
2025-05-05 10:26:03,788 INFO:main.py:408:setup_molecule:Created biomolecule object with 71 residues and 548 atoms.
2025-05-05 10:26:03,788 INFO:main.py:774:main_driver:Setting termini states for biomolecule chains.
2025-05-05 10:26:03,789 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 17 and PHE A 41!
2025-05-05 10:26:03,789 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 43 and ALA A 55!
2025-05-05 10:26:03,789 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 55 and HIS A 57!
2025-05-05 10:26:03,789 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 58 and GLN A 61!
2025-05-05 10:26:03,789 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 61 and PHE A 94!
2025-05-05 10:26:03,789 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LYS A 96 and PRO A 97!
2025-05-05 10:26:03,789 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PRO A 97 and THR A 98!
2025-05-05 10:26:03,789 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 98 and TYR A 99!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 102 and VAL A 138!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 139 and GLY A 142!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 145 and ARG A 146!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 146 and LYS A 147!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 151 and LEU A 158!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between LEU A 158 and VAL A 160!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between VAL A 160 and SER A 172!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 173 and PHE A 174!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between PHE A 174 and ILE A 175!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between THR A 177 and MET A 180!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 185 and GLU A 188!
2025-05-05 10:26:03,790 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 189 and ASP A 190!
2025-05-05 10:26:03,793 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ASP A 190 and CYS A 191!
2025-05-05 10:26:03,793 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between CYS A 191 and GLN A 192!
2025-05-05 10:26:03,793 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLN A 192 and GLY A 193!
2025-05-05 10:26:03,793 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between HIS A 199 and ILE A 212!
2025-05-05 10:26:03,793 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ILE A 212 and TRP A 213!
2025-05-05 10:26:03,793 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TRP A 213 and SER A 214!
2025-05-05 10:26:03,793 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between SER A 214 and ALA A 215!
2025-05-05 10:26:03,794 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 215 and GLY A 216!
2025-05-05 10:26:03,794 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 216 and GLU A 217!
2025-05-05 10:26:03,794 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLU A 217 and ALA A 218!
2025-05-05 10:26:03,794 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ALA A 218 and GLY A 220!
2025-05-05 10:26:03,794 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 220 and ALA A 221!
2025-05-05 10:26:03,794 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between ARG A 222 and LYS A 224!
2025-05-05 10:26:03,794 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between TYR A 225 and GLY A 226!
2025-05-05 10:26:03,794 WARNING:biomolecule.py:615:update_bonds:Gap in backbone detected between GLY A 226 and ILE A 227!
2025-05-05 10:26:03,794 INFO:main.py:604:non_trivial:Loading forcefield.
2025-05-05 10:26:03,815 INFO:main.py:608:non_trivial:Loading hydrogen topology definitions.
2025-05-05 10:26:03,817 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-05-05 10:26:03,817 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-05-05 10:26:03,817 INFO:main.py:618:non_trivial:Attempting to repair 1 missing atoms in biomolecule.
2025-05-05 10:26:03,817 WARNING:biomolecule.py:157:num_missing_heavy:Missing atom OXT in residue THR A 229
2025-05-05 10:26:03,818 INFO:biomolecule.py:1077:repair_heavy:Added atom OXT to residue THR A 229 at coordinates 22.281, 41.961, 60.699
2025-05-05 10:26:03,818 INFO:main.py:623:non_trivial:Updating disulfide bridges.
2025-05-05 10:26:03,818 INFO:main.py:626:non_trivial:Debumping biomolecule.
2025-05-05 10:26:03,829 INFO:main.py:649:non_trivial:Adding hydrogens to biomolecule.
2025-05-05 10:26:03,882 INFO:main.py:652:non_trivial:Debumping biomolecule (again).
2025-05-05 10:26:04,733 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 57
2025-05-05 10:26:04,780 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 95
2025-05-05 10:26:04,801 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump LYS A 96
2025-05-05 10:26:04,803 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PRO A 97
2025-05-05 10:26:05,196 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 98
2025-05-05 10:26:05,256 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 144
2025-05-05 10:26:05,817 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 145
2025-05-05 10:26:07,395 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ARG A 146
2025-05-05 10:26:08,415 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump PHE A 174
2025-05-05 10:26:08,467 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 177
2025-05-05 10:26:08,517 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ASP A 190
2025-05-05 10:26:08,552 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump CYS A 191
2025-05-05 10:26:09,242 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLN A 192
2025-05-05 10:26:09,959 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump HIS A 199
2025-05-05 10:26:11,694 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump TRP A 213
2025-05-05 10:26:11,696 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 215
2025-05-05 10:26:11,697 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump ALA A 218
2025-05-05 10:26:11,698 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump GLY A 220
2025-05-05 10:26:11,770 WARNING:debump.py:172:debump_biomolecule:WARNING: Unable to debump THR A 229
2025-05-05 10:26:11,770 INFO:main.py:654:non_trivial:Optimizing hydrogen bonds
2025-05-05 10:26:11,949 INFO:main.py:666:non_trivial:Applying force field to biomolecule states.
2025-05-05 10:26:11,950 INFO:main.py:713:non_trivial:Regenerating headers.
2025-05-05 10:26:11,950 INFO:main.py:738:non_trivial:Regenerating PDB lines.
2025-05-05 10:26:11,956 WARNING:main.py:311:print_pqr:Ignoring 390 header lines in output.