MakeDOCK 2.0, modified by J.Irwin and M.Mysinger. Previous versions by D.M.Lorber, B.Q.Wei, A.N.Kirschner, and N.Huang Using scripts in /raid5/people/mysinger/xyz/dockenv. Creating binding-site residue list Creating molecular surface real 1m10.812s user 0m0.611s sys 0m0.405s Creating sphgen spheres Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 0:1897 spheres. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 415. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 416. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 420. 420. 420. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 425. 425. 426. 426. 426. 426. 427. 427. 427. 427. 427. 428. 428. 428. 428. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 453. 454. 454. 454. 454. 454. 454. 454. 454. 454. 454. 455. 455. 455. 455. 455. 455. 455. 459. 459. 459. 459. 459. 460. 460. 460. 460. 460. 461. 461. 461. 461. 461. 461. 461. 461. 462. 613. 613. 613. 615. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 616. 621. 621. 623. 642. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 643. 645. 645. 645. 645. 647. 649. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 655. 655. 657. 658. 658. 660. 662. 662. 662. 664. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 670. 670. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 672. 679. 679. 679. 679. 679. 681. 681. 681. 681. 681. 681. 681. 681. 681. 681. 681. 681. 682. 682. 682. 682. 682. 682. 682. 682. 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STOP Converting ligand atoms to spheres Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 22 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22.FORTRAN STOP Adding essential hydrogens to receptor Adding all-atom hydrogens... Working on structure 1 Pre-treating metals... Done treating metals Adding hydrogens... Treating metals... Creating di-sulfur bonds... Created a bond between residue(A:16) and residue(A:5); changed residue names to "CYX " Created a bond between residue(A:26) and residue(A:10); changed residue names to "CYX " Created a bond between residue(A:38) and residue(A:28); changed residue names to "CYX " Created a bond between residue(A:128) and residue(A:6); changed residue names to "CYX " Created a bond between residue(A:544) and residue(A:538); changed residue names to "CYX " Created a bond between residue(A:569) and residue(A:558); changed residue names to "CYX " Created a bond between residue(A:579) and residue(A:563); changed residue names to "CYX " Created a bond between residue(A:591) and residue(A:581); changed residue names to "CYX " Finding het groups... Coloring atoms by element (green carbons in hets)... Running ProtAssign... using exhaustive mode will sample waters done with preparation Writing to file... DONE. Output file: rec.mae Removing non-polar hydrogens... WARNING mmpdb_write: more than 4 bonds for atom (CO ) in residue 1107 (COH ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom (CO ) in residue 1107 (COH ), chain 'A'. Renaming polar hydrogens... Generating matching spheres for delphi Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 90 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.9061.9062.9063.9064.9065.9066.9067.9068.9069.9070.9071.9072.9073.9074.9075.9076.9077.9078.9079.9080.9081.9082.9083.9084.9085.9086.9087.9088.9089.9090.FORTRAN STOP Generating faster matching2 spheres for docking Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 45 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.FORTRAN STOP Coloring matching spheres Generating slower matching3 spheres for docking Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 60 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.FORTRAN STOP Coloring matching spheres Adding spheres to electrostatic grid we were asked to cook *CO * *COH* 22 we had to cook * CHA* we had to cook * CHB* we had to cook * CHC* we had to cook * CHD* we had to cook * NA * we had to cook * C1A* we had to cook * C2A* we had to cook * C3A* we had to cook * C4A* we had to cook * CMA* we had to cook * CAA* we had to cook * CBA* we had to cook * CGA* we had to cook * O1A* we had to cook * O2A* we had to cook * NB * we had to cook * C1B* we had to cook * C2B* we had to cook * C3B* we had to cook * C4B* we had to cook * CMB* we had to cook * CAB* we had to cook * CBB* we had to cook * NC * we had to cook * C1C* we had to cook * C2C* we had to cook * C3C* we had to cook * C4C* we had to cook * CMC* we had to cook * CAC* we had to cook * CBC* we had to cook * ND * we had to cook * C1D* we had to cook * C2D* we had to cook * C3D* we had to cook * C4D* we had to cook * CMD* we had to cook * CAD* we had to cook * CBD* we had to cook * CGD* we had to cook * O1D* we had to cook * O2D* we had to cook * HNA* we had to cook * HO1* we had to cook * HO2* we had to cook * HNB* we had to cook * HNC* we had to cook * HND* Creating DelPhi electrostatic grid real 0m49.591s user 0m26.362s sys 0m0.800s Adding spheres to tarted electrostatic grid we had to cook * HOG* we were asked to cook *CO * *COH* 22 we had to cook * CHA* we had to cook * CHB* we had to cook * CHC* we had to cook * CHD* we had to cook * NA * we had to cook * C1A* we had to cook * C2A* we had to cook * C3A* we had to cook * C4A* we had to cook * CMA* we had to cook * CAA* we had to cook * CBA* we had to cook * CGA* we had to cook * O1A* we had to cook * O2A* we had to cook * NB * we had to cook * C1B* we had to cook * C2B* we had to cook * C3B* we had to cook * C4B* we had to cook * CMB* we had to cook * CAB* we had to cook * CBB* we had to cook * NC * we had to cook * C1C* we had to cook * C2C* we had to cook * C3C* we had to cook * C4C* we had to cook * CMC* we had to cook * CAC* we had to cook * CBC* we had to cook * ND * we had to cook * C1D* we had to cook * C2D* we had to cook * C3D* we had to cook * C4D* we had to cook * CMD* we had to cook * CAD* we had to cook * CBD* we had to cook * CGD* we had to cook * O1D* we had to cook * O2D* we had to cook * HNA* we had to cook * HO1* we had to cook * HO2* we had to cook * HNB* we had to cook * HNC* we had to cook * HND* Creating DelPhi electrostatic grid real 0m47.948s user 0m26.186s sys 0m0.680s Creating box around spheres we were asked to cook *CO * *COH* 22 we had to cook * CHA* we had to cook * CHB* we had to cook * CHC* we had to cook * CHD* we had to cook * NA * we had to cook * C1A* we had to cook * C2A* we had to cook * C3A* we had to cook * C4A* we had to cook * CMA* we had to cook * CAA* we had to cook * CBA* we had to cook * CGA* we had to cook * O1A* we had to cook * O2A* we had to cook * NB * we had to cook * C1B* we had to cook * C2B* we had to cook * C3B* we had to cook * C4B* we had to cook * CMB* we had to cook * CAB* we had to cook * CBB* we had to cook * NC * we had to cook * C1C* we had to cook * C2C* we had to cook * C3C* we had to cook * C4C* we had to cook * CMC* we had to cook * CAC* we had to cook * CBC* we had to cook * ND * we had to cook * C1D* we had to cook * C2D* we had to cook * C3D* we had to cook * C4D* we had to cook * CMD* we had to cook * CAD* we had to cook * CBD* we had to cook * CGD* we had to cook * O1D* we had to cook * O2D* we had to cook * HNA* we had to cook * HO1* we had to cook * HO2* we had to cook * HNB* we had to cook * HNC* we had to cook * HND* Creating chemgrid maps real 0m33.807s user 0m17.291s sys 0m0.230s Atomic solvent excluded volume calculations underway FORTRAN STOP real 24m39.604s user 15m50.823s sys 0m0.069s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: SER 252 has a net charge of 0.2400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: LYS 737 has a net charge of 0.0200 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: SER 252 has a net charge of 0.2400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: LYS 737 has a net charge of 0.0200 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: SER 252 has a net charge of 0.2400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: LYS 737 has a net charge of 0.0200 End of MakeDOCK sphere and grid generation.