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 1m25.902s user 0m0.492s sys 0m0.369s 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 0:1409 spheres. 402. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 405. 425. 427. 427. 427. 427. 427. 427. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 435. 435. 435. 435. 435. 438. 438. 438. 438. 438. 438. 438. 438. 439. 440. 440. 440. 440. 465. 465. 465. 465. 466. 466. 466. 466. 466. 466. 469. 471. 471. 471. 471. 471. 471. 471. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 473. 474. 474. 474. 605. 605. 605. 610. 610. 610. 610. 611. 611. 611. 611. 616. 616. 616. 616. 616. 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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: 25 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25.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:15) and residue(A:4); changed residue names to "CYX " Created a bond between residue(A:25) and residue(A:9); changed residue names to "CYX " Created a bond between residue(A:37) and residue(A:27); changed residue names to "CYX " Created a bond between residue(A:127) and residue(A:5); changed residue names to "CYX " Created a bond between residue(A:543) and residue(A:537); changed residue names to "CYX " Created a bond between residue(B:576) and residue(B:560); changed residue names to "CYX " Created a bond between residue(B:588) and residue(B:578); 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 (FE ) in residue 1103 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom (FE ) in residue 1103 (HEM ), chain 'B'. 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: 120 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.9061.9062.9063.9064.9065.9066.9067.9068.9069.9070.9071.9072.9073.9074.9075.9076.9077.9078.9079.9080.9081.9082.9083.9084.9085.9086.9087.9088.9089.9090.9091.9092.9093.9094.9095.9096.9097.9098.9099.9100.9101.9102.9103.9104.9105.9106.9107.9108.9109.9110.9111.9112.9113.9114.9115.9116.9117.9118.9119.9120.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 Creating DelPhi electrostatic grid real 1m18.362s user 0m25.945s sys 0m0.667s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m6.038s user 0m26.321s sys 0m0.673s Creating box around spheres Creating chemgrid maps real 0m44.215s user 0m17.175s sys 0m0.267s Atomic solvent excluded volume calculations underway FORTRAN STOP real 30m52.283s user 14m49.179s sys 0m0.054s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 End of MakeDOCK sphere and grid generation.