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 0m1.947s user 0m0.328s sys 0m0.212s 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 0:1244 spheres. 65. 65. 67. 67. 67. 67. 67. 67. 67. 67. 67. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 71. 71. 71. 71. 71. 71. 74. 74. 74. 74. 82. 82. 82. 83. 83. 83. 83. 83. 83. 83. 83. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 87. 182. 182. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 189. 197. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 198. 202. 207. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 211. 211. 211. 211. 211. 211. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 215. 215. 215. 218. 219. 219. 219. 219. 219. 220. 220. 221. 221. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 227. 227. 227. 227. 228. 229. 229. 229. 229. 229. 229. 230. 230. 230. 231. 234. 244. 244. 244. 249. 249. 249. 249. 249. 249. 252. 252. 252. 346. 346. 346. 346. 346. 347. 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996.1002.1002.1002.1002.1002.1002.1002.1002.1002.1002.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1011.1011.1109.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1111.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1116.1116.1116.1116.1116.1117.1118.1120.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1136.1141.1141.1142.1142.1142.1142.1142.1142.1142.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1145.1145.1145.1145.1147.1147.1147.1147.1147.1147.1148.1148.1148.1148.1148.1149.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1150.1151.1156.1156.1156.1156.1156.1159.1159.1159.1159.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1163.1163.1165.1165.1170.1170.1204.1205.1205.1206.1206.1206.1206.1206.1206.1206.1207.1324.1328.1343.1360.1360.1360.1360.1360.1361.1361.1361.1362.1362.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1382.1382.1382.1382.1382.1382.1382.1382.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1386.1386.1386.1386.1386.1386.1386.1386.1387.1387.1387.1387.1387.1387.1387.1387.1388.1388.1388.1388.1388.1388.1388.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1395.1396.1396.1396.1396.1396.1396.1396.1396.1396.1396.1402.1402.1403.1403.1403.1403.1403.1403.1418.1418.1418.1418.1424.1424.1424.1424.1424.1424.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1426.1426.1426.1426.1428.1428.1428.1428.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1431.1431.1431.1431.1431.1431.1431.1431.1431.1434.1434.FORTRAN 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: 54 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. 26. 27. 28. 29. 30. 31. 32. 33. 34. 35. 36. 37. 38. 39. 40. 41. 42. 43. 44. 45. 46. 47. 48. 49. 50. 51. 52. 53. 54.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... Detecting missing residue atoms... 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... 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 1m3.690s user 0m53.925s sys 0m2.507s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m56.626s user 0m52.867s sys 0m2.354s Creating box around spheres Creating chemgrid maps real 1m44.699s user 1m43.543s sys 0m0.728s Atomic solvent excluded volume calculations underway FORTRAN STOP real 28m6.806s user 28m6.472s sys 0m0.130s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.