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 0m1.853s user 0m0.258s sys 0m0.174s 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 0:1269 spheres. 70. 70. 70. 70. 70. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 75. 75. 75. 171. 171. 171. 171. 181. 196. 196. 198. 198. 198. 198. 198. 202. 207. 208. 208. 208. 208. 208. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 211. 211. 211. 211. 211. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 215. 218. 218. 218. 219. 219. 220. 220. 220. 220. 220. 222. 222. 222. 222. 226. 227. 227. 227. 227. 227. 228. 229. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 234. 244. 249. 249. 249. 249. 249. 249. 249. 249. 249. 249. 249. 249. 249. 249. 249. 357. 357. 359. 360. 361. 361. 361. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 366. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 368. 369. 369. 369. 369. 371. 372. 372. 372. 372. 372. 372. 372. 372. 373. 373. 373. 373. 373. 373. 373. 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987.1001.1001.1001.1001.1001.1001.1001.1001.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1008.1109.1109.1109.1109.1109.1109.1109.1110.1110.1110.1110.1114.1114.1115.1116.1117.1117.1118.1118.1118.1118.1118.1118.1123.1123.1123.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1129.1129.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1136.1136.1139.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1142.1142.1143.1143.1143.1145.1145.1145.1146.1146.1146.1146.1146.1146.1146.1146.1146.1148.1153.1154.1154.1154.1154.1154.1154.1154.1154.1154.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1163.1164.1166.1166.1166.1168.1168.1168.1168.1168.1168.1168.1168.1168.1168.1168.1168.1168.1168.1168.1169.1169.1169.1169.1169.1170.1170.1173.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1178.1178.1178.1178.1178.1178.1326.1326.1326.1326.1326.1327.1328.1328.1328.1335.1335.1335.1335.1335.1335.1335.1335.1335.1347.1347.1347.1356.1356.1356.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1358.1359.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1363.1363.1363.1363.1363.1363.1365.1365.1365.1365.1365.1370.1370.1372.1372.1372.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1377.1377.1377.1377.1380.1380.1380.1380.1380.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1390.1390.1390.1398.1398.1398.1398.1398.1398.1398.1413.1413.1413.1413.1413.1413.1413.1419.1419.1419.1419.1420.1420.1420.1420.1420.1420.1420.1420.1421.1421.1423.1423.1423.1425.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1427.1427.1429.1429.1429.1429.1429.1429.1429.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: 39 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.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 0m25.743s user 0m22.822s sys 0m0.795s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m27.651s user 0m25.021s sys 0m0.935s Creating box around spheres Creating chemgrid maps real 0m14.145s user 0m13.487s sys 0m0.213s Atomic solvent excluded volume calculations underway FORTRAN STOP real 26m35.027s user 26m34.364s sys 0m0.120s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.