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 0m1.158s user 0m0.205s sys 0m0.136s 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 0:1097 spheres. 66. 66. 67. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 71. 71. 71. 71. 72. 72. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 76. 76. 76. 76. 83. 84. 84. 84. 84. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 182. 182. 183. 188. 188. 197. 199. 199. 199. 199. 199. 199. 206. 206. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 220. 220. 221. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 226. 227. 228. 228. 228. 228. 228. 228. 228. 230. 230. 230. 230. 231. 231. 231. 244. 244. 244. 244. 244. 349. 349. 349. 349. 349. 349. 349. 349. 350. 350. 350. 353. 355. 355. 355. 355. 355. 356. 356. 356. 356. 356. 360. 360. 360. 360. 361. 361. 362. 363. 363. 363. 363. 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992.1004.1004.1010.1010.1017.1017.1018.1018.1018.1018.1018.1018.1021.1021.1021.1021.1022.1022.1109.1109.1109.1109.1109.1109.1109.1109.1109.1109.1110.1110.1115.1115.1115.1115.1115.1115.1115.1115.1116.1116.1116.1116.1116.1116.1116.1120.1120.1120.1120.1122.1123.1123.1124.1124.1124.1124.1124.1124.1124.1124.1124.1126.1126.1129.1129.1129.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1135.1135.1135.1135.1135.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1139.1140.1140.1140.1141.1145.1146.1147.1148.1148.1148.1148.1151.1151.1151.1152.1152.1152.1152.1152.1152.1153.1154.1154.1154.1154.1154.1154.1154.1154.1154.1154.1154.1160.1160.1160.1160.1163.1163.1163.1163.1165.1165.1165.1165.1165.1165.1165.1165.1166.1166.1166.1166.1166.1167.1167.1169.1169.1169.1169.1174.1174.1174.1186.1187.1187.1187.1188.1188.1347.1347.1347.1347.1347.1347.1347.1347.1347.1349.1349.1349.1349.1349.1349.1349.1362.1362.1362.1362.1362.1362.1362.1362.1364.1364.1364.1365.1365.1365.1365.1365.1366.1366.1366.1367.1371.1371.1376.1376.1376.1378.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1381.1387.1387.1387.1387.1387.1387.1387.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1393.1393.1393.1396.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1404.1419.1419.1419.1419.1419.1419.1425.1425.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1427.1429.1429.1429.1429.1431.1431.1431.1431.1432.1432.1432.1432.1432.1432.1432.1433.1433.1433.1433.1433.1433.1433.1433.1435.1435.1435.1435.1435.1435.1435.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: 43 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.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... 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 0m31.608s user 0m29.222s sys 0m1.143s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m7.271s user 0m28.985s sys 0m1.046s Creating box around spheres Creating chemgrid maps real 0m24.871s user 0m10.531s sys 0m0.422s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m41.026s user 18m40.583s sys 0m0.039s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.