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 0m1.831s user 0m0.315s sys 0m0.235s 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 0:1697 spheres. 70. 70. 72. 72. 72. 72. 73. 73. 73. 73. 73. 74. 74. 74. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 75. 188. 188. 188. 188. 202. 202. 204. 204. 204. 204. 204. 204. 214. 214. 214. 214. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 217. 217. 217. 217. 217. 217. 217. 217. 217. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 220. 221. 224. 224. 225. 225. 225. 225. 225. 225. 226. 226. 226. 226. 226. 226. 226. 226. 227. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 233. 233. 233. 233. 233. 233. 233. 233. 233. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 236. 237. 237. 240. 248. 248. 248. 248. 248. 250. 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990.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1092.1092.1092.1093.1098.1098.1098.1098.1099.1099.1099.1099.1103.1103.1103.1103.1105.1105.1105.1105.1105.1105.1105.1107.1107.1107.1107.1107.1107.1107.1107.1109.1109.1113.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1115.1116.1116.1117.1117.1117.1117.1117.1117.1117.1117.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1118.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1120.1121.1121.1121.1121.1121.1121.1121.1121.1122.1122.1122.1122.1122.1124.1126.1126.1127.1127.1127.1127.1127.1127.1127.1127.1127.1127.1128.1128.1129.1129.1129.1129.1129.1129.1129.1130.1130.1132.1132.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1134.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1137.1141.1142.1142.1142.1142.1143.1143.1143.1143.1143.1143.1143.1146.1147.1147.1147.1147.1147.1147.1147.1147.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1154.1154.1154.1154.1154.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1163.1163.1163.1164.1164.1164.1165.1165.1165.1168.1168.1169.1169.1169.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1337.1338.1339.1339.1351.1351.1351.1351.1354.1354.1354.1354.1354.1354.1354.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1355.1356.1356.1356.1356.1356.1356.1356.1356.1356.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1361.1362.1362.1362.1362.1367.1367.1367.1368.1369.1369.1369.1369.1369.1369.1369.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1374.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1386.1386.1386.1386.1386.1387.1388.1388.1388.1396.1396.1396.1396.1396.1396.1396.1414.1420.1420.1420.1420.1420.1420.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1424.1424.1424.1424.1424.1424.1427.1427.1427.1427.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.1428.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: 45 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.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 0m58.922s user 0m51.914s sys 0m2.429s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m57.324s user 0m52.035s sys 0m2.354s Creating box around spheres Creating chemgrid maps real 1m31.152s user 1m30.087s sys 0m0.718s Atomic solvent excluded volume calculations underway FORTRAN STOP real 29m55.496s user 29m53.327s sys 0m0.331s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.