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 0m1.881s user 0m0.340s sys 0m0.242s 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 0:1691 spheres. 65. 65. 67. 68. 68. 68. 68. 68. 68. 68. 68. 68. 68. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 74. 83. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 86. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 181. 181. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 182. 189. 189. 189. 189. 189. 189. 189. 189. 189. 196. 196. 196. 196. 198. 198. 198. 198. 198. 198. 207. 208. 208. 208. 208. 208. 208. 208. 208. 208. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 209. 211. 211. 211. 211. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 214. 215. 215. 218. 218. 219. 219. 219. 220. 220. 220. 220. 220. 220. 220. 220. 221. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 224. 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991.1004.1004.1004.1106.1106.1106.1106.1107.1112.1112.1112.1112.1112.1112.1112.1112.1112.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1116.1116.1117.1117.1117.1117.1117.1117.1117.1117.1118.1118.1118.1118.1118.1119.1119.1119.1119.1119.1120.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1123.1123.1123.1126.1126.1126.1126.1126.1126.1129.1129.1129.1129.1129.1129.1129.1129.1129.1132.1132.1132.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1139.1139.1139.1139.1139.1139.1140.1141.1143.1144.1144.1144.1144.1144.1144.1144.1144.1146.1146.1146.1146.1146.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1148.1151.1151.1151.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1152.1154.1154.1154.1154.1154.1154.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1162.1162.1162.1163.1163.1163.1163.1163.1163.1164.1164.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1166.1167.1167.1167.1167.1167.1167.1169.1169.1169.1174.1174.1174.1174.1176.1179.1180.1180.1180.1180.1182.1182.1183.1183.1183.1183.1183.1183.1183.1183.1183.1183.1183.1183.1183.1183.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1186.1186.1187.1187.1187.1187.1187.1187.1187.1187.1187.1188.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1347.1349.1349.1349.1349.1358.1358.1358.1362.1364.1365.1365.1365.1365.1365.1365.1365.1365.1365.1366.1366.1366.1366.1371.1371.1371.1371.1371.1371.1371.1378.1378.1378.1378.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1381.1381.1381.1381.1381.1381.1381.1381.1383.1383.1386.1386.1386.1386.1386.1386.1386.1386.1386.1386.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1396.1396.1396.1396.1396.1396.1396.1404.1404.1404.1404.1404.1404.1404.1404.1419.1419.1419.1419.1419.1419.1419.1424.1424.1425.1425.1425.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1427.1427.1429.1429.1429.1429.1429.1430.1430.1431.1432.1432.1432.1432.1432.1432.1432.1432.1433.1433.1433.1433.1433.1435.1435.1435.1435.1435.1435.1435.1435.1435.1435.1435.1435.1435.1435.1435.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: 49 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.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 0m44.996s user 0m37.043s sys 0m1.683s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m35.813s user 0m32.714s sys 0m1.377s Creating box around spheres Creating chemgrid maps real 1m1.937s user 1m0.974s sys 0m0.494s Atomic solvent excluded volume calculations underway FORTRAN STOP real 28m52.081s user 28m51.246s sys 0m0.200s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.