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 0m2.070s user 0m0.386s sys 0m0.288s 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 0:1638 spheres. 66. 66. 68. 68. 68. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 70. 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. 72. 72. 72. 72. 72. 72. 72. 72. 72. 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. 75. 84. 84. 85. 85. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 183. 183. 183. 183. 183. 183. 183. 183. 183. 197. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 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. 220. 220. 221. 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987.1001.1006.1006.1006.1006.1006.1006.1006.1006.1006.1097.1097.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1099.1100.1105.1105.1106.1106.1106.1106.1106.1107.1107.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1108.1109.1109.1110.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1114.1115.1115.1116.1116.1116.1116.1116.1116.1116.1116.1117.1117.1117.1117.1117.1117.1117.1118.1118.1118.1118.1118.1123.1123.1123.1123.1123.1123.1123.1123.1125.1125.1125.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1127.1128.1128.1129.1129.1129.1129.1129.1129.1129.1129.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1130.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1138.1139.1139.1140.1140.1142.1142.1142.1142.1142.1142.1142.1145.1145.1146.1146.1146.1146.1148.1148.1148.1148.1148.1153.1153.1154.1154.1154.1154.1154.1154.1154.1157.1157.1157.1158.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1159.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1163.1163.1163.1168.1168.1168.1168.1168.1168.1169.1170.1170.1172.1173.1173.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1174.1175.1175.1175.1175.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1176.1177.1177.1177.1177.1177.1177.1177.1177.1177.1177.1177.1177.1177.1178.1182.1182.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1192.1192.1192.1196.1196.1196.1204.1204.1204.1204.1204.1205.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1213.1221.1221.1221.1221.1221.1222.1222.1222.1222.1225.1321.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1325.1326.1327.1327.1327.1327.1333.1333.1333.1333.1333.1333.1342.1342.1346.1346.1346.1349.1349.1349.1349.1349.1355.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1364.1369.1370.1371.1371.1371.1371.1371.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1372.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1374.1374.1374.1374.1374.1374.1376.1376.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1381.1387.1387.1387.1387.1387.1387.1387.1387.1389.1389.1389.1389.1389.1389.1389.1396.1396.1396.1396.1412.1412.1412.1417.1417.1418.1418.1419.1419.1419.1419.1419.1419.1419.1419.1419.1419.1422.1422.1422.1422.1424.1424.1424.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1426.1426.1426.1428.1428.1428.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: 59 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. 55. 56. 57. 58. 59.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 0m58.619s user 0m53.892s sys 0m2.481s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m58.505s user 0m54.305s sys 0m2.565s Creating box around spheres Creating chemgrid maps real 1m31.843s user 1m30.499s sys 0m0.774s Atomic solvent excluded volume calculations underway FORTRAN STOP real 26m59.758s user 26m59.406s sys 0m0.058s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.