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 0m1.270s user 0m0.196s sys 0m0.159s 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 0:1289 spheres. 65. 66. 66. 66. 67. 68. 68. 68. 68. 68. 68. 68. 68. 68. 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. 74. 74. 75. 75. 82. 82. 83. 83. 83. 83. 86. 86. 86. 86. 86. 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. 87. 87. 87. 87. 87. 87. 181. 181. 181. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 190. 196. 196. 198. 198. 198. 198. 198. 198. 202. 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. 209. 209. 209. 209. 209. 209. 209. 211. 211. 211. 211. 211. 211. 211. 211. 211. 214. 214. 214. 214. 214. 214. 214. 214. 215. 215. 218. 219. 219. 219. 219. 219. 220. 220. 220. 220. 220. 221. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 222. 227. 227. 227. 227. 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819. 819. 819. 819. 819. 819. 820. 820. 820. 820. 820. 821. 821. 821. 821. 821. 821. 821. 821. 821. 821. 822. 822. 822. 822. 822. 822. 822. 822. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 834. 835. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 837. 838. 838. 838. 838. 838. 838. 838. 838. 838. 932. 932. 932. 932. 932. 933. 941. 949. 949. 949. 949. 949. 949. 949. 949. 949. 949. 949. 949. 959. 959. 959. 959. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 960. 962. 962. 962. 962. 962. 962. 962. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 965. 966. 970. 971. 971. 971. 971. 971. 971. 971. 971. 971. 972. 972. 972. 972. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 973. 976. 976. 976. 977. 977. 977. 978. 978. 978. 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994.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1003.1093.1095.1096.1096.1096.1096.1097.1097.1097.1097.1097.1097.1097.1097.1097.1097.1097.1097.1098.1098.1098.1098.1098.1098.1098.1098.1098.1102.1102.1102.1102.1102.1103.1103.1103.1103.1103.1106.1108.1108.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1111.1111.1111.1111.1111.1111.1111.1111.1112.1112.1112.1112.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1113.1114.1114.1114.1114.1114.1114.1114.1114.1114.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1115.1117.1117.1117.1117.1117.1117.1117.1117.1117.1118.1118.1118.1123.1124.1124.1125.1125.1125.1125.1125.1127.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1140.1140.1140.1140.1140.1140.1140.1141.1143.1143.1143.1143.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1144.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1146.1146.1146.1146.1146.1146.1153.1153.1153.1153.1153.1153.1153.1153.1164.1166.1326.1326.1326.1326.1326.1326.1326.1326.1328.1328.1328.1343.1343.1343.1343.1344.1344.1344.1344.1344.1345.1345.1345.1345.1345.1345.1345.1350.1350.1356.1356.1357.1357.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1359.1360.1360.1360.1360.1362.1363.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1367.1373.1373.1373.1373.1373.1373.1373.1373.1373.1375.1375.1375.1375.1383.1383.1383.1383.1383.1383.1383.1383.1383.1391.1391.1391.1391.1391.1391.1391.1391.1391.1391.1398.1403.1403.1403.1404.1404.1405.1405.1405.1405.1405.1405.1405.1405.1405.1406.1406.1406.1408.1408.1408.1408.1411.1411.1411.1411.1411.1411.1411.1411.1412.1412.1412.1412.1412.1412.1412.1412.1414.1414.1414.1414.1414.1414.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: 58 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.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 0m40.404s user 0m30.480s sys 0m1.197s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m21.489s user 0m31.371s sys 0m0.999s Creating box around spheres Creating chemgrid maps real 0m13.487s user 0m9.177s sys 0m0.226s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m5.247s user 18m4.283s sys 0m0.063s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: MET 145 has a net charge of -0.0720 !!! WARNING: MET 145 has a net charge of -0.0720 !!! WARNING: MET 145 has a net charge of -0.0720 End of MakeDOCK sphere and grid generation.