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 0m1.865s user 0m0.331s sys 0m0.223s 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 0:1299 spheres. 66. 66. 69. 69. 69. 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. 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. 75. 76. 76. 76. 84. 84. 84. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 182. 182. 182. 182. 182. 197. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 219. 219. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 222. 223. 223. 223. 223. 227. 228. 228. 228. 228. 228. 228. 228. 228. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 245. 245. 245. 245. 245. 255. 255. 255. 255. 255. 255. 257. 257. 257. 257. 257. 257. 257. 257. 257. 257. 258. 258. 258. 258. 258. 258. 258. 258. 261. 261. 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664. 664. 664. 664. 665. 667. 667. 667. 667. 667. 668. 669. 670. 670. 670. 670. 670. 670. 670. 670. 670. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 671. 673. 823. 823. 823. 823. 823. 826. 826. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 828. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 830. 832. 832. 832. 841. 841. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 940. 940. 940. 940. 940. 940. 940. 940. 940. 954. 954. 954. 954. 955. 955. 956. 956. 956. 956. 956. 966. 966. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 969. 969. 969. 969. 969. 969. 969. 969. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 972. 976. 976. 977. 977. 977. 978. 978. 978. 978. 978. 980. 980. 980. 980. 980. 980. 980. 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988.1002.1002.1002.1002.1002.1002.1002.1002.1007.1007.1012.1012.1012.1012.1012.1015.1015.1015.1015.1015.1015.1015.1017.1018.1018.1018.1018.1019.1019.1019.1105.1110.1110.1110.1110.1110.1110.1111.1111.1111.1111.1111.1111.1111.1111.1115.1115.1115.1116.1116.1116.1116.1117.1117.1117.1119.1119.1119.1119.1121.1124.1124.1124.1124.1124.1124.1126.1127.1127.1127.1128.1128.1130.1130.1130.1130.1130.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1131.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1133.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1139.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1141.1141.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1143.1146.1146.1147.1147.1147.1147.1147.1147.1147.1147.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1149.1150.1155.1155.1155.1155.1155.1155.1158.1158.1158.1158.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1160.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1161.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1162.1167.1167.1167.1167.1169.1181.1181.1342.1342.1342.1342.1342.1342.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1357.1357.1357.1357.1357.1357.1357.1357.1359.1359.1359.1359.1359.1360.1360.1360.1360.1360.1360.1360.1360.1361.1361.1361.1363.1363.1363.1366.1366.1373.1373.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1381.1382.1382.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1383.1390.1390.1390.1391.1391.1391.1391.1391.1391.1391.1391.1391.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1399.1414.1414.1420.1420.1420.1421.1421.1421.1421.1421.1421.1421.1421.1421.1421.1424.1424.1424.1424.1424.1427.1427.1427.1427.1427.1427.1427.1427.1427.1428.1428.1428.1428.1428.1428.1428.1428.1428.1430.1430.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: 51 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.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 1m0.328s user 0m56.163s sys 0m2.065s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m57.778s user 0m54.224s sys 0m2.318s Creating box around spheres Creating chemgrid maps real 1m26.149s user 1m24.858s sys 0m0.926s Atomic solvent excluded volume calculations underway FORTRAN STOP real 25m49.102s user 25m48.730s sys 0m0.186s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.