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 0m1.932s user 0m0.339s sys 0m0.246s 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 0:1223 spheres. 66. 66. 69. 69. 69. 69. 69. 69. 69. 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. 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. 75. 75. 76. 84. 84. 84. 87. 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. 88. 88. 88. 88. 197. 197. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 220. 220. 220. 221. 221. 221. 221. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 226. 226. 226. 227. 227. 228. 228. 228. 228. 230. 231. 231. 244. 244. 244. 244. 244. 244. 341. 341. 342. 342. 347. 347. 347. 347. 347. 347. 348. 348. 348. 348. 352. 353. 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564. 566. 566. 566. 566. 566. 566. 585. 585. 585. 585. 596. 596. 596. 596. 596. 596. 597. 597. 597. 597. 597. 597. 598. 598. 603. 603. 603. 603. 603. 603. 603. 610. 610. 610. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 612. 612. 612. 612. 612. 612. 612. 612. 612. 613. 615. 618. 618. 618. 618. 618. 618. 618. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 620. 628. 628. 628. 628. 628. 634. 634. 636. 636. 636. 651. 651. 651. 651. 651. 651. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 658. 659. 659. 661. 661. 661. 661. 661. 661. 661. 663. 663. 663. 663. 663. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 664. 665. 665. 667. 667. 818. 818. 818. 818. 820. 823. 823. 823. 823. 823. 823. 824. 824. 824. 824. 824. 824. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 827. 827. 827. 827. 836. 836. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 840. 840. 840. 840. 840. 840. 840. 924. 924. 924. 935. 949. 951. 951. 951. 951. 951. 951. 951. 951. 951. 951. 961. 961. 961. 961. 961. 961. 961. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 964. 967. 967. 967. 967. 967. 967. 971. 971. 972. 972. 972. 972. 973. 973. 973. 973. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 980. 980. 980. 980. 981. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 982. 983. 997. 997. 997. 997. 997.1007.1010.1010.1010.1010.1010.1011.1012.1012.1012.1013.1013.1014.1014.1099.1099.1100.1101.1104.1104.1105.1105.1105.1105.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1106.1110.1110.1110.1110.1110.1110.1110.1110.1111.1111.1111.1111.1112.1113.1113.1113.1114.1114.1114.1114.1114.1114.1114.1116.1116.1116.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1119.1121.1121.1122.1122.1122.1123.1123.1123.1124.1124.1125.1125.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1130.1130.1130.1131.1134.1135.1135.1135.1135.1135.1135.1135.1136.1136.1137.1137.1138.1138.1138.1138.1138.1138.1138.1138.1138.1141.1141.1142.1142.1142.1142.1142.1142.1144.1144.1144.1144.1144.1144.1144.1144.1144.1149.1149.1149.1149.1150.1150.1152.1152.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1159.1159.1159.1159.1164.1164.1164.1164.1164.1172.1192.1195.1195.1195.1196.1196.1196.1197.1197.1314.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1320.1320.1320.1320.1320.1320.1339.1339.1345.1345.1345.1345.1345.1345.1345.1345.1348.1348.1348.1348.1348.1348.1350.1350.1350.1350.1350.1350.1350.1350.1350.1350.1351.1351.1351.1351.1351.1351.1351.1352.1352.1352.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1367.1367.1367.1367.1367.1367.1372.1372.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1373.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1375.1375.1375.1382.1382.1382.1382.1382.1389.1390.1390.1390.1405.1405.1411.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1412.1415.1415.1415.1415.1415.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1418.1419.1421.1421.1421.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: 50 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.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 1m23.957s user 0m56.936s sys 0m1.632s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m13.784s user 0m57.954s sys 0m1.788s Creating box around spheres Creating chemgrid maps real 1m32.765s user 1m31.500s sys 0m0.851s Atomic solvent excluded volume calculations underway FORTRAN STOP real 27m35.566s user 27m35.192s sys 0m0.257s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 End of MakeDOCK sphere and grid generation.