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 0m1.594s user 0m0.228s sys 0m0.331s 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 0:1238 spheres. 62. 62. 62. 65. 65. 65. 65. 66. 66. 66. 66. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 71. 71. 80. 80. 80. 80. 83. 83. 83. 83. 83. 83. 83. 84. 84. 195. 195. 195. 195. 197. 197. 197. 197. 197. 197. 197. 197. 197. 197. 197. 207. 207. 207. 207. 208. 208. 208. 208. 208. 208. 208. 208. 208. 210. 210. 210. 210. 210. 210. 210. 210. 213. 213. 213. 213. 213. 213. 213. 214. 217. 217. 218. 218. 219. 219. 219. 219. 221. 221. 221. 221. 221. 221. 222. 222. 226. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 228. 229. 229. 229. 229. 233. 233. 248. 248. 248. 251. 251. 251. 251. 251. 251. 251. 251. 251. 251. 251. 251. 253. 253. 253. 253. 255. 255. 255. 255. 255. 255. 255. 255. 256. 256. 256. 256. 256. 256. 256. 256. 256. 256. 256. 258. 258. 259. 260. 347. 347. 347. 348. 348. 348. 348. 348. 348. 348. 348. 348. 348. 349. 350. 352. 352. 352. 358. 358. 358. 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815. 817. 817. 817. 826. 826. 826. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 829. 830. 830. 830. 937. 939. 939. 939. 939. 949. 949. 949. 949. 949. 950. 950. 950. 950. 950. 950. 950. 950. 950. 950. 950. 952. 952. 952. 952. 952. 952. 955. 955. 955. 955. 955. 955. 955. 955. 955. 955. 955. 955. 955. 956. 959. 960. 960. 960. 960. 961. 961. 961. 961. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 963. 967. 967. 967. 967. 968. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 969. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 971. 971. 971. 971. 971. 971. 971. 971. 971. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 978. 984. 990. 990. 992. 992. 992. 992. 993. 993. 993. 993. 993. 995. 997. 997. 998. 998. 998.1002.1002.1002.1002.1083.1084.1085.1086.1088.1088.1088.1088.1088.1088.1088.1088.1088.1088.1088.1090.1090.1090.1090.1090.1090.1090.1090.1090.1090.1090.1090.1094.1094.1097.1098.1098.1098.1098.1098.1098.1098.1098.1098.1103.1103.1103.1103.1103.1104.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1105.1106.1106.1106.1106.1106.1106.1106.1106.1106.1109.1109.1109.1109.1109.1109.1109.1109.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1110.1112.1112.1112.1112.1112.1112.1112.1112.1112.1112.1114.1114.1114.1114.1120.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1122.1123.1123.1124.1124.1125.1125.1125.1126.1126.1126.1126.1128.1128.1128.1128.1128.1128.1128.1128.1134.1134.1134.1134.1134.1134.1137.1137.1138.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1139.1140.1140.1140.1140.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1141.1143.1143.1144.1146.1148.1148.1148.1148.1148.1148.1148.1156.1158.1176.1176.1176.1176.1176.1178.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1181.1181.1181.1181.1181.1181.1181.1181.1181.1181.1293.1295.1295.1296.1296.1296.1296.1296.1296.1296.1296.1296.1296.1296.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1298.1299.1299.1299.1299.1299.1299.1299.1301.1301.1305.1312.1312.1312.1312.1313.1313.1313.1314.1318.1318.1318.1327.1327.1327.1327.1327.1327.1327.1329.1329.1329.1329.1330.1330.1330.1330.1330.1331.1331.1336.1343.1343.1343.1343.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1345.1351.1351.1351.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1353.1353.1353.1353.1353.1353.1353.1353.1353.1353.1359.1359.1359.1360.1361.1361.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1384.1384.1390.1390.1391.1391.1391.1391.1391.1391.1391.1391.1391.1394.1394.1394.1394.1394.1397.1397.1397.1397.1397.1397.1397.1397.1397.1397.1397.1397.1397.1397.1397.1397.1398.1400.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: 38 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.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 0m25.708s user 0m23.548s sys 0m0.631s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m36.743s user 0m23.562s sys 0m0.723s Creating box around spheres Creating chemgrid maps real 0m21.278s user 0m8.513s sys 0m0.225s Atomic solvent excluded volume calculations underway FORTRAN STOP real 17m57.894s user 17m56.048s sys 0m0.076s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: ASP 159 has a net charge of -0.2080 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: ASP 159 has a net charge of -0.2080 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: ASP 159 has a net charge of -0.2080 End of MakeDOCK sphere and grid generation.