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 0m1.954s user 0m0.344s sys 0m0.241s 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 0:1261 spheres. 68. 69. 69. 69. 69. 69. 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. 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. 76. 84. 84. 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. 183. 183. 197. 197. 199. 199. 199. 199. 199. 199. 199. 199. 199. 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. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 219. 219. 220. 220. 220. 220. 221. 221. 221. 221. 221. 221. 222. 223. 223. 223. 223. 223. 223. 223. 227. 227. 227. 228. 228. 228. 228. 228. 228. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 244. 244. 244. 244. 244. 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659. 661. 661. 661. 661. 661. 661. 661. 663. 663. 663. 664. 664. 664. 664. 664. 664. 664. 664. 664. 665. 818. 818. 818. 818. 818. 820. 820. 820. 821. 821. 821. 822. 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. 827. 827. 827. 836. 836. 836. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 839. 840. 840. 840. 840. 840. 924. 924. 924. 924. 924. 934. 935. 935. 935. 935. 949. 949. 951. 951. 951. 951. 951. 951. 951. 951. 951. 951. 955. 961. 961. 961. 961. 961. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 962. 964. 964. 964. 964. 964. 964. 964. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 967. 971. 971. 972. 972. 972. 973. 973. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 975. 976. 980. 980. 980. 982. 982. 982. 982. 982. 982. 982. 982. 982. 997. 997. 997. 997. 997. 997. 997.1002.1002.1002.1002.1002.1099.1105.1105.1105.1105.1105.1105.1106.1106.1106.1106.1106.1106.1106.1106.1106.1110.1110.1110.1110.1110.1111.1111.1113.1113.1113.1114.1114.1114.1114.1116.1116.1116.1119.1119.1119.1119.1119.1119.1119.1119.1119.1121.1121.1121.1121.1121.1122.1122.1122.1122.1122.1122.1122.1123.1123.1123.1123.1124.1124.1125.1125.1125.1125.1125.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1126.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1128.1129.1129.1130.1130.1134.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1137.1137.1141.1141.1141.1142.1142.1142.1142.1142.1142.1142.1142.1144.1144.1144.1144.1144.1144.1144.1150.1150.1150.1150.1150.1152.1154.1154.1154.1154.1154.1154.1154.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1155.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1157.1164.1164.1164.1165.1178.1178.1196.1199.1199.1199.1199.1200.1200.1200.1200.1201.1201.1322.1322.1322.1322.1322.1322.1322.1322.1322.1322.1322.1324.1324.1324.1324.1324.1324.1324.1343.1343.1343.1343.1343.1343.1343.1343.1352.1352.1354.1354.1354.1354.1354.1354.1354.1355.1355.1355.1355.1355.1355.1361.1361.1361.1361.1361.1361.1361.1361.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1370.1371.1371.1371.1376.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1378.1378.1378.1378.1378.1378.1378.1379.1379.1379.1384.1384.1385.1385.1386.1386.1386.1386.1393.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1394.1409.1409.1415.1415.1416.1416.1416.1416.1416.1416.1416.1416.1416.1416.1419.1419.1419.1419.1421.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1422.1423.1425.1425.1425.1425.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: 46 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.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 1m23.413s user 0m56.039s sys 0m2.197s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m16.842s user 0m58.110s sys 0m2.014s Creating box around spheres Creating chemgrid maps real 1m33.460s user 1m32.145s sys 0m0.800s Atomic solvent excluded volume calculations underway FORTRAN STOP real 28m46.843s user 28m44.877s sys 0m0.167s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: ARG 41 has a net charge of 0.0400 End of MakeDOCK sphere and grid generation.