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 0m1.258s user 0m0.202s sys 0m0.156s 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 0:1375 spheres. 66. 66. 66. 66. 66. 66. 69. 69. 71. 71. 71. 71. 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. 75. 75. 75. 75. 75. 75. 84. 84. 84. 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. 88. 88. 182. 182. 182. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 188. 197. 199. 199. 199. 199. 199. 203. 206. 206. 206. 206. 206. 206. 206. 206. 206. 206. 206. 206. 206. 206. 206. 209. 210. 210. 210. 210. 210. 210. 210. 212. 212. 212. 212. 212. 212. 212. 212. 212. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 215. 216. 219. 219. 219. 219. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 223. 227. 227. 228. 228. 229. 229. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 230. 231. 231. 231. 231. 231. 231. 231. 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644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 659. 659. 659. 659. 660. 660. 664. 665. 665. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 666. 669. 669. 669. 669. 669. 671. 671. 671. 671. 672. 672. 672. 672. 672. 672. 672. 673. 673. 673. 675. 675. 675. 823. 823. 823. 826. 826. 826. 826. 828. 828. 828. 828. 828. 828. 829. 829. 829. 829. 829. 829. 829. 829. 829. 830. 830. 830. 831. 831. 831. 831. 831. 831. 831. 832. 832. 832. 832. 832. 832. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 833. 835. 835. 835. 844. 844. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 848. 932. 932. 932. 943. 957. 957. 957. 957. 958. 959. 959. 959. 959. 959. 963. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 970. 972. 972. 972. 972. 972. 972. 972. 972. 975. 975. 975. 975. 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992.1004.1004.1004.1004.1004.1115.1115.1115.1115.1115.1115.1115.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1116.1123.1124.1124.1124.1129.1129.1129.1129.1129.1131.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1132.1133.1133.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1134.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1135.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1136.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1138.1139.1139.1139.1140.1140.1140.1142.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1146.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1148.1148.1148.1149.1149.1149.1149.1151.1151.1151.1152.1152.1152.1152.1152.1152.1152.1152.1154.1154.1154.1154.1154.1154.1154.1154.1154.1160.1160.1161.1163.1163.1163.1163.1163.1163.1163.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1167.1167.1169.1169.1170.1174.1174.1174.1174.1186.1186.1186.1186.1186.1186.1186.1347.1347.1347.1347.1347.1347.1347.1347.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1362.1362.1362.1364.1364.1364.1364.1364.1364.1364.1364.1364.1364.1364.1364.1364.1365.1365.1365.1367.1367.1367.1367.1371.1371.1377.1378.1378.1378.1378.1378.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1380.1383.1383.1383.1383.1383.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1387.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1394.1395.1396.1396.1396.1396.1396.1396.1396.1396.1396.1404.1404.1404.1404.1404.1404.1404.1404.1404.1419.1419.1419.1419.1420.1425.1425.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1426.1429.1429.1429.1429.1431.1431.1431.1431.1431.1432.1432.1432.1432.1432.1433.1433.1433.1433.1433.1433.1433.1433.1433.1435.1435.1435.1435.1435.1435.1435.1435.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: 42 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.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 0m34.842s user 0m31.958s sys 0m1.023s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m32.585s user 0m28.780s sys 0m1.268s Creating box around spheres Creating chemgrid maps real 0m11.845s user 0m10.162s sys 0m0.449s Atomic solvent excluded volume calculations underway FORTRAN STOP real 19m29.043s user 19m28.333s sys 0m0.054s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.