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 0m1.704s user 0m0.258s sys 0m0.199s 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 0:1194 spheres. 79. 79. 79. 79. 79. 79. 81. 81. 81. 84. 84. 84. 84. 84. 84. 84. 84. 84. 85. 85. 87. 87. 87. 90. 90. 90. 90. 90. 91. 91. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 94. 94. 94. 94. 94. 94. 103. 103. 103. 103. 103. 103. 106. 106. 106. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 230. 230. 230. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 240. 242. 242. 242. 242. 248. 248. 248. 248. 248. 248. 248. 248. 250. 250. 252. 252. 252. 255. 255. 255. 255. 255. 256. 256. 256. 256. 259. 259. 259. 259. 259. 259. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 267. 268. 268. 268. 268. 268. 268. 268. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 272. 272. 272. 272. 272. 272. 274. 277. 279. 279. 279. 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489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 489. 497. 497. 497. 685. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 704. 704. 704. 704. 704. 704. 723. 723. 723. 723. 723. 724. 724. 724. 725. 739. 739. 739. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 740. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 741. 742. 747. 747. 747. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 749. 756. 756. 756. 756. 757. 757. 757. 757. 757. 759. 759. 760. 760. 769. 769. 769. 769. 777. 777. 777. 777. 787. 787. 787. 787. 787. 787. 787. 787. 787. 793. 793. 793. 793. 795. 795. 795. 795. 797. 800. 800. 800. 800. 800. 800. 800. 800. 801. 801. 802. 803. 803. 803. 803. 803. 803. 806. 806. 806. 806. 806. 806. 806. 807. 807. 807. 807. 809. 809. 809. 812. 815. 815. 815. 815. 815. 815. 815. 815. 828. 829. 829. 829. 829. 992. 995. 995.1002.1002.1002.1002.1002.1002.1002.1003.1003.1003.1004.1004.1004.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1007.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1016.1016.1016.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1019.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1020.1137.1137.1137.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1145.1153.1153.1154.1154.1155.1155.1155.1155.1155.1155.1155.1168.1169.1169.1169.1169.1169.1169.1169.1169.1169.1172.1172.1172.1172.1172.1172.1172.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1181.1182.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1185.1185.1185.1185.1190.1190.1190.1190.1190.1191.1191.1191.1192.1192.1192.1192.1192.1192.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1201.1201.1201.1202.1210.1210.1210.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1333.1333.1333.1334.1334.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1341.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1343.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1348.1348.1351.1352.1352.1358.1358.1358.1358.1358.1358.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1364.1364.1364.1364.1365.1365.1365.1365.1365.1365.1365.1365.1365.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1367.1367.1367.1367.1367.1367.1367.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1378.1380.1380.1380.1380.1380.1381.1383.1384.1384.1384.1385.1385.1385.1385.1385.1385.1385.1385.1385.1386.1386.1388.1388.1388.1388.1388.1388.1388.1388.1395.1395.1395.1398.1400.1400.1400.1400.1400.1400.1400.1400.1400.1401.1405.1406.1406.1597.1598.1598.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1600.1602.1602.1602.1602.1602.1602.1602.1602.1602.1602.1618.1618.1618.1634.1634.1634.1634.1635.1637.1637.1637.1637.1637.1637.1637.1637.1643.1643.1647.1652.1652.1652.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1655.1655.1655.1655.1655.1660.1660.1661.1661.1661.1661.1661.1661.1662.1662.1662.1672.1672.1672.1672.1672.1672.1674.1680.1680.1681.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1691.1691.1691.1691.1691.1691.1700.1700.1700.1706.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1712.1714.1714.1714.1716.1716.1716.1716.1716.1719.1719.1719.1719.1720.1720.1720.1722.1722.1725.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: 40 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.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 we had to cook * HE2* we had to cook * HH1* we had to cook * HH2* we had to cook * HD2* Creating DelPhi electrostatic grid real 0m46.755s user 0m31.313s sys 0m0.955s Adding spheres to tarted electrostatic grid we had to cook * HE2* we had to cook * HH1* we had to cook * HH2* we had to cook * HD2* Creating DelPhi electrostatic grid real 1m8.612s user 0m28.250s sys 0m0.875s Creating box around spheres we had to cook * HE2* we had to cook * HH1* we had to cook * HH2* we had to cook * HD2* Creating chemgrid maps real 0m14.483s user 0m9.079s sys 0m0.232s Atomic solvent excluded volume calculations underway FORTRAN STOP real 19m41.024s user 19m39.591s sys 0m0.053s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 has a net charge of -0.6880 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 has a net charge of -0.6880 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 has a net charge of -0.6880 End of MakeDOCK sphere and grid generation.