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 0m2.585s user 0m0.393s sys 0m0.259s 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 0:1452 spheres. 79. 81. 82. 82. 82. 82. 82. 82. 84. 84. 84. 84. 84. 84. 86. 86. 86. 87. 87. 87. 87. 87. 88. 88. 88. 88. 90. 90. 90. 90. 90. 90. 90. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 92. 92. 92. 92. 92. 92. 94. 94. 94. 94. 94. 94. 94. 94. 102. 102. 103. 103. 103. 103. 103. 103. 105. 105. 105. 105. 105. 105. 105. 105. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 106. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 107. 221. 222. 222. 222. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 233. 233. 233. 233. 233. 233. 233. 233. 233. 233. 240. 240. 241. 242. 242. 242. 242. 242. 242. 255. 255. 256. 256. 256. 256. 256. 256. 256. 256. 256. 256. 256. 256. 256. 256. 259. 259. 259. 259. 259. 259. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 267. 267. 268. 268. 268. 268. 268. 269. 269. 269. 269. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 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738. 739. 739. 739. 739. 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. 742. 742. 744. 747. 747. 747. 747. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 748. 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. 757. 757. 757. 757. 757. 757. 758. 758. 758. 758. 759. 759. 759. 759. 759. 759. 759. 759. 760. 760. 760. 769. 769. 769. 769. 769. 769. 769. 769. 769. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 777. 787. 795. 795. 800. 800. 800. 800. 800. 800. 800. 800. 800. 800. 801. 803. 803. 806. 806. 806. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 819. 995. 995. 996. 997. 997. 997. 997. 997. 997. 999. 999. 999.1001.1001.1001.1001.1001.1002.1003.1003.1003.1003.1003.1003.1003.1003.1003.1004.1004.1004.1004.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1134.1134.1135.1135.1135.1135.1135.1136.1136.1144.1144.1144.1144.1144.1144.1144.1146.1146.1146.1146.1146.1146.1146.1146.1153.1155.1155.1155.1155.1155.1155.1155.1155.1168.1168.1168.1168.1169.1169.1169.1169.1169.1172.1172.1172.1172.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1175.1181.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1184.1185.1185.1185.1185.1185.1190.1190.1190.1190.1190.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1191.1192.1192.1192.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1193.1201.1201.1201.1202.1209.1209.1209.1209.1209.1216.1216.1216.1216.1216.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1224.1224.1224.1224.1224.1224.1224.1225.1225.1225.1228.1229.1333.1333.1333.1333.1333.1333.1333.1333.1334.1334.1334.1334.1334.1334.1336.1336.1336.1336.1337.1337.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1338.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1339.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1344.1348.1348.1351.1351.1351.1351.1351.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1352.1358.1358.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1360.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1361.1364.1364.1364.1364.1364.1364.1364.1364.1364.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1365.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1367.1367.1367.1367.1367.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1369.1371.1378.1378.1380.1380.1380.1380.1380.1380.1380.1381.1381.1384.1384.1384.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1385.1386.1388.1388.1388.1388.1388.1388.1388.1388.1388.1388.1395.1395.1395.1395.1398.1398.1398.1398.1398.1399.1399.1399.1399.1399.1399.1399.1400.1400.1400.1400.1400.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1402.1402.1402.1402.1403.1405.1405.1406.1410.1596.1598.1598.1598.1598.1598.1598.1598.1598.1598.1598.1598.1598.1599.1599.1599.1599.1600.1602.1602.1602.1602.1602.1602.1602.1602.1602.1602.1602.1616.1616.1617.1617.1618.1618.1618.1618.1618.1618.1618.1618.1618.1618.1618.1618.1636.1637.1637.1637.1637.1637.1637.1638.1638.1638.1643.1643.1650.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1653.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1654.1655.1655.1655.1655.1660.1660.1660.1660.1660.1661.1661.1661.1661.1661.1661.1661.1661.1661.1661.1661.1662.1662.1662.1662.1662.1662.1662.1662.1662.1662.1662.1662.1662.1667.1670.1670.1670.1670.1672.1672.1673.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1682.1691.1691.1691.1691.1691.1691.1691.1691.1700.1700.1706.1706.1706.1707.1707.1707.1707.1707.1710.1711.1711.1711.1711.1711.1711.1711.1711.1716.1716.1716.1716.1716.1716.1718.1718.1719.1719.1719.1725.1725.1725.1733.1733.1733.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 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 0m31.539s user 0m23.614s sys 0m1.571s 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 0m23.365s user 0m21.281s sys 0m0.553s 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 0m23.050s user 0m22.377s sys 0m0.255s Atomic solvent excluded volume calculations underway FORTRAN STOP real 26m42.387s user 26m41.664s sys 0m0.127s 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.