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 0m2.901s user 0m0.381s sys 0m0.506s 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 0:1505 spheres. 79. 82. 82. 82. 82. 82. 82. 82. 84. 84. 84. 84. 85. 85. 85. 85. 86. 86. 86. 87. 87. 87. 87. 89. 89. 89. 89. 89. 89. 90. 90. 90. 90. 90. 90. 90. 90. 90. 90. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 91. 92. 92. 92. 94. 94. 95. 95. 95. 103. 103. 103. 103. 107. 107. 107. 107. 107. 107. 107. 107. 107. 224. 224. 224. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 240. 242. 242. 242. 242. 242. 242. 242. 242. 242. 242. 242. 242. 255. 255. 255. 255. 255. 255. 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. 262. 267. 268. 268. 268. 269. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 272. 272. 272. 272. 272. 272. 277. 277. 277. 278. 278. 278. 278. 278. 278. 278. 278. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 279. 280. 280. 280. 280. 280. 280. 280. 280. 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830.1002.1002.1003.1003.1003.1005.1005.1005.1005.1005.1005.1005.1005.1005.1005.1007.1007.1007.1007.1007.1007.1007.1008.1009.1010.1013.1013.1013.1013.1013.1013.1013.1013.1013.1013.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1014.1015.1015.1017.1017.1017.1026.1026.1026.1026.1026.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1030.1147.1147.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1156.1163.1164.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1178.1178.1178.1178.1179.1182.1182.1182.1182.1182.1182.1182.1185.1185.1185.1185.1185.1185.1185.1185.1185.1185.1185.1185.1190.1190.1191.1194.1194.1194.1194.1194.1194.1194.1194.1195.1195.1195.1195.1195.1195.1195.1195.1200.1200.1200.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1201.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1202.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1203.1204.1211.1211.1211.1211.1212.1219.1219.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1228.1235.1235.1235.1235.1235.1235.1237.1237.1237.1238.1238.1238.1239.1239.1239.1239.1239.1239.1239.1338.1338.1338.1338.1338.1338.1339.1339.1339.1339.1339.1339.1339.1339.1340.1340.1344.1344.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1349.1352.1352.1352.1354.1354.1354.1354.1358.1358.1358.1358.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1368.1368.1370.1370.1370.1370.1370.1370.1371.1371.1371.1371.1371.1371.1371.1371.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1374.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1375.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1376.1377.1377.1377.1377.1377.1377.1377.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1379.1381.1388.1388.1388.1388.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1390.1391.1391.1394.1394.1395.1395.1395.1395.1395.1395.1395.1395.1396.1396.1396.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1405.1405.1405.1405.1405.1407.1408.1408.1408.1408.1408.1408.1409.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1411.1411.1411.1411.1411.1411.1411.1412.1413.1415.1420.1420.1420.1420.1420.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1438.1438.1438.1438.1438.1438.1438.1439.1464.1464.1464.1464.1464.1464.1464.1464.1464.1464.1464.1468.1468.1468.1468.1472.1472.1472.1472.1472.1613.1614.1614.1615.1615.1615.1615.1615.1615.1615.1615.1615.1615.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1617.1619.1619.1619.1619.1619.1619.1619.1633.1635.1635.1653.1653.1653.1653.1654.1654.1654.1654.1655.1655.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1656.1667.1667.1669.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1670.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1671.1672.1672.1672.1672.1677.1677.1679.1679.1679.1679.1679.1679.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1681.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1684.1694.1694.1694.1695.1695.1701.1701.1701.1701.1701.1701.1701.1701.1701.1701.1701.1711.1711.1711.1711.1711.1711.1711.1711.1711.1711.1711.1720.1720.1720.1726.1726.1726.1727.1727.1732.1732.1732.1732.1732.1732.1732.1732.1733.1733.1736.1736.1736.1736.1736.1736.1736.1738.1739.1739.1739.1739.1739.1739.1739.1739.1739.1739.1740.1740.1740.1740.1740.1740.1740.1744.1753.1753.1753.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: 62 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. 47. 48. 49. 50. 51. 52. 53. 54. 55. 56. 57. 58. 59. 60. 61. 62.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 0m39.308s user 0m33.242s sys 0m1.334s 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 0m36.679s user 0m33.015s sys 0m1.341s 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 1m1.970s user 1m1.009s sys 0m0.509s Atomic solvent excluded volume calculations underway FORTRAN STOP real 29m48.524s user 29m48.114s sys 0m0.196s 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: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 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: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 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: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 End of MakeDOCK sphere and grid generation.