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 0m5.992s user 0m0.505s sys 0m0.356s 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 0:1457 spheres. 75. 75. 112. 116. 116. 116. 116. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 119. 119. 120. 121. 121. 121. 122. 122. 123. 123. 123. 130. 133. 133. 133. 133. 133. 133. 134. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 135. 136. 136. 136. 136. 137. 137. 137. 137. 137. 142. 143. 144. 145. 145. 145. 145. 145. 146. 147. 147. 147. 147. 147. 147. 148. 148. 148. 148. 148. 148. 148. 150. 150. 150. 150. 150. 150. 150. 150. 150. 150. 150. 150. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 158. 168. 168. 168. 168. 168. 168. 168. 169. 171. 171. 171. 171. 171. 171. 171. 171. 175. 175. 178. 179. 179. 179. 179. 180. 180. 183. 189. 189. 189. 189. 189. 192. 194. 194. 194. 351. 351. 354. 354. 354. 354. 354. 354. 354. 355. 355. 355. 355. 355. 355. 355. 355. 355. 356. 356. 356. 356. 357. 357. 357. 357. 360. 360. 360. 360. 360. 379. 380. 380. 389. 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794. 803. 803. 803. 804. 804. 804. 804. 804. 809. 813. 813. 813. 817. 818. 818. 818. 818. 821. 821. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 823. 824. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 825. 832. 832. 832. 832. 832. 832. 833. 833. 834. 834. 834. 834. 834. 834. 834. 834. 834. 841. 841. 841. 844. 844. 844. 844. 844. 845. 848. 848. 848. 850. 850. 884.1176.1179.1179.1179.1179.1179.1179.1237.1242.1244.1244.1244.1246.1246.1246.1247.1247.1247.1247.1250.1250.1250.1252.1256.1256.1256.1256.1256.1256.1256.1270.1270.1270.1270.1270.1271.1271.1271.1271.1271.1271.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1272.1273.1273.1275.1275.1275.1275.1275.1275.1275.1275.1275.1276.1276.1276.1276.1276.1276.1276.1277.1277.1277.1277.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1279.1280.1280.1280.1280.1280.1280.1280.1280.1285.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1286.1287.1287.1287.1287.1289.1290.1290.1290.1290.1293.1293.1293.1293.1293.1293.1293.1293.1293.1295.1295.1295.1296.1304.1304.1309.1309.1309.1309.1309.1309.1309.1309.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1318.1328.1329.1329.1358.1358.1358.1358.1358.1364.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1377.1379.1379.1379.1379.1379.1381.1381.1381.1381.1384.1384.1389.1389.1389.1389.1389.1390.1391.1391.1391.1682.1682.1722.1723.1723.1723.1723.1723.1723.1725.1725.1725.1725.1725.1725.1726.1726.1726.1726.1728.1728.1728.1730.1730.1730.1730.1730.1731.1731.1731.1731.1732.1732.1732.1732.1732.1732.1732.1732.1732.1732.1733.1733.1733.1733.1733.1733.1733.1740.1740.1740.1740.1740.1741.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1742.1743.1743.1743.1743.1743.1743.1743.1743.1743.1744.1744.1744.1747.1752.1752.1752.1752.1752.1752.1754.1754.1754.1754.1754.1754.1754.1755.1755.1755.1755.1755.1756.1756.1756.1757.1757.1757.1757.1757.1757.1757.1757.1757.1757.1757.1757.1757.1760.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1765.1774.1775.1775.1775.1775.1775.1775.1775.1775.1775.1775.1776.1776.1778.1778.1778.1778.1778.1779.1782.1782.1783.1783.1783.1785.1785.1785.1785.1785.1785.1785.1787.1787.1787.1790.1790.1792.1792.1792.1793.1793.1793.1793.1796.1796.1796.1801.1956.1956.1958.1959.1959.1960.1960.1960.1960.1960.1960.1960.1960.1960.1960.1961.1961.1966.1967.1967.1967.1967.1967.1984.1985.1985.1985.1985.1985.1985.1992.1992.2021.2021.2021.2023.2023.2023.2023.2023.2044.2044.2044.2044.2045.2045.2045.2045.2045.2045.2045.2045.2045.2045.2045.2045.2045.2045.2053.2053.2053.2053.2053.2053.2053.2053.2055.2055.2055.2055.2055.2056.2058.2058.2062.2063.2064.2064.2064.2064.2065.2065.2065.2066.2066.2067.2067.2067.2067.2069.2069.2069.2070.2070.2076.2076.2076.2076.2076.2077.2077.2077.2077.2078.2078.2078.2078.2078.2078.2078.2078.2078.2078.2078.2078.2081.2081.2081.2081.2103.2103.2103.2112.2319.2319.2319.2319.2321.2321.2321.2321.2321.2321.2321.2325.2327.2327.2327.2327.2328.2328.2331.2331.2332.2332.2332.2332.2333.2334.2334.2334.2334.2334.2334.2334.2334.2335.2335.2339.2339.2340.2340.2340.2341.2341.2342.2349.2349.2351.2351.2351.2351.2351.2351.2351.2351.2359.2359.2359.2360.2360.2360.2363.2363.2363.2363.2363.2363.2366.2366.2366.2366.2366.2366.2366.2366.2366.2366.2366.2371.2371.2371.2374.2374.2374.2374.2374.2374.2374.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2375.2376.2376.2376.2376.2376.2380.2380.2380.2380.2380.2380.2381.2381.2381.2381.2381.2381.2381.2382.2382.2382.2382.2382.2382.2382.2382.2382.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2384.2391.2391.2391.2393.2394.2394.2395.2395.2397.2398.2398.2398.2398.2398.2398.2407.2407.2408.2408.2408.2409.2409.2409.2417.2422.2422.2422.2424.2427.2427.2427.2427.2427.2427.2427.2427.2427.2427.2427.2427.2427.2427.2428.2428.2429.2429.2429.2429.2429.2429.2429.2429.2429.2430.2432.2432.2436.2436.2436.2436.2436.2436.2436.2436.2436.2436.2436.2437.2437.2437.2437.2437.2437.2437.2438.2438.2438.2438.2438.2438.2438.2438.2438.2438.2438.2438.2438.2448.2448.2448.2452.2452.2452.2455.2488.2488.2488.2488.2488.2488.2488.2488.2488.2494.2815.2815.2819.2819.2819.2819.2819.2819.2819.2841.2841.2846.2846.2846.2848.2848.2850.2850.2850.2850.2850.2850.2850.2851.2851.2851.2852.2853.2854.2856.2860.2860.2860.2860.2860.2860.2860.2860.2874.2875.2875.2875.2875.2875.2875.2875.2876.2876.2876.2876.2876.2876.2876.2876.2876.2876.2878.2879.2879.2879.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2880.2881.2881.2881.2881.2881.2881.2882.2882.2882.2882.2882.2882.2882.2882.2882.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2891.2893.2894.2895.2895.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2899.2900.2900.2900.2900.2900.2900.2900.2913.2913.2913.2922.2922.2922.2922.2922.2922.2929.2932.2932.2932.2933.2933.2933.2933.2933.2933.2933.2962.2962.2962.2962.2964.2968.2968.2969.2969.2969.2970.2981.2981.2981.2981.2981.2981.2981.2981.2981.2983.2983.2983.2983.2983.2985.2988.2993.2993.2993.2993.2993.2993.2995.2995.2995.2997.2997.2997.2997.2997.2997.2997.2997.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: 58 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.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 0m47.967s user 0m31.887s sys 0m1.150s 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 1m21.231s user 0m33.938s sys 0m1.334s 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 0m12.312s user 0m8.828s sys 0m0.344s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m57.271s user 18m56.867s sys 0m0.088s 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: ARG 14 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! 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 106 has a net charge of -0.6880 !!! WARNING: GLN 111 has a net charge of -0.6880 !!! WARNING: ARG 112 has a net charge of -0.4460 !!! WARNING: GLN 122 has a net charge of -0.6880 !!! WARNING: ARG 145 has a net charge of -0.4460 !!! WARNING: ARG 161 has a net charge of -0.4460 !!! WARNING: GLN 162 has a net charge of -0.6880 !!! WARNING: GLN 165 has a net charge of -0.6880 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: ARG 191 has a net charge of -0.4460 !!! WARNING: ASN 192 has a net charge of -0.6880 !!! WARNING: GLN 196 has a net charge of -0.6880 !!! WARNING: ASN 202 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: ARG 14 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! 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 106 has a net charge of -0.6880 !!! WARNING: GLN 111 has a net charge of -0.6880 !!! WARNING: ARG 112 has a net charge of -0.4460 !!! WARNING: GLN 122 has a net charge of -0.6880 !!! WARNING: ARG 145 has a net charge of -0.4460 !!! WARNING: ARG 161 has a net charge of -0.4460 !!! WARNING: GLN 162 has a net charge of -0.6880 !!! WARNING: GLN 165 has a net charge of -0.6880 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: ARG 191 has a net charge of -0.4460 !!! WARNING: ASN 192 has a net charge of -0.6880 !!! WARNING: GLN 196 has a net charge of -0.6880 !!! WARNING: ASN 202 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: ARG 14 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! 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 106 has a net charge of -0.6880 !!! WARNING: GLN 111 has a net charge of -0.6880 !!! WARNING: ARG 112 has a net charge of -0.4460 !!! WARNING: GLN 122 has a net charge of -0.6880 !!! WARNING: ARG 145 has a net charge of -0.4460 !!! WARNING: ARG 161 has a net charge of -0.4460 !!! WARNING: GLN 162 has a net charge of -0.6880 !!! WARNING: GLN 165 has a net charge of -0.6880 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: ARG 191 has a net charge of -0.4460 !!! WARNING: ASN 192 has a net charge of -0.6880 !!! WARNING: GLN 196 has a net charge of -0.6880 !!! WARNING: ASN 202 has a net charge of -0.6880 End of MakeDOCK sphere and grid generation.