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 0m2.677s user 0m0.402s sys 0m0.302s 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 0:1363 spheres. 79. 79. 79. 80. 80. 82. 82. 82. 82. 84. 84. 86. 86. 86. 86. 86. 87. 87. 87. 87. 89. 90. 90. 90. 90. 90. 91. 91. 91. 91. 91. 91. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 92. 103. 103. 103. 103. 103. 103. 106. 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. 107. 107. 107. 224. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 232. 240. 240. 242. 242. 242. 242. 242. 242. 255. 255. 255. 256. 256. 256. 256. 259. 259. 259. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 262. 267. 268. 268. 268. 268. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 271. 272. 272. 272. 272. 272. 275. 275. 275. 275. 276. 276. 276. 277. 277. 277. 277. 277. 278. 278. 278. 278. 278. 278. 278. 279. 279. 279. 279. 280. 280. 280. 280. 281. 281. 281. 295. 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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: 46 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.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 0m56.437s user 0m36.019s sys 0m1.524s 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 1m12.898s user 0m50.492s sys 0m2.173s 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 1m41.179s user 1m27.611s sys 0m1.065s Atomic solvent excluded volume calculations underway FORTRAN STOP real 29m49.565s user 29m47.511s sys 0m0.152s 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.