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 0m1.887s user 0m0.284s sys 0m0.282s 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 0:1077 spheres. 63. 63. 63. 67. 67. 68. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 69. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 73. 73. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 172. 172. 172. 181. 182. 182. 182. 182. 182. 182. 182. 182. 199. 199. 199. 199. 199. 199. 199. 199. 199. 199. 209. 209. 209. 209. 209. 209. 210. 210. 210. 210. 210. 210. 210. 210. 210. 220. 222. 222. 222. 228. 230. 231. 231. 231. 231. 231. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 235. 244. 244. 365. 365. 365. 365. 369. 369. 369. 369. 372. 372. 372. 372. 372. 372. 373. 373. 373. 373. 373. 373. 376. 376. 376. 376. 376. 377. 377. 377. 378. 378. 378. 379. 379. 379. 379. 382. 382. 382. 382. 382. 382. 385. 385. 385. 385. 385. 385. 389. 390. 390. 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626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 626. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 640. 640. 642. 642. 642. 642. 642. 642. 642. 642. 642. 657. 657. 662. 663. 664. 664. 664. 664. 664. 664. 665. 665. 759. 760. 761. 761. 761. 761. 761. 762. 762. 762. 762. 762. 762. 762. 762. 762. 762. 762. 762. 762. 762. 762. 762. 762. 762. 763. 763. 763. 763. 763. 763. 763. 764. 764. 764. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 766. 767. 767. 767. 769. 775. 838. 841. 842. 842. 842. 842. 843. 843. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 844. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 846. 847. 847. 847. 847. 847. 847. 847. 847. 847. 847. 848. 848. 848. 848. 848. 859. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 862. 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997.1003.1003.1006.1006.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1010.1031.1031.1031.1032.1032.1032.1032.1032.1033.1033.1033.1033.1033.1033.1033.1033.1034.1036.1036.1037.1037.1037.1037.1037.1140.1140.1140.1144.1146.1147.1147.1147.1147.1147.1147.1147.1147.1147.1147.1148.1148.1148.1148.1148.1151.1151.1151.1151.1151.1152.1152.1152.1153.1154.1154.1154.1154.1157.1157.1160.1160.1160.1163.1163.1164.1164.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1165.1167.1167.1167.1167.1167.1172.1172.1172.1172.1172.1172.1172.1173.1173.1173.1173.1173.1173.1174.1177.1177.1177.1177.1178.1178.1178.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1179.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1180.1182.1187.1187.1187.1375.1375.1375.1375.1375.1375.1375.1375.1377.1377.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1378.1379.1379.1379.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1392.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1393.1399.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1400.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1409.1409.1409.1409.1409.1415.1417.1417.1417.1417.1417.1417.1417.1417.1432.1432.1432.1432.1438.1438.1439.1439.1439.1439.1439.1439.1440.1534.1535.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1537.1538.1538.1538.1538.1538.1538.1539.1539.1539.1539.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1542.1542.1549.1550.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: 22 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22.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 * HD2* Creating DelPhi electrostatic grid real 1m2.626s user 0m45.805s sys 0m1.972s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 1m12.119s user 0m46.511s sys 0m2.224s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 1m43.483s user 1m42.221s sys 0m0.847s Atomic solvent excluded volume calculations underway FORTRAN STOP real 30m14.981s user 30m14.483s sys 0m0.101s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 127 has a net charge of -0.3190 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 127 has a net charge of -0.3190 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 127 has a net charge of -0.3190 End of MakeDOCK sphere and grid generation.