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 0m2.487s user 0m0.310s sys 0m0.413s 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 0:1061 spheres. 63. 66. 66. 66. 66. 66. 68. 68. 69. 69. 69. 69. 69. 69. 69. 69. 70. 70. 70. 70. 70. 70. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 71. 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. 72. 72. 72. 72. 72. 72. 72. 72. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 73. 75. 75. 76. 76. 76. 83. 84. 87. 87. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 88. 185. 185. 185. 185. 185. 190. 193. 193. 193. 193. 193. 193. 193. 193. 193. 193. 199. 201. 201. 201. 201. 201. 201. 201. 211. 211. 211. 211. 211. 211. 211. 212. 212. 212. 212. 212. 212. 221. 221. 221. 223. 224. 224. 231. 231. 231. 231. 231. 231. 231. 232. 233. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 234. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 240. 255. 255. 255. 255. 255. 255. 255. 255. 255. 255. 371. 371. 371. 371. 371. 371. 371. 371. 378. 378. 379. 379. 379. 379. 379. 379. 379. 379. 379. 379. 379. 379. 380. 380. 380. 380. 380. 380. 381. 381. 381. 381. 381. 381. 381. 381. 384. 384. 384. 387. 391. 392. 392. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 400. 400. 400. 403. 403. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 406. 406. 406. 406. 406. 406. 406. 406. 406. 407. 407. 407. 412. 414. 591. 596. 596. 596. 596. 596. 596. 596. 597. 597. 597. 597. 597. 597. 598. 603. 603. 603. 608. 610. 610. 610. 610. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 611. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 612. 613. 613. 615. 615. 618. 618. 618. 618. 618. 618. 618. 619. 619. 619. 619. 619. 619. 619. 619. 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979.1112.1112.1117.1117.1117.1117.1117.1119.1119.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1121.1122.1123.1123.1123.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1124.1126.1127.1127.1128.1132.1134.1135.1135.1135.1135.1135.1137.1137.1138.1138.1138.1138.1138.1138.1139.1139.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1140.1146.1146.1146.1146.1146.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1151.1152.1152.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1153.1155.1158.1158.1158.1160.1160.1160.1160.1342.1342.1344.1344.1344.1344.1344.1344.1344.1344.1349.1349.1354.1356.1356.1356.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1357.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1358.1359.1359.1359.1359.1359.1359.1359.1361.1361.1365.1365.1365.1365.1365.1365.1365.1365.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1366.1367.1372.1374.1374.1374.1381.1381.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1382.1390.1390.1390.1390.1390.1390.1390.1397.1397.1397.1397.1397.1399.1404.1404.1404.1405.1405.1405.1493.1493.1493.1493.1493.1493.1493.1493.1494.1494.1502.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1505.1505.1505.1505.1505.1505.1505.1505.1505.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1506.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1509.1510.1510.1510.1510.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1516.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1517.1518.1518.1518.1518.1518.1518.1518.1518.1520.1521.1522.1522.1522.1522.1522.1522.1522.1522.1522.1522.1522.1522.1522.1522.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: 19 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19.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 Creating DelPhi electrostatic grid real 0m29.402s user 0m26.284s sys 0m0.641s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m30.619s user 0m28.007s sys 0m0.656s Creating box around spheres Creating chemgrid maps real 0m21.585s user 0m20.269s sys 0m0.322s Atomic solvent excluded volume calculations underway FORTRAN STOP real 35m29.277s user 35m28.507s sys 0m0.104s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation.