make: Warning: File `Makefile' has modification time 0.014 s in the future 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 1m30.233s user 0m0.537s sys 0m0.353s 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 0:1375 spheres. 398. 398. 398. 398. 398. 398. 398. 398. 398. 399. 399. 399. 421. 421. 421. 421. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 426. 426. 426. 429. 429. 429. 429. 431. 432. 432. 432. 433. 434. 434. 434. 434. 434. 434. 434. 434. 459. 460. 460. 460. 460. 460. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 624. 624. 625. 625. 625. 625. 627. 627. 627. 627. 627. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 633. 633. 633. 633. 633. 642. 642. 642. 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717.1274.1274.1274.1274.1275.1275.1276.1276.1276.1276.1276.1276.1276.1276.1276.1277.1277.1277.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1278.1279.1279.1279.1279.1279.1279.1280.1280.1388.1388.1388.1388.1388.1388.1388.1388.1388.1419.1419.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1425.1426.1426.1426.1426.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.2473.2473.2486.2486.2486.2486.2486.2487.2487.2487.2487.2487.2487.2487.2487.2487.2487.2487.2487.2487.2487.2487.2487.2487.2487.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2489.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2490.2491.2491.2493.2496.2497.2497.2497.2497.2497.2497.2498.2498.2498.2498.2498.2498.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2500.2500.2500.2500.2500.2500.2509.2509.2509.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2519.2519.2519.2519.2519.2519.2519.2519.2519.2519.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2525.2526.2526.2526.2526.2526.2526.2527.2527.2530.2530.2535.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2536.2541.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2547.2547.2547.2547.2547.2547.2547.2547.2547.2548.2549.2549.2549.2550.2550.2550.2550.2550.2550.2550.2550.2550.2550.2550.2550.2550.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2554.2554.2554.2555.2555.2555.2555.2555.2555.2555.2555.2555.2555.2555.2559.2565.2565.2565.2565.2565.2565.2565.2566.2566.2566.2567.2567.2567.2567.2567.2567.2567.2567.2567.2567.2567.2570.2571.2571.2571.2571.2571.2571.2574.2574.2574.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2578.2578.2578.2578.2578.2578.2578.2578.2578.2578.2578.2578.2578.2585.2591.2591.2591.2591.2592.2592.2592.2592.2592.2592.2592.2592.2592.2592.2592.2592.2592.2592.2592.2592.2594.2594.2594.2594.2594.2594.2594.2594.2594.2594.2594.2594.2594.2594.2594.2594.2594.2594.2594.2595.2595.2602.2602.2602.2602.2611.2611.2611.2611.2792.2792.2792.2792.2792.2792.2792.2792.2792.2792.2792.2793.2794.2794.2794.2795.2800.2800.2800.2800.2800.2800.2801.2812.2812.2812.2812.2812.2812.2812.2812.2812.2812.2812.2816.2816.2816.2816.2816.2816.2820.2820.2820.2830.2830.2831.2832.2832.2832.2832.2832.2840.2841.2841.2841.2841.2841.2841.2841.2842.2842.2842.2854.2854.2854.2854.2854.2854.2854.2854.2856.3224.3224.3224.3867.3867.3871.3871.3871.3871.3871.3871.3871.3871.3909.3909.3909.3911.3911.3911.3913.3913.3913.3918.3922.3922.3924.3924.3926.3936.3936.3936.3936.3936.3936.3942.3942.3942.3946.3946.3946.3946.3946.3946.3946.3946.3947.3947.3947.3947.3948.3948.3948.3952.3952.3955.3955.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3957.3957.3957.3957.3957.3957.3957.3957.3957.3967.3967.3967.3968.3968.3968.3968.3968.3968.3968.3968.3968.3971.3971.3971.3971.3971.3971.3971.3971.3971.3971.3971.3971.3971.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3983.3985.3985.3985.3988.3988.3988.3988.3988.3988.3988.3988.3988.3988.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3991.3994.3997.3997.3997.3997.3997.3997.3997.3997.3997.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.3998.4004.4004.4005.4005.4005.4005.4005.4006.4006.4006.4006.4006.4006.4006.4006.4006.4006.4012.4012.4012.4012.4012.4012.4015.4015.4015.4015.4015.4015.4015.4015.4015.4015.4015.4015.4015.4015.4015.4015.4015.4017.4017.4017.4017.4017.4017.4017.4017.4017.4017.4017.4017.4017.4017.4017.4018.4018.4018.4018.4018.4018.4019.4019.4019.4019.4025.4025.4025.4025.4025.4026.4026.4026.4026.4027.4027.4034.4034.4034.4034.4034.4034.4034.4034.4034.5391.5391.5391.5391.5391.5392.5392.5392.5392.5392.5392.5392.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5393.5396.5396.5396.5396.5396.5396.5396.5396.5396.5396.5396.5396.5396.5396.5401.5401.5401.5401.5401.5401.5401.5401.5401.5401.5416.5416.5417.5417.5417.5418.5418.5418.5418.5418.5418.5418.5418.5418.5418.5418.5418.5418.5418.5418.5419.5419.5419.5419.5419.5419.5420.5420.5420.5420.5422.5422.5422.5422.5422.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: 18 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18.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... Created a bond between residue(A:16) and residue(A:5); changed residue names to "CYX " Created a bond between residue(A:26) and residue(A:10); changed residue names to "CYX " Created a bond between residue(A:38) and residue(A:28); changed residue names to "CYX " Created a bond between residue(A:128) and residue(A:6); changed residue names to "CYX " Created a bond between residue(A:544) and residue(A:538); changed residue names to "CYX " Created a bond between residue(B:591) and residue(B:581); changed residue names to "CYX " 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... WARNING mmpdb_write: more than 4 bonds for atom (FE ) in residue 1106 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom (FE ) in residue 1106 (HEM ), chain 'B'. 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 1m51.618s user 0m26.938s sys 0m0.670s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m48.743s user 0m27.225s sys 0m0.688s Creating box around spheres Creating chemgrid maps real 0m57.834s user 0m17.397s sys 0m0.216s Atomic solvent excluded volume calculations underway FORTRAN STOP real 44m4.186s user 14m34.161s sys 0m0.205s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: HEM 1106 has a net charge of -4.0000 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: HEM 1106 has a net charge of -4.0000 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: HEM 1106 has a net charge of -4.0000 End of MakeDOCK sphere and grid generation. make: warning: Clock skew detected. Your build may be incomplete.