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 0m30.278s user 0m0.527s sys 0m0.350s 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 0:1777 spheres. 400. 400. 400. 401. 402. 403. 403. 404. 404. 404. 404. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 427. 427. 427. 427. 427. 428. 428. 428. 428. 428. 428. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 432. 432. 432. 432. 435. 435. 435. 435. 435. 435. 435. 435. 437. 437. 437. 437. 437. 437. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 440. 440. 440. 440. 440. 442. 444. 444. 444. 445. 445. 445. 445. 445. 445. 445. 445. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 447. 448. 449. 449. 449. 449. 449. 449. 449. 449. 449. 449. 449. 449. 449. 449. 449. 449. 450. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 471. 471. 471. 471. 471. 471. 471. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 472. 473. 473. 474. 474. 474. 474. 474. 625. 625. 625. 625. 625. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 627. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 633. 636. 636. 636. 636. 636. 652. 652. 652. 652. 652. 653. 653. 653. 653. 653. 653. 653. 654. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 667. 667. 667. 667. 667. 667. 668. 668. 668. 670. 670. 670. 670. 670. 670. 670. 677. 677. 677. 677. 677. 677. 677. 677. 677. 677. 677. 677. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 684. 684. 684. 684. 684. 684. 684. 684. 684. 684. 684. 686. 692. 692. 692. 692. 692. 692. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 693. 694. 694. 694. 694. 694. 694. 694. 694. 694. 694. 695. 695. 695. 695. 695. 695. 695. 695. 695. 698. 699. 699. 699. 699. 700. 701. 701. 701. 701. 701. 701. 701.1245.1245.1245.1245.1245.1245.1245.1245.1245.1245.1245.1245.1245.1245.1245.1245.1258.1258.1258.1258.1258.1258.1258.1258.1258.1259.1260.1260.1260.1260.1262.1262.1263.1263.1263.1263.1263.1263.1263.1263.1263.1264.1264.1265.1273.1273.1273.1273.1273.1273.1273.1273.1273.1275.1275.1369.1372.1372.1372.1372.1372.1372.1372.1372.1403.1403.1403.1403.1403.1406.1406.1406.1408.1408.1408.1408.1408.1408.1408.1408.1408.1408.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1410.1414.1414.2447.2447.2447.2453.2453.2453.2453.2453.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2454.2457.2457.2457.2457.2457.2457.2457.2457.2457.2457.2457.2457.2457.2457.2457.2457.2457.2458.2458.2458.2458.2458.2458.2462.2464.2464.2464.2464.2464.2464.2464.2464.2464.2464.2464.2464.2464.2464.2464.2464.2464.2464.2465.2465.2465.2465.2465.2465.2465.2465.2465.2465.2465.2465.2466.2466.2466.2466.2466.2467.2467.2467.2467.2467.2467.2467.2467.2467.2467.2467.2467.2467.2467.2467.2467.2467.2467.2467.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2485.2492.2492.2492.2492.2492.2492.2492.2492.2492.2492.2492.2492.2493.2493.2493.2493.2494.2495.2497.2497.2499.2499.2502.2502.2503.2503.2503.2503.2503.2503.2503.2503.2503.2503.2503.2506.2506.2507.2507.2507.2508.2508.2508.2508.2508.2508.2508.2509.2509.2509.2509.2511.2512.2512.2512.2512.2512.2512.2512.2512.2512.2512.2512.2512.2512.2512.2512.2512.2512.2512.2512.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2514.2515.2515.2515.2516.2516.2516.2516.2516.2516.2516.2516.2517.2517.2517.2517.2517.2520.2520.2520.2520.2520.2520.2520.2520.2520.2520.2520.2520.2520.2520.2520.2521.2529.2531.2531.2531.2531.2531.2531.2531.2531.2531.2531.2531.2531.2531.2531.2531.2531.2532.2532.2533.2533.2533.2533.2533.2534.2534.2534.2534.2534.2534.2538.2538.2542.2542.2542.2542.2542.2542.2543.2543.2544.2544.2544.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2545.2551.2551.2553.2553.2555.2558.2559.2559.2559.2559.2559.2559.2559.2559.2559.2559.2559.2560.2560.2560.2560.2560.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2562.2566.2569.2569.2569.2570.2570.2570.2570.2570.2570.2570.2570.2570.2570.2570.2570.2570.2574.2574.2574.2574.2574.2574.2574.2574.2574.2574.2574.2578.2578.2578.2578.2578.2578.2578.2578.2578.2578.2578.2578.2578.2747.2747.2747.2747.2747.2747.2747.2747.2747.2747.2747.2747.2759.2759.2759.2759.2759.2759.2759.2759.2759.2759.2759.2759.2759.2759.2759.2759.2759.2759.2761.2761.2761.2761.2761.2761.2761.2762.2762.2762.2768.2768.2768.2768.2768.2768.2768.2770.2770.2770.2770.2770.2770.2770.2770.2770.2770.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2779.2787.2796.2796.2796.2796.2798.2803.2803.2803.2803.2803.2803.2803.2803.2804.2808.2808.2808.2808.2808.2808.2808.2809.2809.2809.2809.2809.2809.2809.2821.2821.2821.2821.2821.2823.2823.2823.3197.3197.3197.3197.3197.3197.3197.3197.3197.3197.3489.3490.3490.3490.3490.3490.3490.3490.3490.3490.3490.3490.3490.3490.3490.3490.3490.3490.3493.3496.3496.3775.3775.3820.3820.3820.3820.3820.3820.3821.3821.3821.3826.3826.3828.3828.3828.3828.3828.3828.3828.3828.3828.3828.3829.3833.3833.3833.3833.3833.3833.3833.3833.3833.3833.3833.3833.3834.3834.3834.3834.3834.3834.3834.3834.3834.3834.3834.3834.3834.3834.3834.3834.3834.3834.3834.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3835.3836.3836.3836.3836.3836.3836.3836.3836.3836.3836.3836.3836.3836.3840.3840.3840.3840.3840.3841.3841.3841.3841.3841.3841.3841.3841.3841.3841.3842.3842.3843.3843.3843.3843.3843.3844.3844.3844.3844.3846.3846.3849.3849.3849.3849.3849.3849.3849.3849.3849.3849.3849.3849.3849.3849.3849.3850.3850.3857.3858.3858.3868.3868.3868.3868.3868.3868.3869.3869.3869.3869.3874.3874.3874.3875.3875.3878.3878.3878.3879.3879.3879.3880.3880.3880.3880.3880.3880.3880.3881.3881.3881.3882.3882.3882.3882.3882.3882.3887.3887.3891.3891.3896.3896.3896.3896.3896.3896.3896.3898.3898.3898.3898.3898.3898.3898.3898.3902.3902.3902.3902.3902.3902.3902.3903.3903.3903.3903.3903.3903.3903.3903.3903.3903.3903.3903.3903.3903.3903.3904.3904.3904.3904.3904.3904.3904.3904.3904.3904.3904.3904.3904.3904.3904.3904.3904.3904.3904.3908.3911.3912.3912.3912.3912.3912.3912.3912.3912.3912.3912.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3913.3918.3918.3918.3920.3920.3923.3923.3923.3923.3923.3923.3923.3923.3924.3924.3924.3924.3926.3926.3926.3926.3927.3927.3927.3927.3927.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3930.3936.3936.3936.3936.3939.3941.3941.3941.3941.3945.3945.3945.3945.3945.3945.3945.3945.3945.3945.3945.3945.3945.3945.3945.3945.3945.3946.3950.3952.3953.3953.3953.3953.3953.3953.3953.3953.3953.3954.3954.3954.3954.3954.3954.3954.3954.3954.3959.3959.3959.3960.3960.3961.3961.3961.3961.3961.3961.3961.3961.3961.3962.3962.3962.3962.3962.3962.3962.3962.3962.3962.3962.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3974.3974.3974.3974.3974.3974.3974.3974.3974.3975.3975.3975.3975.3975.3975.3975.3975.3975.3975.3975.3975.3975.3975.3982.3983.3983.3988.3988.3988.3988.3988.3988.3988.3988.3988.3988.3990.3990.3990.3990.3990.3990.3991.3991.3991.5418.5424.5424.5424.5424.5424.5424.5425.5425.5425.5425.5425.5425.5425.5425.5425.5425.5425.5425.5425.5425.5425.5425.5426.5426.5426.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5427.5428.5428.5428.5428.5428.5428.5428.5428.5428.5429.5429.5429.5429.5429.5429.5430.5430.5430.5430.5430.5430.5430.5435.5435.5435.5435.5435.5435.5435.5435.5435.5435.5435.5435.5435.5435.5435.5450.5450.5450.5450.5451.5451.5452.5452.5453.5453.5453.5454.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: 21 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21.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 " 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 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom (FE ) in residue 1107 (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 we had to cook * HD2* Creating DelPhi electrostatic grid real 0m58.602s user 0m25.596s sys 0m0.663s Adding spheres to tarted electrostatic grid we had to cook * HD2* Creating DelPhi electrostatic grid real 0m49.668s user 0m25.952s sys 0m0.666s Creating box around spheres we had to cook * HD2* Creating chemgrid maps real 0m36.299s user 0m17.479s sys 0m0.311s Atomic solvent excluded volume calculations underway FORTRAN STOP real 37m38.092s user 16m43.297s sys 0m0.091s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: PHE 76 has a net charge of 0.0060 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: ARG 149 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ASH 331 has a net charge of -0.3190 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 407 has a net charge of 0.0400 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: TRP 597 has a net charge of 0.0220 !!! WARNING: HEM 1107 has a net charge of -4.0000 !!! WARNING: PHE 76 has a net charge of 0.0060 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: ARG 149 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ASH 331 has a net charge of -0.3190 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 407 has a net charge of 0.0400 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: TRP 597 has a net charge of 0.0220 !!! WARNING: HEM 1107 has a net charge of -4.0000 !!! WARNING: PHE 76 has a net charge of 0.0060 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: ARG 149 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ASH 331 has a net charge of -0.3190 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 407 has a net charge of 0.0400 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: TRP 597 has a net charge of 0.0220 !!! WARNING: HEM 1107 has a net charge of -4.0000 End of MakeDOCK sphere and grid generation.