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 0m3.588s user 0m0.522s sys 0m0.380s 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 0:1536 spheres. 389. 389. 389. 391. 391. 391. 392. 392. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 393. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 394. 417. 417. 417. 417. 417. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 418. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 419. 421. 424. 424. 424. 424. 427. 427. 427. 427. 427. 427. 427. 427. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 429. 429. 429. 429. 455. 455. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 460. 461. 461. 461. 461. 461. 461. 461. 462. 462. 462. 463. 463. 463. 463. 463. 463. 619. 619. 620. 620. 620. 622. 622. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 623. 628. 628. 628. 630. 630. 631. 637. 637. 637. 637. 638. 639. 639. 642. 642. 642. 644. 647. 648. 648. 648. 648. 648. 649. 649. 649. 649. 649. 649. 649. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 652. 652. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 657. 657. 657. 657. 657. 657. 657. 657. 657. 657. 657. 657. 657. 657. 657. 657. 663. 663. 663. 663. 663. 663. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 665. 671. 671. 672. 677. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 678. 686. 686. 686. 686. 686. 686. 687. 687. 687. 687. 687. 687. 687. 687. 687. 687. 688. 688. 688. 688. 688. 688. 688. 688. 688. 688. 688. 688. 688. 688. 688. 688. 688. 688. 688. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 690. 690. 690. 690. 690. 690. 690. 690. 693. 693. 693. 694. 694. 694. 694. 694. 694. 695. 695. 695. 695. 695. 695.1273.1273.1273.1273.1273.1273.1273.1273.1273.1274.1275.1275.1275.1275.1275.1276.1276.1276.1276.1276.1276.1276.1276.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1277.1278.1278.1278.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1279.1280.1387.1387.1387.1387.1387.1388.1418.1421.1421.1421.1421.1421.1421.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1423.1425.1429.1429.2498.2498.2498.2498.2498.2498.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2499.2500.2501.2501.2501.2501.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2502.2503.2503.2503.2503.2503.2503.2503.2503.2503.2503.2503.2503.2503.2505.2508.2508.2508.2508.2508.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2510.2510.2510.2510.2510.2510.2510.2510.2510.2510.2510.2510.2510.2511.2511.2511.2511.2511.2511.2511.2512.2512.2512.2512.2512.2512.2512.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2530.2531.2531.2531.2531.2531.2531.2531.2537.2537.2537.2537.2537.2537.2537.2537.2537.2537.2537.2538.2538.2538.2538.2538.2538.2539.2539.2540.2542.2542.2542.2546.2547.2547.2548.2548.2548.2548.2548.2548.2548.2548.2548.2548.2548.2548.2548.2548.2548.2548.2548.2552.2553.2554.2554.2555.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2559.2561.2561.2561.2561.2561.2562.2562.2562.2562.2562.2562.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2566.2571.2571.2571.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2576.2578.2578.2579.2579.2579.2579.2579.2579.2582.2582.2583.2583.2583.2583.2583.2588.2588.2588.2588.2588.2588.2588.2588.2588.2588.2588.2588.2588.2588.2588.2588.2588.2588.2588.2590.2590.2597.2600.2600.2603.2603.2604.2604.2604.2604.2604.2604.2604.2604.2604.2604.2604.2604.2604.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2607.2611.2611.2614.2615.2615.2615.2615.2615.2619.2619.2619.2619.2619.2619.2623.2623.2623.2623.2623.2623.2623.2624.2792.2792.2792.2792.2792.2792.2792.2792.2792.2792.2792.2792.2804.2804.2804.2804.2804.2804.2804.2804.2804.2805.2805.2806.2806.2806.2806.2806.2806.2807.2812.2812.2813.2813.2813.2813.2813.2813.2813.2813.2813.2814.2814.2814.2814.2821.2821.2821.2821.2821.2821.2821.2821.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2824.2832.2841.2841.2841.2841.2844.2849.2849.2849.2849.2849.2853.2853.2853.2853.2853.2853.2853.2853.2853.2854.2854.2854.2854.2854.2854.2854.2854.2854.2854.2854.2854.2854.2854.2854.2854.2854.2866.2866.2866.2866.3242.3242.3242.3242.3242.3837.3837.3837.3837.3837.3837.3837.3837.3837.3837.3837.3837.3837.3837.3837.3837.3837.3888.3888.3888.3889.3889.3889.3889.3889.3889.3889.3889.3889.3889.3890.3890.3890.3890.3890.3891.3891.3891.3891.3891.3924.3924.3924.3924.3924.3930.3930.3930.3931.3931.3932.3932.3932.3932.3932.3932.3932.3932.3933.3933.3933.3936.3940.3941.3942.3942.3942.3942.3942.3943.3943.3943.3943.3943.3943.3943.3943.3943.3943.3943.3943.3944.3944.3944.3944.3944.3951.3951.3951.3951.3951.3953.3953.3954.3954.3954.3954.3960.3964.3964.3964.3965.3965.3965.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3966.3970.3970.3970.3970.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3974.3975.3975.3975.3975.3975.3975.3975.3975.3975.3975.3975.3985.3985.3985.3985.3985.3986.3986.3986.3986.3986.3986.3986.3986.3989.3989.3989.3989.3989.3989.3989.3989.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3992.3998.3998.3998.3998.3998.3998.3998.3998.4003.4003.4003.4003.4003.4003.4003.4007.4007.4007.4007.4007.4007.4007.4007.4007.4007.4007.4007.4007.4007.4007.4007.4007.4007.4007.4008.4008.4008.4008.4008.4008.4008.4008.4008.4012.4012.4012.4015.4015.4015.4015.4015.4015.4015.4015.4015.4015.4015.4016.4016.4019.4019.4019.4021.4022.4022.4022.4023.4023.4023.4023.4024.4024.4024.4024.4024.4024.4024.4030.4030.4030.4030.4030.4030.4030.4030.4030.4030.4030.4030.4031.4032.4032.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4035.4035.4035.4035.4035.4035.4035.4035.4035.4035.4035.4035.4035.4035.4035.4036.4036.4036.4036.4036.4036.4036.4036.4037.4037.4044.4044.4045.4045.4045.4045.4050.4050.4050.4050.4050.4050.4050.4050.4050.4050.4050.4052.4052.4052.4052.4052.4052.4052.4052.4052.4052.4052.4052.4052.4052.4053.4053.5464.5467.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5468.5469.5469.5469.5469.5470.5470.5470.5470.5470.5470.5470.5470.5470.5470.5470.5470.5470.5470.5471.5471.5473.5473.5474.5475.5485.5485.5485.5485.5485.5515.5515.5517.5517.5519.5519.5520.5520.5521.5521.5521.5521.5521.5521.5527.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: 17 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17.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 ( C1A) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C1A) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C2A) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C2A) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C3A) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C3A) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C4A) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C4A) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( CGA) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( CGA) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C1B) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C1B) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C2B) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C2B) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C3B) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C3B) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C4B) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C4B) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C1C) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C1C) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C2C) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C2C) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C3C) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C3C) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C4C) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C4C) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C1D) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C1D) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C2D) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C2D) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C3D) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C3D) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C4D) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( C4D) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( CGD) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( CGD) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( NA ) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( NA ) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( NB ) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( NB ) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( NC ) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( NC ) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( ND ) in residue 1107 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom ( ND ) in residue 1107 (HEM ), chain 'A'. 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 'A'. 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 0m50.277s user 0m26.415s sys 0m0.680s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m51.971s user 0m27.070s sys 0m0.771s Creating box around spheres Creating chemgrid maps real 0m22.505s user 0m15.787s sys 0m0.241s Atomic solvent excluded volume calculations underway FORTRAN STOP real 17m39.878s user 14m49.052s sys 0m0.103s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of -4.0000 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of -4.0000 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of -4.0000 End of MakeDOCK sphere and grid generation.