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 0m29.363s user 0m0.466s sys 0m0.444s 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 0:1327 spheres. 400. 400. 400. 401. 401. 402. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 404. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 405. 427. 427. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 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. 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. 432. 432. 435. 435. 435. 435. 435. 435. 435. 438. 438. 438. 438. 440. 440. 440. 440. 440. 466. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 467. 471. 472. 472. 472. 472. 472. 472. 472. 472. 472. 473. 473. 473. 473. 473. 473. 474. 474. 474. 474. 474. 630. 631. 631. 633. 633. 633. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 634. 639. 639. 639. 639. 639. 639. 639. 642. 642. 658. 658. 659. 660. 660. 660. 660. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 661. 663. 663. 663. 663. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 667. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 668. 674. 674. 674. 674. 674. 674. 674. 674. 674. 674. 674. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 679. 680. 682. 682. 683. 683. 683. 683. 687. 688. 688. 688. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 689. 690. 690. 697. 697. 697. 697. 697. 697. 697. 697. 697. 698. 698. 698. 698. 698. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 699. 700. 700. 700. 700. 700. 700. 700. 700. 700. 700. 700. 700. 700. 700. 700. 701. 701. 701. 701. 701. 701. 701. 701. 701. 701. 701. 701. 701. 701. 701. 701. 701. 701. 701. 704. 704. 704. 705. 705. 705. 705. 705. 705. 705. 705. 705. 706. 706. 706. 706. 706. 706. 706. 707. 707. 707. 707. 707. 707. 707. 707. 707. 707.1284.1284.1284.1284.1284.1284.1284.1284.1285.1285.1286.1286.1286.1286.1286.1287.1287.1287.1287.1287.1287.1288.1288.1288.1288.1288.1288.1288.1288.1289.1289.1289.1289.1289.1289.1289.1289.1289.1290.1291.1395.1398.1398.1398.1398.1398.1398.1398.1399.1427.1432.1432.1432.1432.1432.1432.1432.1432.1432.1434.1434.1434.1434.1434.1434.1434.1434.1434.1434.1434.1434.1434.1434.1436.1436.1436.1436.1440.1440.2463.2471.2471.2472.2472.2472.2472.2472.2472.2500.2500.2500.2500.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2508.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2515.2515.2515.2515.2515.2515.2515.2515.2515.2516.2516.2516.2518.2518.2520.2522.2525.2525.2525.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2531.2532.2534.2534.2534.2534.2534.2534.2534.2534.2534.2534.2534.2534.2534.2534.2534.2534.2537.2537.2537.2537.2537.2537.2537.2540.2540.2540.2540.2540.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2543.2544.2545.2545.2549.2549.2549.2549.2549.2549.2549.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2554.2556.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2557.2560.2560.2560.2561.2561.2561.2564.2564.2566.2566.2566.2566.2566.2566.2566.2566.2566.2566.2566.2566.2566.2566.2566.2566.2566.2568.2568.2568.2568.2568.2568.2575.2575.2575.2575.2575.2575.2575.2587.2592.2592.2592.2592.2592.2592.2593.2593.2593.2593.2593.2593.2782.2782.2782.2782.2784.2785.2790.2791.2791.2791.2791.2791.2791.2799.2799.2799.2799.2799.2799.2799.2802.2802.2802.2802.2810.2819.2819.2819.2821.2821.2822.2822.2822.2822.2822.2822.2827.2827.2827.2827.2830.2830.2830.2830.2832.2832.2832.2832.2832.2832.2832.2832.2844.2844.2844.2844.2844.2844.2844.2846.2846.2846.3220.3220.3815.3815.3815.3815.3815.3815.3815.3815.3815.3815.3815.3815.3815.3815.3815.3815.3815.3863.3863.3863.3863.3863.3863.3863.3863.3863.3863.3863.3867.3867.3867.3867.3867.3867.3867.3868.3868.3885.3885.3885.3885.3885.3885.3885.3885.3885.3885.3885.3885.3885.3885.3889.3890.3890.3890.3890.3890.3890.3890.3890.3890.3890.3890.3890.3890.3890.3890.3890.3898.3898.3906.3906.3908.3909.3909.3909.3909.3909.3911.3920.3920.3921.3921.3921.3921.3921.3921.3921.3921.3921.3921.3921.3922.3922.3922.3929.3929.3932.3932.3933.3933.3938.3938.3938.3938.3938.3938.3942.3942.3942.3943.3943.3943.3943.3943.3943.3943.3943.3944.3944.3944.3944.3944.3944.3948.3948.3948.3948.3948.3948.3948.3948.3951.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3952.3953.3953.3953.3953.3953.3953.3953.3953.3953.3953.3963.3963.3963.3963.3963.3964.3964.3964.3964.3966.3967.3967.3967.3967.3967.3967.3967.3967.3967.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3970.3976.3976.3976.3976.3976.3976.3979.3979.3981.3981.3985.3985.3985.3985.3985.3985.3985.3985.3990.3990.3993.3993.3993.3993.3993.3993.3993.3993.3993.3993.3993.3993.3993.3993.3993.3993.3993.3993.3994.3994.3994.3994.3994.3994.3994.3994.3994.3994.3994.3994.3994.3997.3999.4000.4000.4001.4001.4001.4001.4001.4002.4002.4002.4002.4002.4002.4002.4002.4002.4002.4002.4002.4008.4008.4008.4008.4008.4008.4009.4010.4010.4010.4010.4010.4011.4011.4011.4011.4011.4011.4011.4011.4011.4011.4011.4011.4011.4011.4011.4011.4011.4011.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4015.4015.4023.4023.5426.5434.5434.5434.5434.5434.5435.5435.5435.5435.5435.5435.5435.5435.5435.5435.5436.5436.5436.5436.5436.5436.5436.5437.5437.5437.5437.5437.5437.5437.5437.5437.5437.5437.5437.5437.5437.5437.5437.5437.5437.5437.5438.5438.5438.5438.5438.5438.5438.5438.5438.5438.5444.5444.5444.5444.5459.5461.5461.5461.5461.5461.5461.5461.5461.5461.5461.5462.5462.5462.5462.5462.5462.5462.5462.5462.5462.5463.5463.5463.5463.5463.5463.5463.5463.5463.5463.5463.5466.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: 15 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15.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:15) and residue(A:4); changed residue names to "CYX " Created a bond between residue(A:25) and residue(A:9); changed residue names to "CYX " Created a bond between residue(A:37) and residue(A:27); changed residue names to "CYX " Created a bond between residue(A:127) and residue(A:5); changed residue names to "CYX " Created a bond between residue(A:543) and residue(A:537); 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 1103 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom (FE ) in residue 1103 (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 0m48.256s user 0m25.257s sys 0m0.622s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m37.541s user 0m25.978s sys 0m0.766s Creating box around spheres Creating chemgrid maps real 0m31.528s user 0m16.099s sys 0m0.254s Atomic solvent excluded volume calculations underway FORTRAN STOP real 16m58.009s user 16m14.824s sys 0m0.063s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 End of MakeDOCK sphere and grid generation.