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 1m1.884s user 0m0.473s sys 0m0.387s 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 0:1534 spheres. 383. 384. 385. 385. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 388. 388. 388. 388. 388. 388. 388. 388. 410. 410. 410. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 411. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 413. 415. 415. 418. 418. 418. 418. 418. 418. 418. 420. 421. 421. 421. 422. 422. 422. 422. 422. 422. 422. 423. 423. 423. 423. 423. 423. 423. 423. 449. 449. 449. 449. 449. 449. 449. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 454. 455. 455. 455. 455. 455. 455. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 456. 457. 457. 457. 457. 614. 614. 614. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 617. 622. 622. 625. 625. 625. 625. 641. 641. 643. 643. 643. 643. 643. 643. 643. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 646. 646. 646. 650. 650. 650. 650. 650. 650. 650. 650. 650. 650. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 651. 653. 654. 657. 657. 657. 659. 659. 659. 659. 659. 659. 659. 659. 659. 659. 659. 664. 664. 664. 664. 664. 665. 665. 665. 665. 665. 665. 665. 666. 666. 666. 666. 666. 666. 668. 668. 671. 671. 671. 671. 671. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 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690.1251.1251.1251.1251.1251.1251.1252.1253.1253.1253.1253.1253.1254.1254.1254.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1255.1256.1256.1256.1256.1256.1257.1257.1257.1257.1257.1257.1257.1257.1257.1257.1257.1257.1257.1365.1365.1365.1365.1365.1366.1396.1396.1399.1399.1399.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1401.1403.1403.1403.1403.1403.1403.1403.2454.2454.2454.2455.2455.2455.2459.2459.2459.2459.2459.2459.2459.2460.2460.2460.2460.2460.2460.2460.2460.2460.2460.2460.2460.2460.2460.2460.2460.2460.2460.2460.2462.2463.2463.2463.2463.2463.2463.2463.2463.2463.2463.2463.2463.2463.2463.2463.2463.2463.2464.2464.2464.2464.2469.2469.2470.2470.2470.2470.2470.2470.2470.2471.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2472.2473.2473.2473.2473.2473.2473.2473.2473.2473.2473.2490.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2491.2492.2492.2492.2492.2496.2497.2498.2498.2498.2498.2498.2498.2498.2498.2498.2498.2498.2498.2498.2498.2499.2499.2499.2499.2499.2499.2499.2499.2500.2503.2506.2506.2508.2508.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2509.2516.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2518.2520.2520.2520.2520.2520.2520.2520.2520.2522.2522.2522.2522.2522.2522.2522.2522.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2526.2528.2537.2537.2537.2537.2537.2537.2537.2537.2537.2537.2537.2537.2540.2540.2540.2540.2540.2540.2540.2543.2544.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2549.2551.2551.2551.2551.2551.2558.2558.2558.2558.2558.2558.2561.2564.2564.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2565.2568.2568.2568.2568.2568.2568.2568.2568.2568.2572.2575.2575.2575.2575.2575.2575.2575.2575.2575.2576.2580.2580.2580.2580.2580.2580.2584.2584.2584.2765.2765.2765.2765.2765.2765.2765.2765.2765.2765.2765.2765.2765.2765.2765.2765.2767.2767.2767.2767.2767.2768.2768.2768.2774.2774.2774.2774.2774.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2775.2789.2789.2793.2793.2793.2802.2802.2802.2802.2805.2805.2810.2810.2810.2810.2810.2810.2810.2810.2810.2810.2810.2810.2810.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2814.2822.2822.2822.2827.2827.2827.2827.2827.2827.2829.3203.3203.3203.3786.3786.3786.3786.3786.3786.3786.3786.3786.3786.3786.3786.3786.3786.3786.3832.3832.3832.3832.3832.3832.3832.3832.3834.3834.3837.3839.3839.3839.3839.3839.3840.3874.3880.3880.3880.3880.3880.3880.3880.3889.3890.3891.3891.3891.3891.3891.3891.3891.3891.3893.3893.3893.3893.3893.3898.3903.3903.3903.3907.3907.3907.3907.3907.3909.3909.3909.3909.3909.3909.3909.3913.3913.3913.3914.3914.3914.3914.3914.3914.3914.3914.3914.3915.3915.3915.3915.3915.3919.3919.3919.3921.3922.3923.3923.3923.3923.3923.3923.3923.3923.3923.3923.3923.3923.3923.3923.3923.3924.3924.3924.3924.3924.3924.3924.3924.3924.3924.3924.3934.3934.3934.3934.3934.3934.3935.3935.3935.3935.3935.3938.3938.3938.3938.3938.3938.3938.3938.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3941.3947.3947.3947.3947.3947.3947.3947.3947.3947.3947.3950.3950.3950.3952.3952.3952.3952.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3956.3961.3963.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3965.3965.3965.3965.3965.3968.3968.3970.3970.3970.3971.3971.3971.3972.3972.3972.3972.3972.3972.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3978.3978.3978.3979.3981.3981.3981.3981.3981.3981.3981.3981.3981.3981.3981.3981.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3985.3985.3985.3985.3986.3986.3986.3993.3993.3994.3994.3994.3999.3999.3999.3999.3999.3999.4001.4001.4001.4001.4001.4001.4001.4001.4002.4002.5407.5407.5407.5414.5414.5414.5414.5414.5414.5414.5414.5415.5415.5415.5415.5415.5415.5415.5415.5415.5415.5415.5415.5415.5415.5415.5415.5415.5415.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5416.5417.5419.5419.5419.5419.5419.5419.5419.5419.5419.5419.5419.5424.5424.5424.5424.5424.5424.5424.5424.5424.5424.5424.5424.5424.5439.5439.5439.5440.5440.5441.5441.5441.5441.5441.5441.5441.5441.5441.5441.5441.5441.5441.5441.5441.5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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 " 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 1108 (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 0m51.582s user 0m25.975s sys 0m0.755s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m51.278s user 0m27.205s sys 0m0.763s Creating box around spheres Creating chemgrid maps real 0m28.020s user 0m15.268s sys 0m0.224s Atomic solvent excluded volume calculations underway FORTRAN STOP real 18m13.527s user 14m24.208s sys 0m0.065s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LEU 263 has a net charge of -0.0260 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1108 has a net charge of -2.0000 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LEU 263 has a net charge of -0.0260 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1108 has a net charge of -2.0000 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LEU 263 has a net charge of -0.0260 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1108 has a net charge of -2.0000 End of MakeDOCK sphere and grid generation.