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 0m32.796s user 0m0.488s sys 0m0.373s 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 0:1157 spheres. 398. 398. 398. 398. 398. 398. 398. 398. 398. 398. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 400. 402. 402. 405. 405. 405. 405. 405. 405. 405. 407. 407. 408. 408. 408. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 410. 410. 410. 410. 410. 410. 410. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 442. 442. 442. 443. 443. 443. 443. 443. 443. 444. 444. 444. 444. 444. 444. 444. 444. 444. 444. 445. 614. 628. 628. 628. 628. 628. 628. 628. 631. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 633. 634. 634. 634. 634. 634. 635. 635. 635. 635. 635. 635. 635. 635. 637. 637. 637. 640. 640. 640. 640. 640. 640. 640. 640. 640. 641. 641. 641. 641. 641. 641. 642. 642. 642. 642. 642. 642. 648. 648. 648. 648. 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. 661. 661. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 662. 663. 663. 663. 670. 670. 670. 671. 671. 671. 671. 671. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 672. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 674. 674. 674. 674. 674. 674.1249.1249.1249.1249.1251.1253.1253.1253.1253.1253.1253.1253.1253.1253.1253.1253.1254.1254.1254.1254.1254.1254.1254.1255.1255.1255.1256.1256.1326.1326.1328.1328.1328.1328.1328.1328.1328.1354.1354.1354.1357.1359.1359.1359.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1362.1391.1393.1393.1396.1396.1396.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1398.1400.1400.1400.1400.1400.1400.1400.1400.1400.1404.1404.1404.1404.1404.2479.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2488.2515.2515.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2523.2524.2524.2524.2524.2524.2524.2524.2524.2524.2524.2524.2528.2529.2530.2530.2530.2532.2532.2532.2535.2535.2535.2535.2538.2538.2541.2546.2546.2546.2547.2547.2547.2547.2547.2547.2547.2547.2547.2547.2548.2548.2548.2548.2548.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2551.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2553.2554.2554.2554.2555.2555.2555.2556.2556.2556.2559.2559.2559.2559.2559.2559.2559.2559.2559.2559.2559.2561.2561.2565.2565.2570.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2571.2572.2572.2573.2573.2573.2573.2573.2573.2573.2573.2573.2573.2573.2573.2573.2573.2573.2573.2573.2607.2607.2607.2607.2607.2607.2607.2610.2804.2804.2804.2804.2804.2804.2804.2804.2804.2804.2804.2806.2806.2806.2806.2806.2806.2806.2806.2806.2807.2807.2807.2807.2824.2825.2825.2825.2826.2826.2826.2826.2826.2826.2826.2839.2839.2839.2839.2839.2839.2839.2839.2839.2839.2839.2839.2839.2839.2842.2842.2842.2842.2842.2842.2842.2864.2864.2864.2864.2866.2866.2866.3257.3257.3257.3257.3257.3257.3257.3257.3257.3257.3257.3257.3257.3257.3257.3257.3835.3835.3835.3835.3835.3835.3836.3836.3836.3838.3838.3839.3889.3910.3910.3910.3910.3910.3910.3910.3910.3910.3910.3910.3910.3910.3910.3910.3910.3910.3910.3910.3917.3917.3917.3917.3917.3919.3922.3922.3923.3923.3926.3926.3926.3928.3928.3928.3928.3930.3930.3930.3941.3941.3947.3947.3947.3947.3947.3947.3947.3947.3954.3954.3955.3959.3959.3959.3959.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3963.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3964.3968.3968.3968.3968.3968.3968.3968.3968.3968.3968.3971.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3972.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3973.3983.3983.3983.3983.3983.3983.3983.3984.3984.3984.3984.3984.3984.3984.3984.3984.3984.3987.3987.3987.3987.3987.3987.3987.3987.3987.3987.3987.3987.3990.3990.3990.3990.3990.3990.3990.3990.3990.3990.3990.3990.3990.3990.3990.3990.3990.3990.3994.3996.3996.3996.3996.3996.3996.3996.3996.3996.3996.3999.4001.4001.4001.4001.4005.4005.4005.4005.4005.4005.4005.4007.4010.4010.4010.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4013.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4014.4017.4017.4017.4017.4017.4017.4017.4017.4017.4017.4019.4019.4019.4019.4020.4020.4020.4020.4021.4021.4021.4021.4021.4021.4022.4022.4022.4022.4022.4022.4022.4022.4027.4027.4027.4027.4027.4027.4027.4027.4029.4029.4030.4030.4030.4030.4030.4030.4030.4030.4030.4030.4030.4030.4030.4030.4030.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4033.4034.4034.4034.4034.4034.4034.4042.4042.4042.4042.4042.4042.4042.4042.5446.5446.5446.5446.5446.5446.5446.5446.5446.5446.5446.5446.5446.5447.5447.5447.5448.5448.5449.5449.5449.5449.5449.5449.5450.5450.5450.5451.5451.5451.5451.5451.5451.5451.5456.5456.5456.5456.5456.5456.5456.5456.5456.5456.5471.5471.5471.5471.5471.5472.5472.5472.5472.5473.5473.5473.5473.5473.5473.5475.5475.5475.5475.5475.5475.5475.5475.5475.5475.5475.5475.5475.5475.5475.5475.5475.5476.5476.5476.5476.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: 19 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19.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:128) and residue(A:5); 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 1105 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom (FE ) in residue 1105 (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 1m27.507s user 0m27.117s sys 0m0.743s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m5.271s user 0m25.637s sys 0m0.685s Creating box around spheres Creating chemgrid maps real 0m48.425s user 0m17.067s sys 0m0.237s Atomic solvent excluded volume calculations underway FORTRAN STOP real 37m46.893s user 15m35.420s sys 0m0.137s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 End of MakeDOCK sphere and grid generation.