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 0m35.254s user 0m0.507s sys 0m0.303s 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 0:1467 spheres. 394. 395. 396. 396. 396. 396. 396. 396. 398. 398. 398. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 421. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 423. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 424. 426. 426. 429. 429. 429. 429. 429. 429. 433. 433. 433. 433. 433. 433. 433. 433. 459. 460. 460. 460. 460. 460. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 461. 625. 625. 625. 625. 627. 627. 627. 627. 627. 627. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 642. 642. 642. 642. 642. 642. 642. 643. 644. 644. 644. 646. 646. 646. 654. 654. 654. 654. 654. 654. 654. 654. 654. 654. 654. 654. 654. 654. 654. 654. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 655. 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. 662. 662. 662. 662. 662. 662. 662. 662. 667. 668. 668. 668. 670. 670. 670. 670. 670. 670. 670. 675. 676. 676. 676. 676. 676. 677. 677. 677. 677. 677. 677. 677. 681. 682. 682. 682. 682. 682. 682. 682. 682. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 683. 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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 " 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 (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: 118 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.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 1m22.952s user 0m26.120s sys 0m0.685s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m10.934s user 0m26.000s sys 0m0.680s Creating box around spheres Creating chemgrid maps real 0m35.103s user 0m15.430s sys 0m0.260s Atomic solvent excluded volume calculations underway FORTRAN STOP real 39m32.045s user 15m41.853s sys 0m0.090s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 126 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: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! 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: HEM 1107 has a net charge of -4.0000 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 126 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: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! 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: HEM 1107 has a net charge of -4.0000 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 126 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: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: ARG 246 has a net charge of 0.0400 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! 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: HEM 1107 has a net charge of -4.0000 End of MakeDOCK sphere and grid generation.