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 0m35.733s user 0m0.489s sys 0m0.384s 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 0:1380 spheres. 412. 412. 413. 414. 414. 414. 415. 415. 415. 415. 415. 415. 415. 415. 416. 416. 416. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 439. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 440. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 441. 443. 446. 446. 446. 446. 446. 446. 449. 449. 449. 449. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 450. 451. 451. 451. 451. 451. 451. 476. 476. 476. 476. 476. 477. 477. 477. 477. 477. 477. 478. 478. 478. 642. 642. 642. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 644. 645. 645. 645. 645. 645. 645. 645. 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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: 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: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: 114 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.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 1m39.019s user 0m25.500s sys 0m0.633s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m18.802s user 0m25.582s sys 0m0.663s Creating box around spheres Creating chemgrid maps real 1m17.160s user 0m24.185s sys 0m0.226s Atomic solvent excluded volume calculations underway FORTRAN STOP real 38m57.898s user 14m21.882s sys 0m0.054s 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.