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 0m48.955s user 0m0.501s sys 0m0.320s 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 0:1532 spheres. 1502.1502.1502.1502.1502.1502.1502.1502.1502.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1503.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1504.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1505.1506.1506.1506.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1510.1511.1511.1511.1511.1511.1511.1511.1511.1511.1511.1511.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1513.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1514.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1515.1540.1540.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1541.1542.1542.1542.1542.1542.1542.1542.1542.1542.1542.1542.1542.1542.1542.1546.1546.1546.1546.1546.1546.1547.1547.1547.1547.1547.1547.1547.1547.1548.1548.1548.1548.1548.1548.1548.1548.1548.1549.1549.1549.1549.1549.1549.1549.1549.1705.1706.1706.1706.1706.1706.1706.1708.1708.1708.1708.1708.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1709.1714.1717.1717.1717.1730.1733.1734.1734.1734.1734.1734.1734.1734.1735.1735.1735.1735.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1736.1738.1738.1738.1742.1742.1742.1742.1742.1742.1742.1742.1742.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1743.1751.1751.1751.1751.1751.1751.1751.1751.1751.1751.1753.1757.1758.1758.1758.1758.1758.1758.1767.1767.1767.1767.1767.1772.1772.1772.1772.1772.1772.1772.1772.1772.1772.1772.1772.1773.1773.1773.1773.1773.1773.1773.1773.1773.1773.1773.1773.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1774.1775.1775.1775.1775.1776.1776.1776.1776.1776.1776.1776.1776.1776.1779.1780.1780.1780.1780.1782.1782.2335.2335.2335.2335.2335.2337.2337.2337.2339.2339.2339.2339.2339.2339.2339.2339.2339.2339.2339.2339.2339.2339.2339.2339.2339.2339.2340.2340.2340.2340.2341.2341.2341.2341.2341.2341.2341.2341.2341.2341.2341.2341.2341.2341.2341.2341.2412.2413.2415.2415.2441.2441.2441.2441.2441.2441.2441.2441.2444.2444.2444.2444.2444.2444.2446.2449.2449.2449.2449.2449.2449.2483.2483.2483.2483.2485.2485.2485.2485.2485.2485.2485.2487.2487.2487.2487.2487.2491.2491.2491.2615.2615.2615.2615.2615.2615.2615.2615.2615.2615.2615.2621.2621.3493.3493.3493.3493.3493.3493.3493.3493.3494.3494.3494.3494.3494.3494.3494.3494.3494.3494.3513.3513.3538.3538.3538.3538.3539.3539.3539.3539.3539.3539.3539.3539.3539.3539.3539.3539.3542.3542.3542.3542.3542.3542.3542.3542.3542.3542.3545.3548.3548.3548.3549.3549.3549.3549.3549.3549.3549.3549.3550.3550.3550.3551.3551.3551.3551.3551.3551.3552.3552.3552.3552.3552.3552.3552.3552.3552.3552.3562.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3570.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3571.3577.3577.3577.3577.3577.3577.3577.3577.3577.3577.3577.3578.3578.3579.3579.3579.3579.3580.3580.3582.3582.3585.3585.3587.3587.3587.3588.3588.3588.3588.3588.3588.3588.3588.3588.3588.3588.3588.3593.3593.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3597.3601.3601.3601.3601.3602.3605.3605.3605.3605.3605.3605.3605.3605.3605.3605.3605.3605.3605.3605.3605.3605.3605.3605.3605.3607.3607.3611.3611.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3616.3618.3618.3619.3619.3619.3619.3619.3651.3651.3651.3651.3651.3651.3651.3651.3651.3651.3655.3655.3832.3832.3832.3832.3832.3832.3832.3832.3832.3832.3832.3832.3844.3844.3844.3844.3844.3844.3844.3844.3844.3844.3844.3844.3844.3844.3844.3844.3844.3846.3846.3846.3846.3846.3847.3847.3847.3847.3847.3847.3847.3847.3847.3847.3847.3847.3847.3847.3861.3861.3861.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3864.3868.3868.3872.3881.3881.3881.3881.3881.3883.3884.3884.3884.3884.3889.3889.3889.3889.3889.3893.3893.3893.3893.3893.3893.3893.3893.3893.3893.3893.3893.3893.3893.3893.3894.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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:38) and residue(A:28); changed residue names to "CYX " Created a bond between residue(B:569) and residue(B:558); changed residue names to "CYX " Created a bond between residue(B:579) and residue(B:563); changed residue names to "CYX " Created a bond between residue(B:591) and residue(B:581); changed residue names to "CYX " Created a bond between residue(B:681) and residue(B:559); changed residue names to "CYX " Created a bond between residue(B:1096) and residue(B:1090); 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 1106 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom (FE ) in residue 1106 (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: 100 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.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 1m14.512s user 0m25.210s sys 0m0.660s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 1m12.719s user 0m26.089s sys 0m0.759s Creating box around spheres Creating chemgrid maps real 0m38.056s user 0m17.410s sys 0m0.252s Atomic solvent excluded volume calculations underway FORTRAN STOP real 39m18.433s user 16m13.032s sys 0m0.127s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: LYS 690 has a net charge of 0.0730 !!! WARNING: LYS 691 has a net charge of 0.0730 !!! WARNING: GLN 692 has a net charge of 0.0170 !!! WARNING: ARG 701 has a net charge of 0.0400 !!! WARNING: LYS 708 has a net charge of 0.0200 !!! WARNING: LYS 770 has a net charge of 0.0200 !!! WARNING: ARG 799 has a net charge of 0.0400 !!! WARNING: LYS 839 has a net charge of 0.0200 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: ARG 918 has a net charge of 0.0400 !!! WARNING: LYS 975 has a net charge of 0.0200 !!! WARNING: ARG 981 has a net charge of 0.0400 !!! WARNING: LYS 995 has a net charge of 0.0200 !!! WARNING: LYS 1007 has a net charge of 0.0200 !!! WARNING: MET 1009 has a net charge of -0.0720 !!! WARNING: HEM 1106 has a net charge of -4.0000 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: LYS 690 has a net charge of 0.0730 !!! WARNING: LYS 691 has a net charge of 0.0730 !!! WARNING: GLN 692 has a net charge of 0.0170 !!! WARNING: ARG 701 has a net charge of 0.0400 !!! WARNING: LYS 708 has a net charge of 0.0200 !!! WARNING: LYS 770 has a net charge of 0.0200 !!! WARNING: ARG 799 has a net charge of 0.0400 !!! WARNING: LYS 839 has a net charge of 0.0200 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: ARG 918 has a net charge of 0.0400 !!! WARNING: LYS 975 has a net charge of 0.0200 !!! WARNING: ARG 981 has a net charge of 0.0400 !!! WARNING: LYS 995 has a net charge of 0.0200 !!! WARNING: LYS 1007 has a net charge of 0.0200 !!! WARNING: MET 1009 has a net charge of -0.0720 !!! WARNING: HEM 1106 has a net charge of -4.0000 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: LYS 690 has a net charge of 0.0730 !!! WARNING: LYS 691 has a net charge of 0.0730 !!! WARNING: GLN 692 has a net charge of 0.0170 !!! WARNING: ARG 701 has a net charge of 0.0400 !!! WARNING: LYS 708 has a net charge of 0.0200 !!! WARNING: LYS 770 has a net charge of 0.0200 !!! WARNING: ARG 799 has a net charge of 0.0400 !!! WARNING: LYS 839 has a net charge of 0.0200 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: ARG 918 has a net charge of 0.0400 !!! WARNING: LYS 975 has a net charge of 0.0200 !!! WARNING: ARG 981 has a net charge of 0.0400 !!! WARNING: LYS 995 has a net charge of 0.0200 !!! WARNING: LYS 1007 has a net charge of 0.0200 !!! WARNING: MET 1009 has a net charge of -0.0720 !!! WARNING: HEM 1106 has a net charge of -4.0000 End of MakeDOCK sphere and grid generation.