Dear all: When I get the models from modeller, there are always some atom clash。How to solve this problem? Could modeller solve this by itself? I get models from "model-changeopt.py", and set a.md_level = refine.slow a.repeat_optimization = 50 Here is the results for the best model:

Strongest energies for the vdWaals interactions _____________________________ _______________

1 236 .GLU.N - 236 .GLU.CD 2.697 1.7143 2 318 .ASP.CG - 318 .ASP.C 2.844 1.7121 3 278 .ASP.CG - 278 .ASP.C 2.845 1.7029 4 99 .ASP.O - 101 .ASN.N 2.532 1.6450 5 143 .ARG.O - 161 .GLY.N 2.547 1.4700 6 250 .TYR.CG - 250 .TYR.C 2.885 1.3172 7 244 .ASP.O - 248 .ASP.N 2.563 1.3145 8 214 .ASP.CG - 214 .ASP.C 2.888 1.2951 9 411 .THR.O - 412 .LEU.C 2.710 1.2663 10 385 .ALA.O - 386 .ASP.C 2.713 1.2380 11 244 .ASP.N - 249 .ARG.O 2.578 1.1794 12 275 .SER.HA - 285 .ILE.O 2.185 1.1460 13 294 .ASP.O - 295 .GLY.C 2.725 1.1418 14 289 .TRP.CG - 289 .TRP.C 2.907 1.1394 15 276 .PHE.CG - 276 .PHE.C 2.914 1.0910

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Strongest energies for the H-bonds interactions ____________________________________________

1 344 .ASN.HD21- 344 .ASN.O 1.850 -1.5000 2 442 .ALA.O - 445 .SER.H 1.850 -1.5000 3 96 .GLY.O - 105 .VAL.H 1.850 -1.5000 4 397 .GLY.O - 399 .THR.H 1.850 -1.5000 5 230 .LEU.H - 235 .PHE.O 1.850 -1.5000 6 134 .ASP.OD2 - 164 .ARG.HH12 1.850 -1.5000 7 353 .ILE.O - 511 .ALA.H 1.850 -1.5000 8 398 .SER.HG - 398 .SER.O 1.849 -1.5000 9 106 .GLN.HE22- 142 .PHE.O 1.849 -1.5000 10 71 .PRO.O - 74 .LYS.H 1.849 -1.5000 11 206 .SER.HG - 208 .GLN.O 1.848 -1.4999 12 478 .ASP.O - 480 .SER.H 1.848 -1.4999 13 365 .VAL.O - 475 .SER.H 1.852 -1.4999 14 56 .LEU.O - 59 .TRP.HE1 1.848 -1.4999 15 177 .ASN.OD1 - 180 .LYS.H 1.852 -1.4999

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Strongest energies for the Elect. interactions ____________________________________________

1 31 .HIS.HE2 - 117 .PRO.O 1.872 -6.9175 2 50 .HIS.HE2 - 118 .TYR.O 1.940 -6.4947 3 406 .PRO.O - 513 .ASN.OD1 2.707 6.0365 4 348 .ASP.O - 513 .ASN.O 2.771 5.8644 5 294 .ASP.O - 295 .GLY.C 2.725 -5.8603 6 385 .ALA.O - 386 .ASP.C 2.713 -5.8427 7 340 .VAL.O - 524 .LEU.O 2.774 5.7495 8 411 .THR.O - 412 .LEU.C 2.710 -5.7430 9 326 .GLN.O - 488 .GLY.O 2.738 5.6908 10 9 .HIS.HE2 - 483 .GLU.OE2 1.871 -5.6896 11 134 .ASP.O - 135 .ILE.C 2.798 -5.6414 12 201 .ASP.O - 225 .VAL.O 2.878 5.5602 13 362 .GLN.OE1 - 530 .ASP.O 2.901 5.5484 14 386 .ASP.O - 387 .LEU.C 2.822 -5.5457 15 441 .ASP.CG - 441 .ASP.O 2.899 -5.4778

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Non-bonded contributions _________________________

Normal pairs

H-bonds : N.pairs= 14516 energy= -861. Elect. : N.pairs= 687078 energy= -0.402E+04 vdWaals : N.pairs= 699117 energy= -0.443E+04

1-4 pairs H-bonds : N.pairs= 5 energy= -0.137 Elect. : N.pairs= 21311 energy= 0.430E+04 vdWaals : N.pairs= 21306 energy= 288.

Total H-bonds : N.pairs= 14521 energy= -861. Elect. : N.pairs= 708389 energy= 282. vdWaals : N.pairs= 720423 energy= -0.414E+04

Total non-bonded energy : -0.472E+04