Table 1. RMSDs of the Models Built with Respect to Native Structure over All Residues and over All Residues in Secondary Structure Elements (in Parentheses)^I.

protein	starta	MDFF1b	Rosetta1c	MDFF2d	Rosetta2e	MDFF3f	Rosetta3g	besth
1X91	1.82(1.19)	1.42(0.88)	1.53(0.94)	1.38(0.89)	1.37(0.85)	1.41(0.92)	1.29(0.79)	0.98(0.74)
1DVO	2.50(1.65)	2.18(1.28)	2.16(1.19)	1.56(0.99)	1.89(1.01)	2.14(1.17)	2.14(0.98)	1.54(1.01)
1ICX	2.65(2.14)	1.90(1.45)	2.05(1.72)	1.75(1.38)	2.21(1.87)	1.84(1.39)	1.80(1.37)	1.80(1.37)
2FD5	2.16(1.46)	1.89(1.17)	2.03(1.26)	1.94(1.19)	2.07(1.31)	1.96(1.27)	2.01(1.38)	1.55(1.29)

^aRMSDs of the starting models.

^bRMSDs of the models after 1 ns of the first round of MDFF (step 1, density map scaling factor 0.3).

^cRMSDs of the top scoring model after the first round of Rosetta refinement.

^dRMSDs of the models after 1 ns of the second round of MDFF (step 1, density map scaling factor 0.3).

^eRMSDs of the top scoring model after the second round of Rosetta refinement.

^fRMSDs of the models after 1 ns of the third round of MDFF (step 1, density map scaling factor 0.3).

^gRMSDs of the top scoring model after the third round of Rosetta refinement.

^hRMSDs of the best Rosetta models ever built during the iterative MD–Rosetta refinement protocol.

^IAll RMSDs shown are in Å.