Model,RMSDens N=10↓,RMSDens N=100↓,RMSDens N=500↓,RMSDens N=1000↓,RMSD Cluster 3 N=10↓,RMSD Cluster 3 N=100↓,RMSD Cluster 3 N=500↓,RMSD Cluster 3 N=1000↓,Pairwise RMSD,CA clash (%)↓,CA break (%)↓,PepBond break (%)↓ EigenFold ,1.56,1.5,1.47,1.46,2.54,2.48,2.46,2.46,0.85,1.4,4.3,NaN MSA-depth256,1.57,1.54,1.52,1.52,2.51,2.47,2.45,2.45,0.2,0,0,9.2 MSA-depth64,1.6,1.54,1.51,1.5,2.48,2.4,2.35,2.33,0.55,0,0,7.9 MSA-depth32,1.67,1.53,1.45,1.41,2.39,2.21,1.93,1.87,2.14,0.6,0,10.6 Str2Str-ODE (Tmax=0.15),2.36,2.19,2.1,2.08,3.03,2.68,2.6,2.56,1.86,0,0,13.9 Str2Str-SDE (Tmax=0.15),2.83,2.48,2.28,2.25,3.42,2.92,2.52,2.48,3.6,0.3,0,16 AlphaFlow-PDB,1.53,1.45,1.42,1.41,2.48,2.43,2.41,2.4,0.86,0,0,13.2 AlphaFlow-MD,1.74,1.51,1.45,1.43,2.44,2.32,2.28,2.24,1.26,0,0.1,26.2 ESMFlow-PDB,1.61,1.49,1.44,1.42,2.47,2.41,2.37,2.35,0.74,0,0,6 ESMFlow-MD,1.66,1.5,1.41,1.4,2.49,2.29,2.2,2.18,1.17,0,0,14.3 ConfDiff-Open-ClsFree,1.65,1.48,1.41,1.37,2.56,2.3,2.16,2.03,1.77,0.5,0,5.5 ConfDiff-Open-MD,1.64,1.5,1.44,1.42,2.49,2.39,2.32,2.31,1.37,0.2,0,4.6 ConfDiff-ESM-ClsFree,1.58,1.45,1.41,1.39,2.5,2.39,2.35,2.33,1.52,0.5,0,7.5 ConfDiff-ESM-MD,1.61,1.47,1.42,1.4,2.45,2.32,2.26,2.24,1.42,0.1,0,5 ConfDiff-ESM-Energy,1.63,1.47,1.43,1.42,2.55,2.43,2.41,2.4,1.26,0.1,0,7.5 ConfDiff-ESM-Force,1.58,1.44,1.37,1.36,2.45,2.33,2.23,2.22,1.76,0.1,0,8.9