Table 1. Annotated scorefile headers.

Metric	Purpose
CA_sup_RMSD	Whole complex Cα RMSD after superimposition
I_sup_bb_RMSD	Interface main chain atom RMSD, after superimposition
ch1_CA_RMSD	Chain 1 Cα RMSD without superimposition
ch1_CA_sup_RMSD	Chain 1 Cα RMSD with superimposition
ch2_CA_RMSD	Chain 2 Cα RMSD without superimposition
ch2_CA_sup_RMSD	Chain 2 Cα RMSD with superimposition
loop_CA_sup_RMSD	Loop residues' Cα RMSD with superimposition
dSASA_int	SASA buried by the interface
dG_cross	Interface binding energy, calculated from residue interactions between chains
dG_cross/dSASAx100	dG_cross, scaled by dSASA_int and a constant factor
dG_separated	Interface binding energy, calculated by separating components
dG_separated/dSASAx100	dG_separated, scaled by dSASA_int and a constant factor
delta_unsatHbonds	Number of unsatisfied hydrogen bonds in the interface
total_score	Weighted, summed score of the scorefunction
LAM_total	A sensitive descriptor of loop closure quality
description	The trajectory label (e.g., 2OBG_0001)

This table annotates the regions of the scorefile produced by AnchoredDesign. The first column lists metrics useful for analyzing benchmark or designed structures, and the second lists the meanings of those metrics. Of particular interest are total_score, loop_CA_sup_RMSD (loop RMSD), I_sup_bb_RMSD (IRMSD), and ch2_CA_RMSD (LRMSD), which provide the metrics used for the other plots and tables in this paper. Scorefile columns not listed here are either scorefunction terms [31], [36] or InterfaceAnalyzerMover metrics not useful for AnchoredDesign.