We evaluated the performance of Emap2sec+ at three levels: the voxel, the amino acid residue/nucleotide, and the protein secondary structure segment levels. The voxel-level considers if the assigned structure by Emap2sec+ agrees with the structure(s) within a 3 Å radius to the voxel center. We also evaluated with multiple structure labels for a voxel if the structures were observed within the radius. For the voxel-level evaluation, we used the F1-score, which is computed from the precision and the recall of the assignments given to the entire map or to each secondary structure class:

where precision is the fraction of voxels with correctly assigned structure among all the voxels that were structure-assigned by Emap2sec+ and recall is the fraction of the voxels with correctly assigned structure among all the voxels that belong to the structure class. The overall accuracy (recall) and F1-score of maps were computed as the weighted average of different classes. For the residue-level evaluation, we defined Q4 accuracy. Q4 is the average of the fractions of residues or nucleotides in each structure class whose class label is correctly assigned by Emap2sec+.

For each residue or nucleotide, labels were assigned to voxels within 3.0 Å to any heavy atoms of the residue/nucleotide were considered and the assignment was considered as correct if the majority vote from the voxels agreed with the correct class of the residue/nucleotide. For the protein secondary structures, we further reported the segment-level accuracy. A segment was defined as consecutive amino acids with the same secondary structure type with the minimum length of 6 amino acids for α helix and 3 residues for a β strand. If at least 50% of the residues in a segment were assigned with the correct label, the assignment to the segment was considered correct.

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