HNMMC refinement of the native structure of the ribonuclease P S-domain against the cryo-EM map of the folding intermediate. (A) The flow chart of the refinement protocol of the S-domain. DOF 1 is applied in the first step to generate 10,000 conformations without the restraint from the cryo-EM density. DOF 2 with two levels is applied in the last step for a detailed refinement. (B) The conformational difference between the 500 representative conformations from clustering the 10,000 conformations. The scatter plot shows the differences among the 500 models by multidimensional scaling computed using the matrix of the pairwise C4′ RMSD among the 500 conformations. Each point represents one conformation. The 18 unique conformations with high cross-correlation to the target map are marked as solid purple or red dots, with the red dot representing the conformation with the highest cross-correlation. (C) The heat map of the normalized cross-correlation of the 500 representative conformations to the target map. The 18 unique conformations with high cross-correlations are marked as stars. The red star at the top-left corner indicates the conformation with the highest cross-correlation.
