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![[Figure 6]](ji5028fig6mag.jpg)
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Figure 6
Analysis of initial and refined models of two 2Ver targets using the DAQ(AA) score. Left: the initial model (the first version of the PDB entry). The color of the chain reflects the deviation of Cα-atom positions from the native structure (the revised version of the entry). Color is scaled from green (deviation < 1.0 Å) to magenta (deviation > 3.0 Å). Middle and right: the initial and refined models colored by the DAQ(AA) score. The color is scaled from red [DAQ(AA) < −1.0] to blue [DAQ(AA) > 1.0]. The radius of the chain tube is thicker if the region has a low DAQ(AA) score. The enlargements show model regions with a low DAQ(AA) score. The initial, refined and revised models are indicated in magenta, cyan and orange, respectively. Surface meshes represent the EM map at the author's recommended contour level. Plots show the DAQ(AA) scores along the sequence position. Gray in the plot represents residue positions where the deviation of the Cα-atom position between the model and native (the revised structure) is larger than 3.0 Å. (a) PDB entry 7jsn chain A, which was built from the EM map (EMDB entry EMD-22458). A region containing Leu241, Trp243 and Ly247, which has a residue shift in sequence assignment in the initial model, is enlarged. The corresponding position in the plot is indicated by a red arrow. In the refined model, residue conformations in the native (the revised model) are shown in orange and cyan residues are those refined by DAQ-refine. (b) PDB entry 7ksm chain C with the EM map (EMDB entry EMD-23020) from which the chain structure was built. A region with a residue shift in the initial model, which includes Asn326 and Phe330, is enlarged. |
![[Figure 6]](ji5028fig6.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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