Before revision:  In the end, we compared the EM results under different forcefields, showing that our reconstructed configurations are robust to the forcefields selection. Availability and implementation: The software and its MATLAB source codes are available at URLContact: qzhaoyuping@bit.edu.cn or xubiaopeng@bit.edu.cn.
After revision:  In the end, we compared our calculation results with PDB models by checking the structural similarity to X-ray crystallographic structure for a special dataset. The software and its MATLAB source codes are available at URLContact: qzhaoyuping@bit.edu.cn or xubiaopeng@bit.edu.cn.