Thank you very much, Pavel. I don't save H's when I modify the model in coot (the input PDB file that I sent you was the output from coot). I did the refinement again, now in version 2247, without NCS. I got the same results, higher R factors and RMS deviations for the newer version. I got better results when I used "update waters" (both in Rfactors and RMS). Below, I list the statistics for refinement without updating waters. Significant differences remain. Could it be any difference in settings of default parameters between versions?

version: dev-2247

Start: r_work = 0.1687 r_free = 0.2011 bonds = 0.046 angles = 1.321
Final: r_work = 0.1753 r_free = 0.2040 bonds = 0.030 angles = 0.593

version: 1.9-1692

Start: r_work = 0.1651 r_free = 0.2018 bonds = 0.013 angles = 1.409
Final: r_work = 0.1663 r_free = 0.2017 bonds = 0.011 angles = 1.321