to_mmcif: add a few more items in _refine and _refine_ls_shell #1197

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Job	Run time
AlmaLinux 8	4m 57s
macOS 13 (w/o python)	3m 1s
Ubuntu 20.04	6m 42s
macOS 15	2m 18s
Ubuntu 22.04	3m 1s
Ubuntu 24.04	2m 54s
Ubuntu 20.04 with Clang 8	3m 58s
Windows 2022	7m 27s
	34m 18s