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This may be close to what you want, with some modifications to better handle the initial part of the data in each timestep section.
$ cat atoms.awk
BEGIN { printf ("CRYST1 200.000 200.000 200.000...

Both next and getline get the next record (next line).

The difference is:
- next restarts the script
- getline continues the script

Please use code tags as required by forum rules!

Replace the next command with getline. BTW, there's much opportunities to improve / trim / prune your code. First, indent code so the logics...