I would have coded it this way:
/usr/bin/rm -v `ls -1|egrep -ve '(^ZMAT|^out|^Out|^GENBAS|^Note)'`
And bash is a shell, but you mean a script. Likely in interactive bash the * are getting expanded so you might have to use noglob to suppress it or something similar.
Or you might have to use a single quote to suppress the expansion so that rm gets the *, otherwise the shell expands the * and rm gets a list of files.
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