That is the percentage of structures with that particular rotamer out of the population sampled (either the backbone bin or for the residue type as a whole).  PyMOL presents the rotamers in order of decreasing prevalence.
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From: pymol-users-bounces@lists.sourceforge.net [mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf Of Jamaine Saydu C. Davis
Sent: Tuesday, January 02, 2007 7:41 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] mutagenesis

When making mutations using the mutagenesis wizard, what are the percentages that are displayed in the toggle/selection area? Is there a way to do an energy minimization after creating mutations?