SPACI score report for 3lyo in ASTRAL 2.06:

PDB Entry: 3lyo
SPACI score: 0.46
AEROSPACI score: 0.46

Experiment type: XRAY
Resolution: 1.93
R-factor: 0.179
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -0.4
WCK2 WHAT_CHECK Ramachandran: -2.015
WCK3 WHAT_CHECK Chi angles: -2.598
WCK4 WHAT_CHECK Backbone: -0.095

Note: Here are links to pages about PROCHECK and WHAT_CHECK.

Here is the full WHAT_CHECK report on this protein (linked from the WHAT_CHECK site).