SPACI score report for 3ly6 in ASTRAL 2.07:

PDB Entry: 3ly6
SPACI score: 0.17
AEROSPACI score: 0.17

Experiment type: XRAY
Resolution: 3.14
R-factor: 0.233
PCK1 PROCHECK Ramachandran: 2
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -2.507
WCK2 WHAT_CHECK Ramachandran: -4.063
WCK3 WHAT_CHECK Chi angles: -3.91
WCK4 WHAT_CHECK Backbone: -0.894

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).