SPACI score report for 1yl3 in ASTRAL 2.04:

PDB Entry: 1yl3
SPACI score: -0.12
AEROSPACI score: -0.12

Experiment type: XRAY
Resolution: 5.5
R-factor: 0.307
PCK1 PROCHECK Ramachandran: 4
PCK2 PROCHECK Chi-1 angle: 3
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -5.008
WCK2 WHAT_CHECK Ramachandran: -8.476
WCK3 WHAT_CHECK Chi angles: -6.085
WCK4 WHAT_CHECK Backbone: -8.902

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).