SPACI score report for 1y46 in ASTRAL 1.75:

PDB Entry: 1y46
SPACI score: 0.42
AEROSPACI score: 0.42

Experiment type: XRAY
Resolution: 2.22
R-factor: 0.192
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 2
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -0.183
WCK2 WHAT_CHECK Ramachandran: -2.07
WCK3 WHAT_CHECK Chi angles: -2.823
WCK4 WHAT_CHECK Backbone: 0.844

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).