SPACI score report for 2ypp in ASTRAL 2.08:

PDB Entry: 2ypp
SPACI score: 0.44
AEROSPACI score: 0.44

Experiment type: XRAY
Resolution: 2.3
R-factor: 0.14046
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -0.726
WCK2 WHAT_CHECK Ramachandran: -0.958
WCK3 WHAT_CHECK Chi angles: -1.572
WCK4 WHAT_CHECK Backbone: 3.167

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).