SPACI score report for 3se9 in ASTRAL 2.04:

PDB Entry: 3se9
SPACI score: 0.45
AEROSPACI score: 0.45

Experiment type: XRAY
Resolution: 2
R-factor: 0.192
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -1.397
WCK2 WHAT_CHECK Ramachandran: -1.374
WCK3 WHAT_CHECK Chi angles: -0.847
WCK4 WHAT_CHECK Backbone: 2.639

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).