SPACI score report for 3nqd in ASTRAL 2.01:

PDB Entry: 3nqd
SPACI score: 0.69
AEROSPACI score: 0.69

Experiment type: XRAY
Resolution: 1.42
R-factor: 0.166
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 1
PCK3 PROCHECK H-bonds: 2
WCK1 WHAT_CHECK Packing: -1.069
WCK2 WHAT_CHECK Ramachandran: -0.413
WCK3 WHAT_CHECK Chi angles: 1.828
WCK4 WHAT_CHECK Backbone: -1.018

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).