SPACI score report for 1nyr in ASTRAL 2.07:

PDB Entry: 1nyr
SPACI score: 0.18
AEROSPACI score: 0.18

Experiment type: XRAY
Resolution: 2.8
R-factor: 0.239
PCK1 PROCHECK Ramachandran: 1
PCK2 PROCHECK Chi-1 angle: 3
PCK3 PROCHECK H-bonds: 3
WCK1 WHAT_CHECK Packing: -2.172
WCK2 WHAT_CHECK Ramachandran: -5.402
WCK3 WHAT_CHECK Chi angles: -4.467
WCK4 WHAT_CHECK Backbone: -1.813

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).