Table 6.

All-Atom RMSD's for RAPPER Using Two Different Restraint Derivations Compared to Those for MODELLER.

	All-atom RAPPER PDF (Å)	All-atom RAPPER Standard (Å)	Modeller (Å)
Az	1.24	1.62	1.30
Asp	1.89	2.47	1.54
Blm	1.56	2.06	1.55
Cyt3	1.50	1.99	1.19
Cytc	2.07	2.53	2.11
Egf	2.64	2.28	2.64
Fabp	2.18	2.36	2.15
Flav‡	2.30	1.78	1.65
Fn3	2.02	2.35	2.02
Ghf22	1.73	2.50	1.88
Glob‡	2.00	2.10	1.50
Gluts	2.24	3.66	2.84
Gtp	1.88	2.21	1.78
Igvar-h	2.32	2.79	2.36
Igvar-l	1.66	1.78	1.41
Ltn	1.66	1.78	1.41
MHC_II_N	2.61	2.62	2.45
Parv	1.14	1.73	1.21
Phc	1.46	1.81	1.52
Phoslip	1.87	2.56	1.90
Response_reg	2.41	2.64	2.26
Sh3	1.76	2.34	1.88
Tim	1.18	1.58	1.18
Mean	1.87	2.23	1.81

The RMSD for models of each of the family targets generated using RAPPER with restraints derived from PDF's, RAPPER with the standard restraint derivation procedure and MODELLER. The RMSD's for MODLLER and Standard RAPPER differ from the equivalent RMSD's in Tables 3 and 4 as they are calculated over the equivalent number of residues for all models in each family. The two families with difficulties in PDF generation are indicated by ‡.