Table 2.

Changes in RMSD (Å) from the experimental structure relative to the RMSDs of the initial models during MD simulations with and without restraints over different simulation lengths. For all cases, the ΔRMSD for the final conformation and the overall lowest RMSD are given. Improved cases with negative ΔRMSD values are highlighted in bold.

Target	NO RESTRAINTS		WITH RESTRAINTS
	24 ns		24 ns		8 × 3 ns		200 ns
	Final	Best	Final	Best	Final	Best	Final	Best
TR592	0.42	−0.05	−0.07	−0.18	−0.12	−0.16	−0.12	−0.20
TR453	0.34	0.08	0.16	−0.09	0.17	−0.10	0.44	−0.09
TR432	1.39	−0.12	−0.13	−0.30	−0.26	−0.34	−0.18	−0.31
TR462a	0.53	0.04	0.44	0.04	−0.04	−0.26	0.42	−0.07
TR594	1.37	0.13	0.75	0.00	0.05	−0.12	0.34	0.00
TR614	1.11	0.03	0.40	−0.13	0.25	−0.11	0.08	−0.13
TR435	0.13	−0.31	0.30	0.03	0.07	−0.08	0.78	0.03
TR530	−0.27	−0.64	0.18	−0.27	−0.22	−0.40	0.26	−0.35
TR488	1.29	−0.08	0.00	−0.25	−0.16	−0.23	−0.13	−0.26
TR469	0.72	−0.14	−0.02	−0.19	−0.09	−0.20	0.15	−0.19
TR462b	0.23	−0.16	0.10	−0.11	−0.02	−0.14	0.17	−0.11
TR389	0.81	0.01	−0.27	−0.62	−0.11	−0.51	0.31	−0.62
TR464	0.89	−0.14	−0.02	−0.16	0.03	−0.15	−0.12	−0.23
TR569	0.46	−0.03	−0.24	−0.50	−0.26	−0.47	−0.28	−0.69
TR454	0.89	−0.31	0.06	−0.15	−0.10	−0.19	−0.12	−0.20
TR567	−1.00	−1.46	0.02	−0.18	−0.03	−0.11	−0.06	−0.20
TR574	1.82	0.15	1.07	0.07	0.09	−0.50	1.16	−0.40
TR557	−0.01	−0.75	−0.58	−0.67	−0.35	−0.57	−0.61	−0.84
TR429a	2.32	−1.19	0.20	−0.20	−0.08	−0.21	−0.03	−0.26
TR517	3.05	0.03	0.50	−0.12	0.15	−0.17	0.46	−0.12
TR606	1.76	0.01	1.63	−0.28	0.58	−0.93	−0.80	−1.51
TR429b	−0.35	−0.59	−0.02	−0.17	−0.04	−0.25	0.01	−0.23
TR624	−0.90	−1.83	−0.21	−0.68	−0.03	−0.37	−0.63	−0.89
TR568	0.59	0.13	0.07	−0.31	0.32	−0.10	0.29	−0.43
TR622	0.20	0.03	0.23	−0.05	0.06	−0.72	1.63	−0.32
TR576	1.01	0.51	0.74	0.49	0.70	0.37	0.28	0.00
Avg.	0.72	−0.26	0.20	−0.19	0.02	−0.27	0.14	−0.33
#better	5	15	9	21	15	25	11	23