DNATCO v4.1: results

Molecular dynamics re-refinement of domain 5 of the yeast ai5(gamma) group II intron

Results of the assignment of 165 detected steps in 5 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

Click a row in table or a step in viewer for analysis of results. Click column headers to sort data.

Define restraints for steps within Å cartesian RMSD, global sigma scaling factor or use per step sigma scaling.

step number	Step name	CANA	NtC	confal	rmsd	NtCs
001	2lps-m1_A_G1_A2	AAA	AA00	85	0.13	AA00
002	2lps-m2_A_G1_A2	AAA	AA00	77	0.23	AA00
003	2lps-m3_A_G1_A2	AAA	AA00	84	0.15	AA00
004	2lps-m4_A_G1_A2	AAA	AA00	85	0.13	AA00
005	2lps-m5_A_G1_A2	AAA	AA00	83	0.14	AA00
006	2lps-m1_A_A2_G3	AAA	AA00	79	0.22	AA00
007	2lps-m2_A_A2_G3	AAA	AA00	73	0.20	AA00
008	2lps-m3_A_A2_G3	AAA	AA00	64	0.27	AA00
009	2lps-m4_A_A2_G3	AAA	AA00	82	0.23	AA00
010	2lps-m5_A_A2_G3	AAA	AA00	86	0.19	AA00
011	2lps-m1_A_G3_C4	AAA	AA00	81	0.28	AA00
012	2lps-m2_A_G3_C4	AAA	AA00	84	0.23	AA00
013	2lps-m3_A_G3_C4	AAA	AA00	79	0.28	AA00
014	2lps-m4_A_G3_C4	AAA	AA00	79	0.26	AA00
015	2lps-m5_A_G3_C4	AAA	AA00	83	0.26	AA00
016	2lps-m1_A_C4_C5	AAA	AA00	79	0.22	AA00
017	2lps-m2_A_C4_C5	AAA	AA00	82	0.22	AA00
018	2lps-m3_A_C4_C5	AAA	AA00	85	0.20	AA00
019	2lps-m4_A_C4_C5	AAA	AA00	88	0.20	AA00
020	2lps-m5_A_C4_C5	AAA	AA00	82	0.20	AA00
021	2lps-m1_A_C5_G6	AAA	AA00	83	0.20	AA00
022	2lps-m2_A_C5_G6	AAA	AA00	85	0.15	AA00
023	2lps-m3_A_C5_G6	AAA	AA00	91	0.14	AA00
024	2lps-m4_A_C5_G6	AAA	AA00	86	0.15	AA00
025	2lps-m5_A_C5_G6	AAA	AA00	89	0.13	AA00
026	2lps-m1_A_G6_U7	AAA	AA00	90	0.20	AA00
027	2lps-m2_A_G6_U7	AAA	AA00	76	0.24	AA00
028	2lps-m3_A_G6_U7	AAA	AA00	87	0.18	AA00
029	2lps-m4_A_G6_U7	AAA	AA00	85	0.21	AA00
030	2lps-m5_A_G6_U7	AAA	AA00	89	0.20	AA00
031	2lps-m1_A_U7_A8	AAA	AA00	79	0.22	AA00
032	2lps-m2_A_U7_A8	AAA	AA00	70	0.25	AA00
033	2lps-m3_A_U7_A8	AAA	AA00	82	0.24	AA00
034	2lps-m4_A_U7_A8	AAA	AA00	79	0.28	AA00
035	2lps-m5_A_U7_A8	AAA	AA00	82	0.24	AA00
036	2lps-m1_A_A8_U9	AAA	AA00	68	0.34	AA00
037	2lps-m2_A_A8_U9	AAA	AA04	45	0.52	AA04
038	2lps-m3_A_A8_U9	AAA	AA00	63	0.37	AA00
039	2lps-m4_A_A8_U9	AAA	AA00	24	0.48	AA00
040	2lps-m5_A_A8_U9	AAA	AA00	77	0.28	AA00
041	2lps-m1_A_U9_G10	AAA	AA00	26	0.47	AA00
042	2lps-m2_A_U9_G10	AAA	AA00	22	0.47	AA00
043	2lps-m3_A_U9_G10	AAA	AA00	38	0.42	AA00
044	2lps-m4_A_U9_G10	AAA	AA00	67	0.32	AA00
045	2lps-m5_A_U9_G10	AAA	AA00	19	0.46	AA00
046	2lps-m1_A_G10_C11	AAA	AA00	81	0.22	AA00
047	2lps-m2_A_G10_C11	AAA	AA00	90	0.14	AA00
048	2lps-m3_A_G10_C11	AAA	AA00	83	0.21	AA00
049	2lps-m4_A_G10_C11	AAA	AA00	75	0.24	AA00
050	2lps-m5_A_G10_C11	AAA	AA00	77	0.22	AA00
051	2lps-m1_A_C11_G12	AAA	AA00	89	0.14	AA00
052	2lps-m2_A_C11_G12	AAA	AA00	77	0.21	AA00
053	2lps-m3_A_C11_G12	AAA	AA00	88	0.14	AA00
054	2lps-m4_A_C11_G12	AAA	AA00	89	0.13	AA00
055	2lps-m5_A_C11_G12	AAA	AA00	88	0.15	AA00
056	2lps-m1_A_G12_A13	AAA	AA00	86	0.14	AA00
057	2lps-m2_A_G12_A13	AAA	AA00	79	0.18	AA00
058	2lps-m3_A_G12_A13	AAA	AA00	85	0.14	AA00
059	2lps-m4_A_G12_A13	AAA	AA00	88	0.11	AA00
060	2lps-m5_A_G12_A13	AAA	AA00	86	0.14	AA00
061	2lps-m1_A_A13_U14	AAA	AA00	79	0.26	AA00
062	2lps-m2_A_A13_U14	AAA	AA00	81	0.23	AA00
063	2lps-m3_A_A13_U14	AAA	AA00	82	0.18	AA00
064	2lps-m4_A_A13_U14	AAA	AA00	82	0.23	AA00
065	2lps-m5_A_A13_U14	AAA	AA00	82	0.22	AA00
066	2lps-m1_A_U14_G15	AAA	AA00	60	0.30	AA00
067	2lps-m2_A_U14_G15	AAA	AA00	67	0.29	AA00
068	2lps-m3_A_U14_G15	AAA	AA00	59	0.37	AA00
069	2lps-m4_A_U14_G15	AAA	AA00	67	0.31	AA00
070	2lps-m5_A_U14_G15	AAA	AA00	57	0.37	AA00
071	2lps-m1_A_G15_A16	NAN	NANT	0	0.34	OP04
072	2lps-m2_A_G15_A16	NAN	NANT	0	0.35	OP04
073	2lps-m3_A_G15_A16	NAN	NANT	0	0.41	OP04
074	2lps-m4_A_G15_A16	NAN	NANT	0	0.46	OP04
075	2lps-m5_A_G15_A16	NAN	NANT	0	0.33	OP04
076	2lps-m1_A_A16_A17	NAN	NANT	0	0.56	AA04
077	2lps-m2_A_A16_A17	NAN	NANT	0	0.55	AA04
078	2lps-m3_A_A16_A17	NAN	NANT	0	0.61	AA04
079	2lps-m4_A_A16_A17	NAN	NANT	0	0.63	AA04
080	2lps-m5_A_A16_A17	NAN	NANT	0	0.51	AA04
081	2lps-m1_A_A17_A18	AAA	AA00	47	0.29	AA00
082	2lps-m2_A_A17_A18	AAA	AA00	49	0.30	AA00
083	2lps-m3_A_A17_A18	AAA	AA00	55	0.26	AA00
084	2lps-m4_A_A17_A18	AAA	AA00	44	0.30	AA00
085	2lps-m5_A_A17_A18	AAA	AA00	52	0.28	AA00
086	2lps-m1_A_A18_G19	NAN	NANT	0	0.76	AA00
087	2lps-m2_A_A18_G19	NAN	NANT	0	0.76	AA04
088	2lps-m3_A_A18_G19	NAN	NANT	0	0.69	AA00
089	2lps-m4_A_A18_G19	NAN	NANT	0	0.79	AA04
090	2lps-m5_A_A18_G19	NAN	NANT	0	0.71	AA00
091	2lps-m1_A_G19_U20	AAA	AA00	78	0.29	AA00
092	2lps-m2_A_G19_U20	AAA	AA00	81	0.26	AA00
093	2lps-m3_A_G19_U20	AAA	AA00	81	0.28	AA00
094	2lps-m4_A_G19_U20	AAA	AA00	77	0.30	AA00
095	2lps-m5_A_G19_U20	AAA	AA00	80	0.27	AA00
096	2lps-m1_A_U20_C21	AAA	AA00	83	0.18	AA00
097	2lps-m2_A_U20_C21	AAA	AA00	81	0.24	AA00
098	2lps-m3_A_U20_C21	AAA	AA00	83	0.15	AA00
099	2lps-m4_A_U20_C21	AAA	AA00	78	0.18	AA00
100	2lps-m5_A_U20_C21	AAA	AA00	84	0.17	AA00
101	2lps-m1_A_C21_G22	AAA	AA00	81	0.16	AA00
102	2lps-m2_A_C21_G22	AAA	AA00	77	0.21	AA00
103	2lps-m3_A_C21_G22	AAA	AA00	75	0.17	AA00
104	2lps-m4_A_C21_G22	AAA	AA00	82	0.14	AA00
105	2lps-m5_A_C21_G22	AAA	AA00	77	0.17	AA00
106	2lps-m1_A_G22_C23	AAA	AA00	87	0.20	AA00
107	2lps-m2_A_G22_C23	AAA	AA00	77	0.18	AA00
108	2lps-m3_A_G22_C23	AAA	AA00	74	0.22	AA00
109	2lps-m4_A_G22_C23	AAA	AA00	86	0.17	AA00
110	2lps-m5_A_G22_C23	AAA	AA00	82	0.21	AA00
111	2lps-m1_A_C23_A24	AAA	AA00	53	0.28	AA00
112	2lps-m2_A_C23_A24	AAA	AA00	61	0.23	AA00
113	2lps-m3_A_C23_A24	AAA	AA00	57	0.31	AA00
114	2lps-m4_A_C23_A24	AAA	AA00	63	0.27	AA00
115	2lps-m5_A_C23_A24	AAA	AA00	70	0.24	AA00
116	2lps-m1_A_A24_C25	A-B	AB04	53	0.36	AB04
117	2lps-m2_A_A24_C25	NAN	NANT	0	0.53	AB04
118	2lps-m3_A_A24_C25	A-B	AB05	57	0.24	AB05
119	2lps-m4_A_A24_C25	A-B	AB05	17	0.27	AB05
120	2lps-m5_A_A24_C25	NAN	NANT	0	0.57	AA01
121	2lps-m1_A_C25_G26	NAN	NANT	0	1.03	AB2S
122	2lps-m2_A_C25_G26	NAN	NANT	0	1.86	OP08
123	2lps-m3_A_C25_G26	NAN	NANT	0	1.11	AB2S
124	2lps-m4_A_C25_G26	NAN	NANT	0	1.02	AB2S
125	2lps-m5_A_C25_G26	NAN	NANT	0	1.20	AB2S
126	2lps-m1_A_G26_U27	NAN	NANT	0	1.04	OP27
127	2lps-m2_A_G26_U27	NAN	NANT	0	1.08	OP07
128	2lps-m3_A_G26_U27	NAN	NANT	0	1.66	OP24
129	2lps-m4_A_G26_U27	NAN	NANT	0	1.67	OP24
130	2lps-m5_A_G26_U27	NAN	NANT	0	1.64	OP24
131	2lps-m1_A_U27_A28	AAA	AA00	72	0.26	AA00
132	2lps-m2_A_U27_A28	AAA	AA00	63	0.31	AA00
133	2lps-m3_A_U27_A28	AAA	AA00	65	0.27	AA00
134	2lps-m4_A_U27_A28	AAA	AA00	37	0.36	AA00
135	2lps-m5_A_U27_A28	AAA	AA00	30	0.38	AA00
136	2lps-m1_A_A28_C29	AAA	AA00	79	0.18	AA00
137	2lps-m2_A_A28_C29	AAA	AA00	76	0.22	AA00
138	2lps-m3_A_A28_C29	AAA	AA00	83	0.17	AA00
139	2lps-m4_A_A28_C29	AAA	AA00	86	0.17	AA00
140	2lps-m5_A_A28_C29	AAA	AA00	74	0.24	AA00
141	2lps-m1_A_C29_G30	AAA	AA00	82	0.17	AA00
142	2lps-m2_A_C29_G30	AAA	AA00	85	0.18	AA00
143	2lps-m3_A_C29_G30	AAA	AA00	81	0.16	AA00
144	2lps-m4_A_C29_G30	AAA	AA00	90	0.12	AA00
145	2lps-m5_A_C29_G30	AAA	AA00	86	0.16	AA00
146	2lps-m1_A_G30_G31	AAA	AA00	89	0.17	AA00
147	2lps-m2_A_G30_G31	AAA	AA00	86	0.20	AA00
148	2lps-m3_A_G30_G31	AAA	AA00	83	0.17	AA00
149	2lps-m4_A_G30_G31	AAA	AA00	88	0.13	AA00
150	2lps-m5_A_G30_G31	AAA	AA00	91	0.18	AA00
151	2lps-m1_A_G31_U32	AAA	AA00	75	0.26	AA00
152	2lps-m2_A_G31_U32	AAA	AA00	82	0.23	AA00
153	2lps-m3_A_G31_U32	AAA	AA00	81	0.21	AA00
154	2lps-m4_A_G31_U32	AAA	AA00	78	0.25	AA00
155	2lps-m5_A_G31_U32	AAA	AA00	82	0.23	AA00
156	2lps-m1_A_U32_U33	AAA	AA00	83	0.21	AA00
157	2lps-m2_A_U32_U33	AAA	AA00	89	0.17	AA00
158	2lps-m3_A_U32_U33	AAA	AA00	85	0.20	AA00
159	2lps-m4_A_U32_U33	AAA	AA00	86	0.18	AA00
160	2lps-m5_A_U32_U33	AAA	AA00	82	0.23	AA00
161	2lps-m1_A_U33_C34	AAA	AA00	87	0.15	AA00
162	2lps-m2_A_U33_C34	AAA	AA00	84	0.20	AA00
163	2lps-m3_A_U33_C34	AAA	AA00	68	0.26	AA00
164	2lps-m4_A_U33_C34	AAA	AA00	85	0.17	AA00
165	2lps-m5_A_U33_C34	AAA	AA00	84	0.19	AA00

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.

step:
Table of conformers

	δ1	ε1	ζ1	α2	β2	γ2	δ2	χ1	χ2	μ	NN	CC
step_torsions
ntC_average
Δ torsions
torsion scores

comments	step confal = NaN cartesian RMSD = NaN Å pseudorotation: NA details: NA

Similarity of step to class averages

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A

A-B

B-A

B

IC

OPN

Z

N

Results of the assignment of 165 detected steps in 5 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Restraints

User-based restraints

Definitions

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