Detailed results of SSR10_XRay_em_bcr3 by PSVS
Output from PDBStat
Output from PROCHECK
Ramachandran Plot for all models
Text summary of Ramachandran Plot
+----------<<< P R O C H E C K S U M M A R Y >>>----------+
| |
| SSR10_XRay_em_bcr3_noHs_000.rin 0.0 242 residues |
| |
| Ramachandran plot: 91.7% core 8.3% allow 0.0% gener 0.0% disall |
| |
+| All Ramachandrans: 6 labelled residues (out of 236) |
+| Chi1-chi2 plots: 1 labelled residues (out of 153) |
JPEG image for all model Ramachandran Plot
Residue Properties for all models
JPEG for all model Residue Properties - page $num_n
JPEG for all model Residue Properties - page $num_n
JPEG for all model Residue Properties - page $num_n
JPEG for all model Residue Properties - page $num_n
JPEG for all model Residue Properties - page $num_n
Model Secondary Structures from Procheck
JPEG for Model Secondary Structures - page $num_n
JPEG for Model Secondary Structures - page $num_n
JPEG for Model Secondary Structures - page $num_n
JPEG for Model Secondary Structures - page $num_n
JPEG for Model Secondary Structures - page $num_n
Ramachandran Plots for each residue
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
Ramachandran analysis for each residue from Molprobity
Chi1-Chi2 Plots for each residue
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
Procheck G-factors for phi-psi for each residue
JPEG image for residue phi-psi G-factors
Table of Procheck G-factors for phi-psi for ordered residues
#phipsi_gfactor
#Residue\Model average
3 0.29
4 -0.10
5 -0.18
6 1.09
7 0.76
8 0.61
9 0.56
10 1.22
11 1.17
12 0.86
13 0.87
14 0.76
15 0.86
16 0.72
17 1.05
18 0.82
19 0.83
20 -0.38
21 1.14
22 -0.48
23 1.13
24 0.98
25 0.65
26 0.66
27 0.40
28 1.08
29 0.85
30 1.22
31 1.18
32 1.04
33 0.99
34 0.99
35 0.72
36 0.87
37 0.99
38 1.01
39 0.95
40 0.88
41 0.65
42 0.98
43 0.80
44 0.87
45 0.11
46 -1.82
47 -3.77
48 0.28
49 -1.21
50 -0.41
51 0.87
52 1.05
53 -0.19
54 -0.48
59 -0.57
60 -1.57
61 -0.27
62 0.13
63 0.87
64 1.13
65 0.99
66 1.22
67 0.95
68 0.66
69 1.19
70 -1.30
71 -2.58
72 -0.72
73 0.04
74 0.88
75 1.05
76 -1.44
77 -1.19
78 0.33
79 0.06
80 0.47
81 -0.78
82 0.84
83 1.03
84 0.95
85 0.95
86 0.76
87 0.95
88 0.84
89 0.88
90 0.66
91 -4.34
92 0.14
93 -1.94
94 1.22
95 -1.12
96 -0.21
97 -2.47
98 -1.55
99 -0.17
100 -0.44
101 0.86
102 1.22
103 0.82
104 0.98
105 0.95
106 0.95
107 0.63
108 0.71
109 0.87
110 0.93
111 0.98
112 0.90
113 0.95
114 0.63
115 0.81
116 0.47
117 1.22
118 -1.02
119 -0.85
120 0.93
121 0.64
122 -3.77
135 0.10
136 -0.18
137 1.09
138 0.76
139 1.08
140 1.05
141 0.79
142 1.22
143 0.72
144 0.44
145 0.65
146 0.87
147 0.87
148 1.05
149 0.82
150 0.14
151 -0.91
152 0.89
153 -1.07
154 0.01
155 1.05
156 0.13
157 0.05
158 1.18
159 1.08
160 0.07
161 1.22
162 1.18
163 0.95
164 0.76
165 0.66
166 0.86
167 0.82
168 0.66
169 1.01
170 1.04
171 1.13
172 1.13
173 0.98
174 0.58
175 0.33
176 0.34
177 0.37
178 -2.39
179 0.17
180 0.86
181 -0.49
182 0.29
183 1.39
184 1.05
185 0.57
186 -3.05
187 -2.58
188 -3.05
189 -0.39
190 -0.90
191 -2.78
192 -0.88
193 0.95
194 0.86
195 1.39
196 1.13
197 1.22
198 0.95
199 0.82
200 1.19
201 0.68
202 0.88
203 -0.35
204 0.90
205 0.64
206 -2.04
207 -1.23
208 -0.93
209 -0.56
210 0.71
211 0.45
212 0.69
213 0.99
214 1.03
215 0.95
216 1.19
217 0.76
218 1.26
219 1.24
220 1.13
221 1.39
222 0.56
223 1.08
224 0.98
225 1.22
226 -0.04
227 -2.57
228 -1.71
229 -2.30
230 -0.59
231 -0.24
232 -0.39
233 0.71
234 0.08
235 0.98
236 0.95
237 0.95
238 0.84
239 0.49
240 0.87
241 0.99
242 1.05
243 0.36
244 0.71
245 0.84
246 0.22
247 0.06
248 1.22
249 0.99
250 1.05
251 0.93
252 0.88
253 -1.07
254 -3.23
#Reported_Model_Average 0.318
#Overall_Average_Reported 0.318
Procheck G-factors for all dihedral angles for each residue
JPEG image for residue all dihedral G-factors
Table of Procheck G-factors for all dihedrals for ordered residues
#alldih_gfactor
#Residue\Model average
2 -0.72
3 -0.18
4 0.14
5 0.29
6 0.87
7 0.76
8 0.92
9 0.35
10 0.04
11 0.83
12 0.86
13 0.75
14 0.76
15 0.37
16 0.79
17 0.47
18 -0.51
19 0.40
20 0.29
21 1.14
22 -0.62
23 0.84
24 0.56
25 -0.37
26 0.66
27 0.27
28 -0.35
29 -0.14
30 0.42
31 0.82
32 1.08
33 0.99
34 0.99
35 0.76
36 0.65
37 0.99
38 0.40
39 1.12
40 0.59
41 0.50
42 0.95
43 0.39
44 0.57
45 -0.49
46 -1.25
47 -2.45
48 0.28
49 -1.79
50 -0.73
51 0.00
52 1.00
53 -0.95
54 0.13
55 0.00
58 0.00
59 0.25
60 -1.52
61 0.52
62 -0.29
63 0.46
64 0.65
65 -0.25
66 0.32
67 0.79
68 0.66
69 0.92
70 -1.30
71 -1.81
72 0.09
73 0.04
74 0.62
75 -0.20
76 -0.88
77 -1.03
78 0.18
79 -1.50
80 0.47
81 -1.52
82 -0.11
83 0.87
84 1.06
85 0.12
86 0.76
87 0.46
88 0.96
89 0.46
90 -0.19
91 -1.80
92 0.68
93 -1.94
94 0.69
95 -0.01
96 0.41
97 -1.79
98 -0.79
99 0.23
100 -0.44
101 -0.99
102 1.22
103 -0.48
104 0.79
105 0.90
106 0.74
107 0.59
108 -0.73
109 0.06
110 0.80
111 0.74
112 0.12
113 0.54
114 0.40
115 0.74
116 0.23
117 -0.56
118 -1.02
119 -0.23
120 -0.04
121 0.50
122 -1.44
123 0.00
134 0.00
135 -0.31
136 0.44
137 0.87
138 0.76
139 0.85
140 0.77
141 0.12
142 0.76
143 0.45
144 0.63
145 0.65
146 0.38
147 0.75
148 0.47
149 0.57
150 -0.29
151 -0.13
152 0.89
153 -0.49
154 0.27
155 0.96
156 -0.51
157 0.05
158 1.02
159 0.29
160 0.14
161 0.01
162 0.82
163 1.06
164 0.76
165 0.66
166 0.71
167 0.72
168 0.66
169 0.21
170 1.11
171 0.83
172 0.75
173 -0.05
174 0.74
175 0.30
176 0.44
177 0.32
178 -1.72
179 -0.08
180 0.85
181 -0.25
182 0.46
183 0.97
184 0.19
185 0.65
186 -3.05
187 -2.58
188 -3.05
189 -0.39
190 -0.10
191 -1.43
192 -0.08
193 1.00
194 0.47
195 1.36
196 -0.02
197 -0.36
198 0.49
199 0.82
200 1.03
201 0.92
202 0.14
203 0.28
204 0.85
205 -0.04
206 -0.85
207 -0.55
208 0.02
209 -0.01
210 0.66
211 0.45
212 0.75
213 -0.71
214 0.83
215 0.47
216 0.78
217 0.76
218 0.73
219 0.76
220 0.88
221 1.01
222 0.35
223 0.85
224 0.98
225 0.93
226 -0.48
227 -2.57
228 -0.41
229 -2.30
230 0.16
231 -0.24
232 -1.16
233 0.71
234 0.65
235 0.69
236 1.03
237 -0.28
238 0.70
239 -1.20
240 -0.34
241 1.04
242 0.98
243 0.21
244 0.72
245 0.50
246 0.57
247 0.08
248 -0.55
249 0.99
250 -0.02
251 1.07
252 1.17
253 -1.12
254 -1.68
255 0.00
#Reported_Model_Average 0.159
#Overall_Average_Reported 0.159
Output from Verify3D
Verify3D Score over a window of $winsize_s residues
JPEG image for Verify3D Score
Table of Verify3D scores for ordered residues across all models
#verify3d
#Residue\Model only_model
2 0.34
3 -0.94
4 0.17
5 0.55
6 0.59
7 0.49
8 -0.59
9 0.66
10 1.25
11 1.14
12 0.00
13 -1.13
14 0.49
15 -0.59
16 0.28
17 1.04
18 0.77
19 0.34
20 0.47
21 1.10
22 0.34
23 -0.33
24 -0.74
25 -0.57
26 0.49
27 1.29
28 -2.01
29 0.08
30 0.52
31 1.14
32 0.08
33 0.49
34 0.49
35 -1.13
36 -0.46
37 0.49
38 0.93
39 -2.12
40 0.77
41 0.77
42 1.00
43 -0.94
44 0.28
45 -0.26
46 0.41
47 0.29
48 0.00
49 0.28
50 0.93
51 0.55
52 0.41
53 0.51
54 -0.74
55 0.00
58 1.10
59 0.24
60 0.96
61 0.47
62 0.59
63 0.28
64 -0.56
65 1.06
66 -1.29
67 0.47
68 0.49
69 0.59
70 0.00
71 -0.33
72 1.06
73 0.00
74 0.34
75 0.51
76 -0.26
77 0.08
78 -0.59
79 0.93
80 0.64
81 -0.94
82 0.77
83 0.96
84 0.47
85 0.59
86 0.49
87 1.12
88 0.55
89 1.06
90 1.04
91 -0.74
92 0.28
93 1.10
94 0.71
95 0.20
96 0.28
97 -0.68
98 0.34
99 0.77
100 0.00
101 0.28
102 0.00
103 0.28
104 1.00
105 0.47
106 -0.10
107 0.29
108 0.08
109 0.28
110 0.51
111 1.00
112 0.24
113 0.47
114 1.06
115 1.00
116 -0.94
117 0.71
118 0.49
119 -0.74
120 0.41
121 0.59
122 -0.33
123 0.00
134 0.00
135 0.17
136 0.55
137 0.59
138 0.49
139 -0.59
140 1.00
141 1.14
142 1.14
143 0.28
144 -1.13
145 0.49
146 -0.59
147 0.28
148 1.04
149 0.29
150 0.34
151 0.47
152 1.10
153 0.34
154 0.77
155 -0.74
156 -0.57
157 0.49
158 1.29
159 0.28
160 -2.12
161 0.52
162 1.14
163 0.08
164 0.49
165 0.49
166 -1.13
167 -1.13
168 0.49
169 0.93
170 -2.12
171 1.06
172 0.77
173 1.00
174 -0.28
175 -0.59
176 -0.26
177 0.41
178 0.77
179 0.47
180 0.28
181 0.93
182 0.55
183 0.41
184 0.51
185 -0.40
186 0.00
187 0.00
188 0.00
189 1.10
190 -0.41
191 0.96
192 0.47
193 0.59
194 0.04
195 -0.26
196 0.77
197 0.71
198 0.47
199 0.49
200 0.59
201 0.47
202 -0.33
203 1.06
204 0.24
205 0.34
206 0.51
207 -0.26
208 0.08
209 -0.59
210 0.93
211 0.64
212 -0.94
213 1.06
214 0.96
215 0.47
216 0.59
217 0.49
218 1.12
219 0.55
220 1.06
221 0.54
222 -0.09
223 -0.59
224 1.10
225 -0.84
226 0.20
227 0.00
228 -1.14
229 0.00
230 0.77
231 0.00
232 0.28
233 0.00
234 0.28
235 1.00
236 0.47
237 0.47
238 0.29
239 -2.12
240 0.28
241 0.34
242 1.00
243 0.71
244 0.47
245 1.06
246 1.00
247 -0.94
248 0.71
249 0.49
250 -0.74
251 0.41
252 0.59
253 -0.33
254 0.28
255 0.00
#Reported_Model_Average 0.264
#Overall_Average_Reported 0.264
Output from ProsaII
ProsaII Score over a window of $winsize_s residues
JPEG image for ProsaII Score
Table of Verify3D scores for ordered residues across all models
#verify3d
#Residue\Model only_model
2 0.34
3 -0.94
4 0.17
5 0.55
6 0.59
7 0.49
8 -0.59
9 0.66
10 1.25
11 1.14
12 0.00
13 -1.13
14 0.49
15 -0.59
16 0.28
17 1.04
18 0.77
19 0.34
20 0.47
21 1.10
22 0.34
23 -0.33
24 -0.74
25 -0.57
26 0.49
27 1.29
28 -2.01
29 0.08
30 0.52
31 1.14
32 0.08
33 0.49
34 0.49
35 -1.13
36 -0.46
37 0.49
38 0.93
39 -2.12
40 0.77
41 0.77
42 1.00
43 -0.94
44 0.28
45 -0.26
46 0.41
47 0.29
48 0.00
49 0.28
50 0.93
51 0.55
52 0.41
53 0.51
54 -0.74
55 0.00
58 1.10
59 0.24
60 0.96
61 0.47
62 0.59
63 0.28
64 -0.56
65 1.06
66 -1.29
67 0.47
68 0.49
69 0.59
70 0.00
71 -0.33
72 1.06
73 0.00
74 0.34
75 0.51
76 -0.26
77 0.08
78 -0.59
79 0.93
80 0.64
81 -0.94
82 0.77
83 0.96
84 0.47
85 0.59
86 0.49
87 1.12
88 0.55
89 1.06
90 1.04
91 -0.74
92 0.28
93 1.10
94 0.71
95 0.20
96 0.28
97 -0.68
98 0.34
99 0.77
100 0.00
101 0.28
102 0.00
103 0.28
104 1.00
105 0.47
106 -0.10
107 0.29
108 0.08
109 0.28
110 0.51
111 1.00
112 0.24
113 0.47
114 1.06
115 1.00
116 -0.94
117 0.71
118 0.49
119 -0.74
120 0.41
121 0.59
122 -0.33
123 0.00
134 0.00
135 0.17
136 0.55
137 0.59
138 0.49
139 -0.59
140 1.00
141 1.14
142 1.14
143 0.28
144 -1.13
145 0.49
146 -0.59
147 0.28
148 1.04
149 0.29
150 0.34
151 0.47
152 1.10
153 0.34
154 0.77
155 -0.74
156 -0.57
157 0.49
158 1.29
159 0.28
160 -2.12
161 0.52
162 1.14
163 0.08
164 0.49
165 0.49
166 -1.13
167 -1.13
168 0.49
169 0.93
170 -2.12
171 1.06
172 0.77
173 1.00
174 -0.28
175 -0.59
176 -0.26
177 0.41
178 0.77
179 0.47
180 0.28
181 0.93
182 0.55
183 0.41
184 0.51
185 -0.40
186 0.00
187 0.00
188 0.00
189 1.10
190 -0.41
191 0.96
192 0.47
193 0.59
194 0.04
195 -0.26
196 0.77
197 0.71
198 0.47
199 0.49
200 0.59
201 0.47
202 -0.33
203 1.06
204 0.24
205 0.34
206 0.51
207 -0.26
208 0.08
209 -0.59
210 0.93
211 0.64
212 -0.94
213 1.06
214 0.96
215 0.47
216 0.59
217 0.49
218 1.12
219 0.55
220 1.06
221 0.54
222 -0.09
223 -0.59
224 1.10
225 -0.84
226 0.20
227 0.00
228 -1.14
229 0.00
230 0.77
231 0.00
232 0.28
233 0.00
234 0.28
235 1.00
236 0.47
237 0.47
238 0.29
239 -2.12
240 0.28
241 0.34
242 1.00
243 0.71
244 0.47
245 1.06
246 1.00
247 -0.94
248 0.71
249 0.49
250 -0.74
251 0.41
252 0.59
253 -0.33
254 0.28
255 0.00
#Reported_Model_Average 0.264
#Overall_Average_Reported 0.264
Output from MolProbity
VdW violations from MAGE
JPEG image for MAGE VdW violation
Table of MAGE VdW violations for ordered residues across all models
#mage_clash
#Residue\Model only_model
2.000 0
3.000 0
4.000 0
5.000 0
6.000 0
7.000 0
8.000 0
9.000 1
10.000 0
11.000 0
12.000 0
13.000 1
14.000 2
15.000 1
16.000 0
17.000 1
18.000 1
19.000 0
20.000 0
21.000 0
22.000 0
23.000 0
24.000 0
25.000 0
26.000 0
27.000 0
28.000 0
29.000 2
30.000 3
31.000 1
32.000 0
33.000 0
34.000 0
35.000 1
36.000 0
37.000 0
38.000 1
39.000 4
40.000 2
41.000 2
42.000 2
43.000 1
44.000 1
45.000 2
46.000 0
47.000 1
48.000 1
49.000 0
50.000 3
51.000 2
52.000 0
53.000 0
54.000 1
55.000 0
56.000 0
57.000 0
58.000 0
59.000 0
60.000 2
61.000 1
62.000 1
63.000 1
64.000 2
65.000 1
66.000 0
67.000 2
68.000 2
69.000 1
70.000 0
71.000 1
72.000 1
73.000 0
74.000 0
75.000 2
76.000 0
77.000 0
78.000 3
79.000 5
80.000 6
81.000 1
82.000 1
83.000 0
84.000 0
85.000 0
86.000 0
87.000 0
88.000 0
89.000 0
90.000 1
91.000 0
92.000 1
93.000 0
94.000 0
95.000 0
96.000 1
97.000 0
98.000 0
99.000 0
100.000 1
101.000 2
102.000 0
103.000 0
104.000 2
105.000 4
106.000 0
107.000 0
108.000 5
109.000 0
110.000 0
111.000 1
112.000 0
113.000 0
114.000 0
115.000 1
116.000 1
117.000 1
118.000 3
119.000 0
120.000 0
121.000 0
122.000 2
123.000 0
124.000 0
125.000 0
126.000 0
127.000 0
128.000 0
129.000 0
130.000 0
131.000 0
132.000 0
133.000 0
134.000 0
135.000 0
136.000 1
137.000 0
138.000 0
139.000 0
140.000 1
141.000 0
142.000 0
143.000 1
144.000 1
145.000 0
146.000 0
147.000 1
148.000 1
149.000 0
150.000 0
151.000 0
152.000 0
153.000 0
154.000 0
155.000 0
156.000 0
157.000 0
158.000 0
159.000 0
160.000 0
161.000 0
162.000 2
163.000 0
164.000 0
165.000 0
166.000 2
167.000 0
168.000 0
169.000 0
170.000 1
171.000 0
172.000 2
173.000 0
174.000 0
175.000 0
176.000 0
177.000 0
178.000 0
179.000 1
180.000 0
181.000 0
182.000 1
183.000 0
184.000 0
185.000 1
186.000 0
187.000 1
188.000 0
189.000 0
190.000 0
191.000 0
192.000 0
193.000 0
194.000 0
195.000 0
196.000 1
197.000 0
198.000 0
199.000 0
200.000 0
201.000 0
202.000 0
203.000 0
204.000 0
205.000 0
206.000 0
207.000 0
208.000 0
209.000 1
210.000 0
211.000 0
212.000 0
213.000 1
214.000 0
215.000 2
216.000 0
217.000 0
218.000 0
219.000 0
220.000 0
221.000 2
222.000 1
223.000 0
224.000 0
225.000 1
226.000 0
227.000 0
228.000 0
229.000 0
230.000 0
231.000 0
232.000 0
233.000 0
234.000 0
235.000 0
236.000 0
237.000 0
238.000 0
239.000 0
240.000 0
241.000 0
242.000 1
243.000 0
244.000 1
245.000 0
246.000 1
247.000 1
248.000 0
249.000 2
250.000 0
251.000 0
252.000 0
253.000 0
254.000 0
255.000 0
#Reported_Model_Average 0.504
#Overall_Average_Reported 0.504
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 3788:M 122 LEU 1HD2 :M 40 LEU 1HD1 : -0.783: 80
: 3788:M 40 LEU 3HD2 :M 118 ALA 1HB : -0.573: 57
: 3788:M 122 LEU 3HD2 :M 44 GLU CD : -0.500: 81
: 3788:M 41 LEU 1HD2 :M 118 ALA HA : -0.452: 58
: 3788:M 41 LEU CD2 :M 118 ALA HA : -0.427: 58
: 3788:M 45 ASN 1HD2 :M 75 ASN 2HD2 : -0.747: 93
: 3788:M 45 ASN 1HD2 :M 75 ASN ND2 : -0.435: 93
: 3788:M 79 ILE 3HD1 :M 80 PRO 2HD : -0.681: 75
: 3788:M 79 ILE 3HD1 :M 80 PRO CD : -0.654: 75
: 3788:M 80 PRO 2HD :M 79 ILE CD1 : -0.583: 75
: 3788:M 72 LEU C :M 79 ILE 1HD1 : -0.542: 75
: 3788:M 78 GLU O :M 82 LEU 3HD1 : -0.520: 53
: 3788:M 80 PRO HA :M 69 SER 2HB : -0.501: 58
: 3788:M 79 ILE N :M 80 PRO 1HD : -0.480: 55
: 3788:M 78 GLU O :M 81 ILE 2HG1 : -0.445: 64
: 3788:M 80 PRO 1HD :M 78 GLU C : -0.413: 55
: 3788:M 166 GLU 2HG :M 196 LEU 1HD2 : -0.656: 51
: 3788:M 166 GLU 1HG :M 170 LYS 2HE : -0.415: 52
: 3788:M 215 LYS 2HE :M 215 LYS HA : -0.655: 66
: 3788:M 68 ALA 2HB :M 50 ILE CD1 : -0.649: 99
: 3788:M 64 ASN 2HB :M 50 ILE 1HD1 : -0.553: 99
: 3788:M 68 ALA 2HB :M 50 ILE 2HD1 : -0.502: 99
: 3788:M 64 ASN 2HD2 :M 61 LYS 1HB : -0.449: 79
: 3788:M 213 LEU 2HD2 :M 209 GLU O : -0.620: 52
: 3788:M 92 GLU HA :M 96 GLU 1HB : -0.619: 76
: 3788:M 105 LYS HA :M 108 LYS 2HD : -0.586: 51
: 3788:M 105 LYS 2HE :M 101 GLU CD : -0.581: 90
: 3788:M 108 LYS 1HE :M 15 GLU OE1 : -0.517: 57
: 3788:M 30 TYR OH :M 18 LEU 2HD1 : -0.491: 52
: 3788:M 108 LYS CD :M 105 LYS HA : -0.464: 51
: 3788:M 30 TYR CD2 :M 14 ALA 1HB : -0.460: 45
: 3788:M 17 PHE CE2 :M 29 LYS 2HD : -0.447: 59
: 3788:M 14 ALA 2HB :M 29 LYS 2HB : -0.440: 48
: 3788:M 104 VAL O :M 108 LYS 2HB : -0.427: 46
: 3788:M 101 GLU O :M 105 LYS 2HG : -0.422: 70
: 3788:M 104 VAL 3HG2 :M 100 ASN O : -0.413: 68
: 3788:M 108 LYS 2HG :M 30 TYR CE1 : -0.413: 46
: 3788:M 185 VAL C :M 187 ASN H : -0.576: 94
: 3788:M 147 GLU 2HG :M 143 GLU O : -0.570: 55
: 3788:M 65 LEU 3HD2 :M 62 SER HA : -0.566: 67
: 3788:M 48 LYS HA :M 51 THR OG1 : -0.559: 99
: 3788:M 54 VAL 3HG2 :M 51 THR HA : -0.421: 99
: 3788:M 179 LYS HA :M 182 THR OG1 : -0.544: 67
: 3788:M 13 GLU 2HG :M 9 VAL O : -0.539: 57
: 3788:M 39 LYS 1HE :M 60 TRP CD1 : -0.534: 71
: 3788:M 39 LYS O :M 43 ILE 1HG1 : -0.520: 74
: 3788:M 60 TRP CZ2 :M 39 LYS 1HG : -0.477: 70
: 3788:M 39 LYS 2HE :M 35 GLU 1HG : -0.475: 55
: 3788:M 42 VAL 3HG2 :M 38 ILE O : -0.533: 53
: 3788:M 42 VAL 3HG1 :M 47 LEU 1HB : -0.430: 87
: 3788:M 148 PHE CE2 :M 144 GLU 1HG : -0.517: 58
: 3788:M 222 VAL O :M 225 PHE 2HB : -0.509: 63
: 3788:M 221 HIS 1HB :M 162 TYR CD1 : -0.506: 37
: 3788:M 221 HIS 1HB :M 162 TYR CG : -0.467: 41
: 3788:M 71 LEU 3HD1 :M 67 LYS O : -0.499: 82
: 3788:M 67 LYS 2HG :M 63 GLU O : -0.419: 61
: 3788:M 136 THR O :M 140 VAL 3HG2 : -0.448: 43
: 3788:M 244 LYS HA :M 247 ILE 1HG1 : -0.437: 66
: 3788:M 90 HIS 1HB :M 31 TYR CD1 : -0.431: 51
: 3788:M 111 VAL O :M 115 VAL 3HG2 : -0.427: 50
: 3788:M 246 VAL 3HG2 :M 242 VAL O : -0.426: 43
: 3788:M 117 PHE N :M 116 ILE 2HG1 : -0.425: 72
: 3788:M 172 LEU CD2 :M 249 ALA HA : -0.409: 48
: 3788:M 249 ALA HA :M 172 LEU 1HD2 : -0.402: 48
#sum2 ::16.90 clashscore : 2.58 clashscore B<40
#summary::3788 atoms:387 atoms B<40:427639 potential dots:26730.0 A^2:64 bumps:1 bumps B<40:1373 score
Output from PDB validation software
Summary from PDB validation
May. 11, 00:57:07 2013
Greetings,
[ Text modified to reflect that this was run under PSVS - Aneerban Bhattacharya: Dec 2005 ]
The following checks were made on :
-----------------------------------------
DISTANCES AND ANGLES
We have checked your intra and intermolecular distances and angles with the
procedures currently in place at PDB:
==> The following solvent molecules are further away than 3.5 Angstroms from
macromolecule atoms which are available for hydrogen bonding in the
asymmetric unit.
none
The coordinates for water molecules which could be translated back into
the asymmetric unit are listed. If you do not indicate otherwise we will
replace the solvent coordinates in the entry with the ones below:
none
==> Close contacts in same asymmetric unit. Distances smaller than 2.2
Angstroms are considered as close contacts.
none
==> Close contacts based on crystal symmetry. Distances smaller than 2.2
Angstroms are considered as close contacts.
none
==> Bond and angle checks are performed by first computing the average rms
error for all bonds and angles relative to standard values for nucleotide
units [L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous
Bases, J.Am.Chem.Soc. 1996, 118, 509-518; A. Gelbin et al., Geometric
Parameters in Nucleic Acids: Sugar and Phosphate Constituents, J.Am.Chem.Soc.
1996, 118, 519-529] and amino acid units [R.A. Engh and R. Huber, Accurate
Bond and Angle Parameters for X-ray protein structure refinement, Acta
Crystallogr. 1991, A47, 392-400]. Any bond or angle which deviates from the
dictionary values by more than six times this computed rms error is
identified as an outlier.
*** Covalent Bond Lengths:
The RMS deviation for covalent bonds relative to the standard
dictionary is 0.008 Angstroms
All covalent bonds lie within a 6.0*RMSD range about the
standard dictionary values.
*** Covalent Angle Values:
The RMS deviation for covalent angles relative to the standard
dictionary is 1.1 degrees.
The following table contains a list of the covalent bond angles
greater than 6.0*RMSD.
Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary
Name ID Number Angle Value
--------------------------------------------------------------------------------
9.0 GLU A 78 N - CA - C 120.2 111.2
-7.9 PRO A 80 C - N - CA 114.7 122.6
7.0 ILE B 79 N - CA - C 118.2 111.2
7.7 LEU B 82 CA - CB - CG 124.0 116.3
9.3 GLU B 123 N - CA - C 120.5 111.2
TORSION ANGLES
The torsion angle distributions have been checked. The postscript file of the
conformation rings showing the torsion angle distributions will be sent in a
separate E-mail message.
CHIRALITY
The chirality has been checked and there are no incorrect carbon chiral centers.
Some of O1P and O2P atoms do not follow the convention defined in the standard
IUBMB nomenclature (Liebecq, C. Compendium of Biochemical Nomenclature and Related
Documents, 2nd ed.; Portland Press: London and Chapel Hill, 1992). If you do not
indicate otherwise, we will switch the labels of O1P and O2P as shown below.
OTHER IMPORTANT ISSUES
==> Please check carefully REMARKS 3 and 200 and fill in the parameters as
appropriate.
SEQUENCE WARNING: Residue (A LYS 55 ) and Residue (A GLY 58 ) are not linked
Distance of C-N bond is 7.06
==> The following residues have missing atoms:
RES MOD#C SEQ ATOMS
GLU( A 12) CG CD OE1 OE2
LYS( A 48) CG CD CE NZ
LYS( A 55) CG CD CE NZ
LYS( A 70) CG CD CE NZ
ARG( A 73) CG CD NE CZ NH1 NH2
ASN( A 100) CG OD1 ND2
LYS( A 102) CG CD CE NZ
GLU( A 123) CG CD OE1 OE2
ILE( B 3) CG1 CG2 CD1
LYS( B 55) CG CD CE NZ
ASN( B 56) CG OD1 ND2
LYS( B 57) CG CD CE NZ
GLU( B 96) CG CD OE1 OE2
SER( B 98) OG
ASN( B 100) CG OD1 ND2
LYS( B 102) CG CD CE NZ
HIS( B 124) CG ND1 CD2 CE1 NE2
SSR10_XRay_em_bcr3.pdb: Error: Z value is 32. It should be 16.