Detailed results of DRR147D_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 >>>----------+
| |
| DRR147D_XRay_em_bcr3_noHs_000.rin 0.0 260 residues |
| |
+| Ramachandran plot: 89.7% core 9.3% allow 0.9% gener 0.0% disall |
| |
*| All Ramachandrans: 10 labelled residues (out of 252) |
+| Chi1-chi2 plots: 2 labelled residues (out of 136) |
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
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
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
4 0.31
5 0.57
6 -0.51
7 -0.51
8 -0.39
9 -0.32
10 0.42
11 0.31
12 -2.67
13 -0.48
14 0.40
15 0.80
16 0.87
17 0.90
18 0.84
19 1.17
20 0.58
21 0.98
22 0.60
23 -0.10
24 -0.38
25 0.88
26 0.35
27 -0.20
28 0.50
29 -0.33
30 0.04
31 0.04
32 -1.55
33 -3.61
34 0.27
35 -0.22
36 -1.19
37 -1.24
38 -0.40
39 -0.52
40 -0.32
41 -0.96
42 -1.09
43 0.39
44 -1.27
45 -0.48
46 0.03
47 -0.52
48 -0.56
49 0.13
50 -0.05
51 -0.59
52 -1.08
53 -1.55
54 -0.16
55 -1.74
56 0.09
57 -2.46
58 -0.07
59 -0.03
60 0.18
61 -0.36
62 -0.61
63 -0.55
64 -0.62
65 -0.18
66 -0.25
67 -0.93
68 -1.24
69 -1.69
70 -1.55
71 0.51
72 -3.52
73 -1.22
74 -0.21
75 -0.53
76 0.05
77 -0.90
78 0.11
79 -0.70
80 0.03
81 0.45
82 -0.66
83 -1.96
84 -0.46
85 -0.85
86 -0.72
87 0.03
88 -0.37
89 -1.46
90 0.57
91 -0.31
92 -0.81
93 -0.17
94 0.40
95 -0.39
96 0.07
97 -3.49
98 -3.46
99 -1.76
100 -0.37
101 0.49
102 -0.43
103 -0.13
104 0.31
105 0.57
106 -0.72
107 -0.31
108 0.13
109 -0.83
128 -0.58
129 0.95
130 1.23
131 0.90
132 0.84
133 0.36
134 1.14
135 1.08
136 1.13
137 1.12
138 0.90
139 1.22
140 0.29
141 0.90
142 0.72
143 1.01
144 0.05
145 -1.19
146 -0.83
159 -3.61
160 0.10
161 -0.03
162 -0.64
163 -0.51
164 -0.39
165 -0.32
166 0.24
167 0.20
168 -2.67
169 -0.28
170 0.62
171 0.66
172 0.09
173 0.85
174 1.13
175 1.22
176 0.82
177 0.30
178 0.73
179 0.33
180 -0.46
181 0.09
182 0.35
183 -0.08
184 0.88
185 -0.33
186 -0.02
187 -0.24
188 -1.45
189 -0.12
190 0.27
191 -0.31
192 -1.60
193 0.03
194 -0.40
195 -0.74
196 -0.42
197 -1.84
198 -2.86
199 -0.97
200 -1.27
201 -0.56
202 0.13
203 -0.44
204 -0.91
205 -0.57
206 -0.05
207 -0.91
208 -0.72
209 -0.91
210 -1.02
211 -0.58
212 -3.77
213 -3.49
214 -2.54
215 0.57
216 -0.13
217 -0.27
218 -0.49
219 -1.08
220 -0.43
221 -0.27
222 -0.03
223 -2.00
224 -1.28
225 -1.46
226 -1.55
227 -0.01
228 -3.52
229 -0.92
230 -0.21
231 -0.54
232 -0.25
233 -1.60
234 0.11
235 -0.70
236 0.62
237 0.91
238 -0.45
239 0.60
240 -0.61
241 -0.39
242 -0.84
243 -0.04
244 -0.37
245 -1.05
246 0.38
247 -0.49
248 -1.00
249 -0.39
250 -0.59
251 -0.77
252 -2.64
253 -3.49
254 -3.46
255 -2.93
256 -0.79
257 0.51
258 -0.84
259 -0.27
260 0.53
261 0.57
262 -0.72
263 -0.31
264 -0.01
265 0.37
266 -2.09
267 -0.61
285 0.75
286 0.90
287 1.23
288 0.99
289 0.90
290 1.01
291 1.14
292 1.13
293 1.12
294 1.14
295 1.05
296 0.37
297 0.90
298 0.87
299 1.04
300 0.44
301 -0.82
302 1.03
#Reported_Model_Average -0.342
#Overall_Average_Reported -0.342
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
3 -0.88
4 0.23
5 0.58
6 -1.68
7 -1.08
8 -0.39
9 0.14
10 0.53
11 0.56
12 -2.67
13 -0.15
14 0.40
15 0.80
16 -0.08
17 0.79
18 0.86
19 0.59
20 0.58
21 0.74
22 0.59
23 -0.43
24 -0.58
25 0.56
26 0.35
27 -0.20
28 0.53
29 -0.33
30 -0.60
31 0.46
32 -0.33
33 -1.27
34 0.14
35 0.17
36 -0.29
37 0.11
38 0.23
39 0.13
40 0.28
41 -0.04
42 -0.82
43 -0.90
44 -0.28
45 0.30
46 -0.34
47 0.05
48 -1.97
49 0.45
50 -0.15
51 -0.11
52 -1.08
53 -1.55
54 -0.16
55 -1.74
56 0.50
57 -2.46
58 -0.47
59 0.28
60 0.07
61 -0.46
62 -0.90
63 -0.55
64 0.13
65 0.35
66 0.02
67 -0.93
68 -0.70
69 -0.53
70 -1.55
71 0.51
72 -1.23
73 -1.15
74 0.33
75 -0.53
76 -0.10
77 -1.26
78 -0.30
79 -0.76
80 0.03
81 0.45
82 -0.66
83 -1.96
84 -0.09
85 -1.15
86 -0.98
87 -0.34
88 -0.37
89 -0.34
90 0.01
91 0.28
92 0.05
93 -0.65
94 0.40
95 -0.39
96 0.07
97 -3.49
98 -3.46
99 -1.93
100 -0.37
101 0.63
102 0.00
103 0.13
104 0.49
105 0.69
106 0.05
107 0.10
108 -0.37
109 -0.83
110 0.00
127 0.00
128 -0.58
129 1.00
130 0.68
131 0.34
132 0.69
133 -0.23
134 1.14
135 1.11
136 1.02
137 0.96
138 0.68
139 0.19
140 0.10
141 0.72
142 0.99
143 0.74
144 -0.04
145 -0.16
146 -0.83
147 0.00
158 0.00
159 -1.32
160 0.04
161 -0.03
162 -0.64
163 -0.82
164 -0.39
165 -0.70
166 0.15
167 0.54
168 -2.67
169 -0.05
170 0.62
171 0.66
172 0.38
173 0.66
174 1.00
175 -0.57
176 0.82
177 0.52
178 0.55
179 -0.21
180 -0.76
181 0.16
182 0.35
183 -0.08
184 0.75
185 -0.33
186 0.29
187 0.32
188 -1.20
189 0.09
190 -0.18
191 0.28
192 -0.64
193 0.45
194 0.00
195 -0.42
196 0.16
197 -0.49
198 -2.39
199 0.10
200 -0.38
201 0.25
202 0.05
203 -1.09
204 -2.15
205 -0.26
206 -0.04
207 -0.27
208 -0.72
209 -0.91
210 -1.02
211 -0.58
212 -1.62
213 -3.49
214 -1.71
215 0.77
216 0.37
217 -0.38
218 0.03
219 -1.08
220 -0.57
221 0.32
222 0.37
223 -2.00
224 -0.71
225 -0.53
226 -1.55
227 -0.01
228 -1.28
229 -1.27
230 0.04
231 -0.54
232 -0.37
233 -0.87
234 0.04
235 -0.81
236 0.62
237 0.91
238 -0.45
239 0.89
240 -0.31
241 -0.01
242 -1.36
243 0.42
244 -0.37
245 -0.19
246 -0.09
247 0.19
248 -0.04
249 -0.60
250 -0.59
251 -0.77
252 -2.64
253 -3.49
254 -3.46
255 -2.93
256 -0.79
257 0.57
258 -0.20
259 0.16
260 0.70
261 0.58
262 0.04
263 -0.24
264 0.02
265 0.37
266 -2.09
267 -0.61
268 0.00
284 0.00
285 0.90
286 0.53
287 -0.27
288 0.76
289 0.33
290 1.10
291 1.20
292 0.88
293 1.10
294 1.03
295 0.44
296 0.40
297 0.76
298 0.95
299 0.53
300 -0.01
301 0.05
302 1.03
303 -1.94
#Reported_Model_Average -0.235
#Overall_Average_Reported -0.235
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
3 0.08
4 -0.74
5 -0.09
6 0.24
7 0.51
8 -0.25
9 0.66
10 0.08
11 0.93
12 1.10
13 0.47
14 0.44
15 0.49
16 0.28
17 0.25
18 1.06
19 1.14
20 0.14
21 -0.09
22 0.96
23 0.71
24 0.23
25 0.77
26 0.44
27 1.10
28 1.06
29 -0.11
30 -0.68
31 1.06
32 0.91
33 0.08
34 -1.21
35 1.06
36 0.71
37 0.34
38 1.00
39 0.28
40 -0.74
41 0.29
42 0.51
43 0.23
44 0.47
45 0.71
46 0.59
47 0.24
48 0.96
49 0.08
50 -0.09
51 0.28
52 0.49
53 0.25
54 0.14
55 0.25
56 -0.68
57 1.10
58 0.08
59 -0.09
60 0.17
61 1.62
62 0.28
63 0.49
64 -1.13
65 0.77
66 0.08
67 -0.25
68 0.51
69 0.28
70 0.44
71 1.10
72 -0.10
73 0.71
74 0.93
75 -0.25
76 0.96
77 0.24
78 0.59
79 -0.68
80 0.25
81 1.10
82 -0.25
83 0.00
84 -0.28
85 0.28
86 -0.26
87 0.17
88 1.10
89 -0.59
90 1.00
91 0.29
92 1.40
93 0.71
94 0.25
95 0.49
96 0.25
97 1.10
98 0.14
99 0.24
100 1.10
101 0.55
102 -0.46
103 1.00
104 -0.40
105 1.00
106 -0.88
107 0.77
108 0.08
109 0.00
110 0.00
127 0.00
128 0.25
129 0.34
130 0.25
131 0.25
132 1.06
133 0.71
134 0.51
135 -0.83
136 1.06
137 -0.83
138 0.71
139 1.40
140 0.08
141 0.71
142 -0.59
143 -0.87
144 0.28
145 0.29
146 1.10
147 0.00
158 0.00
159 0.08
160 -0.74
161 0.66
162 0.00
163 0.51
164 -0.25
165 -0.09
166 0.08
167 0.93
168 1.10
169 0.47
170 0.25
171 0.49
172 0.04
173 0.25
174 1.06
175 1.14
176 0.14
177 -0.09
178 0.96
179 0.71
180 0.23
181 0.77
182 0.44
183 1.10
184 1.06
185 -0.11
186 -0.68
187 1.06
188 0.91
189 0.08
190 -1.21
191 1.06
192 0.71
193 0.17
194 1.00
195 0.28
196 -0.09
197 0.29
198 0.51
199 0.23
200 0.47
201 0.71
202 0.59
203 0.71
204 0.96
205 0.55
206 -0.09
207 0.28
208 0.49
209 0.00
210 0.14
211 0.00
212 -0.68
213 1.10
214 0.08
215 -0.09
216 0.59
217 1.62
218 -0.46
219 0.49
220 -0.59
221 0.29
222 0.08
223 -0.25
224 0.51
225 0.28
226 0.44
227 1.10
228 0.47
229 0.71
230 0.93
231 0.49
232 0.96
233 0.24
234 0.59
235 -0.68
236 0.25
237 1.10
238 -0.25
239 0.24
240 0.81
241 0.04
242 -0.26
243 0.17
244 1.10
245 -0.59
246 1.00
247 0.29
248 1.40
249 0.24
250 0.25
251 0.49
252 0.25
253 1.10
254 0.14
255 0.00
256 1.10
257 0.55
258 -0.46
259 1.00
260 -0.09
261 1.00
262 0.24
263 0.77
264 0.08
265 0.00
266 0.00
267 0.00
268 0.00
284 0.00
285 0.34
286 -0.03
287 0.25
288 1.06
289 0.24
290 0.51
291 0.51
292 1.06
293 -0.83
294 0.71
295 1.40
296 0.47
297 0.71
298 0.28
299 -0.87
300 -0.59
301 0.29
302 1.10
303 0.77
#Reported_Model_Average 0.351
#Overall_Average_Reported 0.351
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
3 0.08
4 -0.74
5 -0.09
6 0.24
7 0.51
8 -0.25
9 0.66
10 0.08
11 0.93
12 1.10
13 0.47
14 0.44
15 0.49
16 0.28
17 0.25
18 1.06
19 1.14
20 0.14
21 -0.09
22 0.96
23 0.71
24 0.23
25 0.77
26 0.44
27 1.10
28 1.06
29 -0.11
30 -0.68
31 1.06
32 0.91
33 0.08
34 -1.21
35 1.06
36 0.71
37 0.34
38 1.00
39 0.28
40 -0.74
41 0.29
42 0.51
43 0.23
44 0.47
45 0.71
46 0.59
47 0.24
48 0.96
49 0.08
50 -0.09
51 0.28
52 0.49
53 0.25
54 0.14
55 0.25
56 -0.68
57 1.10
58 0.08
59 -0.09
60 0.17
61 1.62
62 0.28
63 0.49
64 -1.13
65 0.77
66 0.08
67 -0.25
68 0.51
69 0.28
70 0.44
71 1.10
72 -0.10
73 0.71
74 0.93
75 -0.25
76 0.96
77 0.24
78 0.59
79 -0.68
80 0.25
81 1.10
82 -0.25
83 0.00
84 -0.28
85 0.28
86 -0.26
87 0.17
88 1.10
89 -0.59
90 1.00
91 0.29
92 1.40
93 0.71
94 0.25
95 0.49
96 0.25
97 1.10
98 0.14
99 0.24
100 1.10
101 0.55
102 -0.46
103 1.00
104 -0.40
105 1.00
106 -0.88
107 0.77
108 0.08
109 0.00
110 0.00
127 0.00
128 0.25
129 0.34
130 0.25
131 0.25
132 1.06
133 0.71
134 0.51
135 -0.83
136 1.06
137 -0.83
138 0.71
139 1.40
140 0.08
141 0.71
142 -0.59
143 -0.87
144 0.28
145 0.29
146 1.10
147 0.00
158 0.00
159 0.08
160 -0.74
161 0.66
162 0.00
163 0.51
164 -0.25
165 -0.09
166 0.08
167 0.93
168 1.10
169 0.47
170 0.25
171 0.49
172 0.04
173 0.25
174 1.06
175 1.14
176 0.14
177 -0.09
178 0.96
179 0.71
180 0.23
181 0.77
182 0.44
183 1.10
184 1.06
185 -0.11
186 -0.68
187 1.06
188 0.91
189 0.08
190 -1.21
191 1.06
192 0.71
193 0.17
194 1.00
195 0.28
196 -0.09
197 0.29
198 0.51
199 0.23
200 0.47
201 0.71
202 0.59
203 0.71
204 0.96
205 0.55
206 -0.09
207 0.28
208 0.49
209 0.00
210 0.14
211 0.00
212 -0.68
213 1.10
214 0.08
215 -0.09
216 0.59
217 1.62
218 -0.46
219 0.49
220 -0.59
221 0.29
222 0.08
223 -0.25
224 0.51
225 0.28
226 0.44
227 1.10
228 0.47
229 0.71
230 0.93
231 0.49
232 0.96
233 0.24
234 0.59
235 -0.68
236 0.25
237 1.10
238 -0.25
239 0.24
240 0.81
241 0.04
242 -0.26
243 0.17
244 1.10
245 -0.59
246 1.00
247 0.29
248 1.40
249 0.24
250 0.25
251 0.49
252 0.25
253 1.10
254 0.14
255 0.00
256 1.10
257 0.55
258 -0.46
259 1.00
260 -0.09
261 1.00
262 0.24
263 0.77
264 0.08
265 0.00
266 0.00
267 0.00
268 0.00
284 0.00
285 0.34
286 -0.03
287 0.25
288 1.06
289 0.24
290 0.51
291 0.51
292 1.06
293 -0.83
294 0.71
295 1.40
296 0.47
297 0.71
298 0.28
299 -0.87
300 -0.59
301 0.29
302 1.10
303 0.77
#Reported_Model_Average 0.351
#Overall_Average_Reported 0.351
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
3.000 0
4.000 2
5.000 0
6.000 0
7.000 1
8.000 0
9.000 1
10.000 1
11.000 1
12.000 0
13.000 0
14.000 0
15.000 0
16.000 0
17.000 0
18.000 0
19.000 1
20.000 0
21.000 0
22.000 2
23.000 0
24.000 1
25.000 0
26.000 1
27.000 0
28.000 1
29.000 2
30.000 3
31.000 2
32.000 5
33.000 0
34.000 1
35.000 0
36.000 0
37.000 1
38.000 0
39.000 0
40.000 0
41.000 0
42.000 2
43.000 0
44.000 5
45.000 1
46.000 0
47.000 0
48.000 0
49.000 0
50.000 0
51.000 0
52.000 1
53.000 1
54.000 0
55.000 0
56.000 0
57.000 0
58.000 0
59.000 0
60.000 0
61.000 1
62.000 0
63.000 0
64.000 8
65.000 1
66.000 0
67.000 0
68.000 0
69.000 0
70.000 1
71.000 0
72.000 0
73.000 1
74.000 0
75.000 0
76.000 1
77.000 0
78.000 1
79.000 3
80.000 0
81.000 0
82.000 2
83.000 0
84.000 0
85.000 1
86.000 0
87.000 0
88.000 1
89.000 0
90.000 1
91.000 1
92.000 0
93.000 0
94.000 0
95.000 0
96.000 0
97.000 0
98.000 0
99.000 6
100.000 0
101.000 0
102.000 0
103.000 0
104.000 0
105.000 0
106.000 2
107.000 4
108.000 0
109.000 1
110.000 0
111.000 0
112.000 0
113.000 0
114.000 0
115.000 0
116.000 0
117.000 0
118.000 0
119.000 0
120.000 0
121.000 0
122.000 0
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 1
134.000 0
135.000 1
136.000 0
137.000 0
138.000 0
139.000 0
140.000 3
141.000 0
142.000 0
143.000 0
144.000 0
145.000 0
146.000 0
147.000 0
148.000 0
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 1
163.000 1
164.000 1
165.000 1
166.000 2
167.000 1
168.000 0
169.000 0
170.000 0
171.000 0
172.000 0
173.000 0
174.000 0
175.000 2
176.000 0
177.000 1
178.000 1
179.000 0
180.000 0
181.000 1
182.000 1
183.000 0
184.000 1
185.000 1
186.000 0
187.000 2
188.000 6
189.000 0
190.000 2
191.000 1
192.000 0
193.000 0
194.000 0
195.000 0
196.000 0
197.000 0
198.000 1
199.000 0
200.000 0
201.000 2
202.000 0
203.000 0
204.000 1
205.000 1
206.000 1
207.000 0
208.000 4
209.000 0
210.000 0
211.000 0
212.000 2
213.000 1
214.000 1
215.000 1
216.000 1
217.000 0
218.000 1
219.000 0
220.000 1
221.000 0
222.000 2
223.000 0
224.000 0
225.000 1
226.000 1
227.000 0
228.000 0
229.000 1
230.000 0
231.000 0
232.000 2
233.000 0
234.000 0
235.000 1
236.000 0
237.000 0
238.000 0
239.000 1
240.000 2
241.000 0
242.000 0
243.000 1
244.000 2
245.000 0
246.000 2
247.000 0
248.000 1
249.000 0
250.000 0
251.000 0
252.000 1
253.000 1
254.000 0
255.000 0
256.000 0
257.000 0
258.000 1
259.000 1
260.000 1
261.000 1
262.000 0
263.000 4
264.000 1
265.000 0
266.000 0
267.000 1
268.000 0
269.000 0
270.000 0
271.000 0
272.000 0
273.000 0
274.000 0
275.000 0
276.000 0
277.000 0
278.000 0
279.000 0
280.000 0
281.000 0
282.000 0
283.000 0
284.000 0
285.000 0
286.000 0
287.000 0
288.000 0
289.000 0
290.000 0
291.000 1
292.000 1
293.000 0
294.000 0
295.000 0
296.000 4
297.000 0
298.000 2
299.000 0
300.000 1
301.000 2
302.000 0
303.000 9
#Reported_Model_Average 0.565
#Overall_Average_Reported 0.565
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 3976:M 32 MET 2HE :M 107 LEU 1HD1 : -1.121: 29
: 3976:M 32 MET 1HE :M 107 LEU 1HD2 : -0.832: 29
: 3976:M 32 MET CE :M 107 LEU 1HD2 : -0.731: 29
: 3976:M 32 MET 2HE :M 107 LEU CD1 : -0.627: 29
: 3976:M 32 MET 2HB :M 34 HIS CE1 : -0.460: 24
: 3976:M 79 LEU 1HD1 :M 64 GLU 2HG : -1.028: 34
: 3976:M 79 LEU 1HD1 :M 64 GLU CG : -0.768: 34
: 3976:M 64 GLU 2HB :M 44 LYS 1HE : -0.755: 28
: 3976:M 65 LEU O :M 44 LYS 2HE : -0.728: 28
: 3976:M 64 GLU 2HG :M 79 LEU CD1 : -0.708: 34
: 3976:M 44 LYS 1HG :M 64 GLU 2HB : -0.643: 27
: 3976:M 64 GLU 1HG :M 45 ARG 1HG : -0.566: 31
: 3976:M 64 GLU CB :M 44 LYS 1HE : -0.520: 28
: 3976:M 44 LYS O :M 64 GLU HA : -0.475: 23
: 3976:M 188 MET 1HE :M 263 LEU 1HD2 : -0.989: 34
: 3976:M 188 MET 2HE :M 263 LEU 1HD1 : -0.869: 34
: 3976:M 188 MET 2HB :M 190 HIS CE1 : -0.705: 32
: 3976:M 188 MET CE :M 263 LEU 1HD1 : -0.586: 34
: 3976:M 188 MET 2HB :M 190 HIS HE1 : -0.526: 32
: 3976:M 263 LEU 1HD2 :M 188 MET CE : -0.424: 34
: 3976:M 7 ASP OD2 :M 133 ARG 1HD : -0.743: 36
: 3976:M 215 VAL 3HG2 :M 208 ALA 2HB : -0.708: 43
: 3976:M 208 ALA 3HB :M 213 GLY H : -0.569: 52
: 3976:M 208 ALA 1HB :M 212 LEU 2HD1 : -0.450: 52
: 3976:M 212 LEU 1HB :M 208 ALA CB : -0.425: 52
: 3976:M 9 VAL 1HG1 :M 140 LYS 1HB : -0.675: 26
: 3976:M 140 LYS 1HE :M 10 THR O : -0.575: 26
: 3976:M 140 LYS 2HG :M 11 ILE 1HG1 : -0.434: 23
: 3976:M 99 ARG HE :M 99 ARG HA : -0.616: 53
: 3976:M 99 ARG NE :M 99 ARG HA : -0.581: 53
: 3976:M 99 ARG NE :M 99 ARG CA : -0.413: 53
: 3976:M 201 ARG 1HD :M 218 GLU OE2 : -0.602: 35
: 3976:M 198 ASP OD2 :M 201 ARG NE : -0.453: 37
: 3976:M 135 ASP 2HB :M 31 LEU O : -0.595: 28
: 3976:M 296 LYS O :M 300 GLU 2HG : -0.595: 28
: 3976:M 90 VAL 1HG2 :M 22 TRP CE3 : -0.561: 21
: 3976:M 31 LEU 3HD1 :M 22 TRP CE2 : -0.532: 27
: 3976:M 165 VAL CG2 :M 296 LYS 1HD : -0.439: 21
: 3976:M 166 THR HA :M 258 GLU HA : -0.439: 23
: 3976:M 296 LYS 2HG :M 167 ILE 1HG1 : -0.432: 22
: 3976:M 296 LYS 1HE :M 166 THR O : -0.415: 25
: 3976:M 291 ASP 2HB :M 187 LEU O : -0.570: 31
: 3976:M 177 VAL 2HG1 :M 187 LEU 1HD1 : -0.482: 29
: 3976:M 235 LEU 1HD1 :M 220 GLU 2HB : -0.558: 25
: 3976:M 240 ILE 3HD1 :M 239 ARG O : -0.556: 32
: 3976:M 267 PRO HA :M 240 ILE 2HD1 : -0.400: 43
: 3976:M 244 GLY 2HA :M 232 TRP CZ2 : -0.535: 20
: 3976:M 232 TRP CE2 :M 244 GLY 2HA : -0.473: 20
: 3976:M 253 GLY C :M 252 PRO O : -0.526: 38
: 3976:M 175 TYR CZ :M 226 PRO HA : -0.518: 23
: 3976:M 248 PHE CZ :M 175 TYR HA : -0.492: 18
: 3976:M 246 VAL 1HG2 :M 178 TRP CE3 : -0.505: 21
: 3976:M 260 VAL O :M 246 VAL HA : -0.435: 17
: 3976:M 30 LEU HG :M 303 LEU 3HD1 : -0.502: 44
: 3976:M 303 LEU 3HD1 :M 30 LEU CG : -0.488: 44
: 3976:M 298 GLU 1HG :M 303 LEU 1HD1 : -0.474: 44
: 3976:M 30 LEU CD2 :M 303 LEU 3HD1 : -0.471: 44
: 3976:M 298 GLU HA :M 303 LEU 1HD1 : -0.443: 44
: 3976:M 303 LEU 3HD2 :M 301 LEU CB : -0.439: 42
: 3976:M 303 LEU 2HD1 :M 303 LEU C : -0.420: 44
: 3976:M 303 LEU 3HD2 :M 301 LEU 1HB : -0.411: 42
: 3976:M 29 PRO 1HG :M 37 SER HA : -0.493: 19
: 3976:M 28 LEU N :M 29 PRO CD : -0.429: 15
: 3976:M 184 LEU N :M 185 PRO CD : -0.492: 19
: 3976:M 181 LEU 1HB :M 182 PRO 2HD : -0.491: 21
: 3976:M 19 TYR CZ :M 70 PRO HA : -0.478: 22
: 3976:M 82 ALA 1HB :M 61 TRP 1HB : -0.471: 41
: 3976:M 78 SER 2HB :M 82 ALA CB : -0.426: 41
: 3976:M 225 GLU OE2 :M 229 ARG 1HD : -0.457: 34
: 3976:M 106 ARG NH1 :M 4 VAL 1HG1 : -0.452: 38
: 3976:M 4 VAL CG1 :M 106 ARG NH1 : -0.436: 38
: 3976:M 162 ARG HA :M 261 VAL O : -0.449: 29
: 3976:M 88 GLY 2HA :M 76 TRP CZ2 : -0.446: 21
: 3976:M 91 LEU 3HD2 :M 73 ARG 1HB : -0.446: 22
: 3976:M 243 SER HG :M 264 THR HG1 : -0.443: 30
: 3976:M 222 THR O :M 222 THR 2HG2 : -0.431: 30
: 3976:M 24 ASP OD1 :M 26 PRO 1HD : -0.419: 26
: 3976:M 191 LEU HA :M 206 VAL 2HG1 : -0.418: 30
: 3976:M 204 TRP O :M 216 SER 2HB : -0.415: 29
: 3976:M 205 THR CG2 :M 214 THR 2HG2 : -0.414: 42
: 3976:M 42 ASP C :M 42 ASP OD2 : -0.411: 30
: 3976:M 164 ALA HA :M 259 VAL O : -0.410: 21
: 3976:M 109 TYR HA :M 85 GLU O : -0.406: 32
: 3976:M 163 ASP 2HB :M 292 LEU CD1 : -0.401: 24
: 3976:M 53 PRO 2HD :M 52 ALA HA : -0.400: 24
#sum2 ::21.38 clashscore : 17.87 clashscore B<40
#summary::3976 atoms:3694 atoms B<40:447376 potential dots:27960.0 A^2:85 bumps:66 bumps B<40:1031 score
Output from PDB validation software
Summary from PDB validation
May. 10, 03:11:30 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 0.009 Angstroms
The following table contains a list of the covalent bonds
greater than 6.0*RMSD.
Deviation Residue Chain Sequence AT1 - AT2 Bond Dictionary
Name ID Number Distance Value
------------------------------------------------------------------------
-0.289 LEU B 147 CG - CD1 1.232 1.521
-0.187 LEU B 147 CG - CD2 1.334 1.521
*** Covalent Angle Values:
The RMS deviation for covalent angles relative to the standard
dictionary is 1.3 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
--------------------------------------------------------------------------------
7.7 THR A 33 N - CA - C 118.9 111.2
-8.0 VAL A 59 N - CA - C 103.2 111.2
-8.5 PHE A 92 N - CA - C 102.7 111.2
-7.6 PHE B 92 N - CA - C 103.6 111.2
11.8 LEU B 147 CD1 - CG - CD2 122.6 110.8
10.3 LEU B 147 CB - CG - CD1 121.0 110.7
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 ARG 110 ) and Residue (A GLU 127 ) are not linked
Distance of C-N bond is 17.61
SEQUENCE WARNING: Residue (B PRO 112 ) and Residue (B PRO 128 ) are not linked
Distance of C-N bond is 17.73
==> The following residues have missing atoms:
RES MOD#C SEQ ATOMS
ARG( A 83) CG CD NE CZ NH1 NH2
TYR( A 109) CG CD1 CD2 CE1 CE2 CZ OH
ARG( A 110) CG CD NE CZ NH1 NH2
GLU( A 127) CG CD OE1 OE2
LEU( A 147) CG CD1 CD2
GLU( B 2) CG CD OE1 OE2
ARG( B 6) CG CD NE CZ NH1 NH2
PRO( B 53) CG CD
PRO( B 55) CG CD
ARG( B 99) CG CD NE CZ NH1 NH2
TYR( B 109) CG CD1 CD2 CE1 CE2 CZ OH
ARG( B 110) CG CD NE CZ NH1 NH2
PRO( B 111) CG CD
PRO( B 112) CG CD
PRO( B 128) CG CD
DRR147D_XRay_em_bcr3.pdb: Error: Z value is 4. It should be 2.