Detailed results of SR213_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 >>>----------+
| |
| SR213_XRay_em_bcr3_noHs_000.rin 0.0 233 residues |
| |
+| Ramachandran plot: 92.9% core 6.7% allow 0.5% gener 0.0% disall |
| |
+| All Ramachandrans: 6 labelled residues (out of 219) |
+| Chi1-chi2 plots: 1 labelled residues (out of 165) |
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
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
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 0.57
4 1.01
5 0.94
6 0.99
7 0.82
11 0.87
15 1.08
16 0.77
17 0.76
18 0.82
19 0.68
20 1.25
21 0.99
22 1.32
23 1.14
24 1.17
25 1.23
26 0.87
27 0.57
28 0.85
29 0.29
30 -1.73
31 -1.33
32 -0.02
33 -2.30
34 -0.14
35 -0.14
36 0.66
37 0.18
38 -0.89
39 -2.67
40 -1.01
41 0.95
42 0.47
43 0.65
44 0.98
45 0.72
46 1.08
47 0.59
48 1.08
49 0.87
50 0.82
51 0.82
52 0.76
53 0.85
54 1.09
55 0.66
56 1.08
57 0.73
58 0.76
59 1.13
60 0.87
61 0.88
62 -1.07
63 -0.25
64 0.22
65 -0.51
66 -2.09
67 0.13
68 -0.25
69 -0.73
70 0.04
71 -0.29
72 -0.21
73 0.86
74 1.04
75 1.01
76 0.61
77 0.21
78 0.81
79 -1.44
80 1.14
81 1.05
82 1.22
83 0.85
84 0.87
85 0.82
86 0.30
87 0.82
88 0.45
89 1.09
90 -1.33
91 -1.46
92 -2.52
93 0.20
94 -2.01
95 -0.67
96 0.28
97 0.95
98 1.14
99 1.20
100 1.08
101 1.01
102 0.69
103 1.14
104 1.08
105 0.91
106 0.98
107 0.88
108 1.18
109 1.24
110 0.99
111 1.43
112 0.76
113 1.05
114 0.95
115 1.08
116 0.87
117 0.27
118 0.82
119 1.01
120 -0.13
121 0.16
122 -0.67
136 0.29
137 -0.17
138 -0.72
139 1.13
140 0.99
144 0.87
148 1.08
149 1.05
150 0.65
151 0.87
152 1.04
153 1.25
154 0.80
155 0.99
156 1.14
157 1.18
158 0.85
159 1.08
160 1.25
161 0.95
162 -0.69
163 -1.24
164 0.44
165 0.06
166 -0.71
167 -0.50
168 -0.11
169 0.79
170 0.18
171 -0.89
172 -4.21
173 0.27
174 0.95
175 0.42
176 0.76
177 0.98
178 0.72
179 0.87
180 0.37
181 0.64
182 1.08
183 0.29
184 0.82
185 0.36
186 1.14
187 1.09
188 0.14
189 0.55
190 0.98
191 0.36
192 0.29
193 0.10
194 1.13
195 0.30
196 -3.05
197 -0.85
198 -1.54
199 -0.46
205 -3.52
206 -3.23
207 -1.66
208 0.30
209 0.87
210 0.76
211 0.73
212 1.04
213 -0.23
214 1.17
215 0.66
216 0.88
217 0.87
218 0.99
219 0.98
220 0.82
221 0.45
222 0.64
223 -1.44
224 -0.69
225 -0.98
226 -1.20
227 -2.01
228 -0.32
229 0.71
230 0.37
231 0.85
232 1.20
233 1.22
234 1.32
235 1.01
236 1.14
237 1.08
238 0.09
239 0.22
240 0.88
241 1.17
242 1.24
243 0.24
244 0.48
245 0.99
246 0.37
247 0.95
248 0.27
249 0.14
250 -3.15
251 -3.46
#Reported_Model_Average 0.330
#Overall_Average_Reported 0.330
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 0.91
3 0.81
4 -0.48
5 0.61
6 -0.50
7 0.69
8 0.88
10 0.63
11 0.34
12 -0.56
14 0.91
15 0.95
16 0.58
17 0.76
18 0.85
19 0.82
20 1.25
21 0.99
22 0.43
23 0.98
24 0.93
25 0.49
26 0.23
27 0.57
28 0.30
29 0.39
30 -0.68
31 -1.17
32 -0.07
33 -0.96
34 0.11
35 -0.82
36 0.35
37 0.50
38 -0.14
39 -1.19
40 -0.20
41 0.85
42 0.47
43 0.65
44 0.83
45 0.88
46 0.97
47 0.73
48 -0.03
49 1.07
50 0.38
51 0.82
52 0.76
53 0.81
54 0.82
55 0.66
56 -0.65
57 0.73
58 0.76
59 1.02
60 0.87
61 0.51
62 -0.54
63 -0.12
64 -0.43
65 0.25
66 -0.77
67 0.13
68 -0.13
69 -0.79
70 -0.52
71 0.47
72 0.09
73 0.46
74 0.89
75 0.32
76 0.87
77 0.21
78 0.84
79 -0.57
80 1.02
81 0.99
82 0.88
83 -0.10
84 0.69
85 -1.28
86 0.45
87 0.58
88 0.49
89 0.19
90 -0.24
91 -0.66
92 -1.47
93 0.40
94 -0.96
95 0.29
96 -0.11
97 0.82
98 0.44
99 0.84
100 0.92
101 1.10
102 0.27
103 0.95
104 1.17
105 1.06
106 0.63
107 0.75
108 0.86
109 0.86
110 0.95
111 0.51
112 0.76
113 0.77
114 0.89
115 1.11
116 0.77
117 0.44
118 0.82
119 0.91
120 -0.32
121 -0.08
122 -0.69
123 0.57
135 0.91
136 -0.21
137 0.13
138 -0.21
139 0.65
140 0.46
141 1.12
143 0.76
144 0.27
145 0.13
147 0.91
148 0.98
149 0.93
150 0.65
151 0.75
152 0.35
153 1.25
154 0.80
155 1.06
156 0.50
157 0.85
158 0.50
159 0.87
160 1.25
161 0.31
162 0.13
163 -0.18
164 0.09
165 0.41
166 -0.71
167 0.17
168 -0.57
169 0.66
170 0.11
171 -0.16
172 -1.72
173 0.28
174 0.40
175 0.42
176 0.76
177 0.56
178 0.92
179 0.84
180 0.67
181 -0.14
182 0.95
183 0.23
184 0.82
185 0.36
186 0.95
187 0.65
188 0.14
189 0.69
190 0.98
191 0.36
192 -0.86
193 0.46
194 0.77
195 0.13
196 -1.09
197 -0.96
198 -0.32
199 0.21
200 0.00
204 1.24
205 -1.76
206 -1.20
207 -1.29
208 -0.78
209 0.26
210 0.76
211 -0.18
212 0.74
213 -0.02
214 1.24
215 0.40
216 -0.08
217 0.48
218 -0.66
219 0.56
220 0.49
221 0.30
222 0.65
223 -0.30
224 -0.47
225 -0.70
226 -1.01
227 -0.96
228 -0.91
229 0.42
230 0.54
231 0.30
232 0.84
233 0.30
234 1.11
235 0.94
236 0.89
237 1.17
238 0.23
239 0.31
240 0.75
241 0.86
242 1.15
243 0.57
244 0.22
245 0.99
246 0.62
247 0.83
248 0.43
249 -0.23
250 -1.32
251 -3.46
252 -0.43
#Reported_Model_Average 0.311
#Overall_Average_Reported 0.311
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
1 -0.83
2 -1.14
3 0.59
4 0.25
5 0.55
6 1.06
7 -0.33
8 0.04
9 1.00
10 0.55
11 0.28
12 0.25
13 0.91
14 -0.54
15 0.04
16 -0.09
17 0.49
18 0.28
19 0.47
20 1.10
21 0.49
22 0.23
23 0.71
24 1.14
25 -0.03
26 0.04
27 1.10
28 0.08
29 0.51
30 0.34
31 0.51
32 0.20
33 0.34
34 1.25
35 0.51
36 -1.29
37 -0.84
38 0.04
39 0.08
40 0.93
41 0.47
42 0.44
43 -0.25
44 -0.09
45 0.28
46 0.28
47 -0.26
48 0.34
49 0.28
50 0.29
51 0.49
52 0.14
53 0.24
54 0.96
55 0.49
56 0.28
57 1.10
58 0.49
59 -0.33
60 0.28
61 0.77
62 0.81
63 -0.10
64 -0.74
65 0.24
66 -0.41
67 -0.11
68 0.47
69 1.25
70 1.00
71 1.04
72 0.47
73 0.04
74 0.10
75 0.93
76 0.28
77 0.14
78 1.00
79 0.47
80 0.23
81 0.51
82 1.40
83 0.77
84 0.28
85 1.06
86 1.00
87 -0.33
88 -0.84
89 0.59
90 1.14
91 -0.09
92 1.04
93 0.20
94 -0.54
95 -0.41
96 0.47
97 -0.10
98 0.24
99 1.40
100 0.47
101 0.51
102 -0.54
103 0.55
104 0.28
105 0.34
106 1.00
107 0.77
108 1.25
109 0.55
110 1.06
111 -1.21
112 0.49
113 1.00
114 0.47
115 0.34
116 -1.13
117 0.93
118 0.14
119 0.24
120 -0.46
121 0.51
122 0.34
123 -0.41
134 -1.30
135 -1.14
136 0.34
137 -0.57
138 0.08
139 0.77
140 -0.68
141 0.28
142 1.00
143 0.55
144 -0.46
145 0.25
146 0.91
147 0.81
148 0.28
149 -0.09
150 0.49
151 0.28
152 -0.10
153 1.10
154 0.49
155 0.23
156 0.71
157 1.14
158 0.25
159 0.28
160 1.10
161 0.08
162 0.51
163 0.34
164 0.41
165 0.20
166 0.34
167 1.14
168 0.51
169 -1.29
170 -0.84
171 0.04
172 0.55
173 0.93
174 0.47
175 0.44
176 -0.25
177 -0.09
178 0.28
179 0.04
180 -2.61
181 0.51
182 0.28
183 0.77
184 0.49
185 0.14
186 0.24
187 0.96
188 0.49
189 0.04
190 1.10
191 0.49
192 -0.68
193 0.28
194 0.77
195 0.93
196 -0.10
197 -0.74
198 0.24
199 -0.41
200 0.44
204 0.20
205 -0.10
206 0.28
207 -0.03
208 0.93
209 0.28
210 0.14
211 0.66
212 0.08
213 0.51
214 -0.26
215 1.40
216 -0.33
217 0.28
218 0.77
219 1.00
220 -0.68
221 -0.87
222 0.59
223 1.14
224 -0.09
225 1.04
226 0.20
227 -0.54
228 -0.41
229 0.47
230 -0.10
231 0.24
232 1.40
233 0.47
234 0.51
235 0.81
236 0.55
237 -1.13
238 0.17
239 1.00
240 1.06
241 1.25
242 0.55
243 1.06
244 -0.61
245 -0.25
246 1.00
247 0.08
248 0.51
249 0.28
250 0.81
251 0.14
252 0.71
#Reported_Model_Average 0.301
#Overall_Average_Reported 0.301
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
1 -0.83
2 -1.14
3 0.59
4 0.25
5 0.55
6 1.06
7 -0.33
8 0.04
9 1.00
10 0.55
11 0.28
12 0.25
13 0.91
14 -0.54
15 0.04
16 -0.09
17 0.49
18 0.28
19 0.47
20 1.10
21 0.49
22 0.23
23 0.71
24 1.14
25 -0.03
26 0.04
27 1.10
28 0.08
29 0.51
30 0.34
31 0.51
32 0.20
33 0.34
34 1.25
35 0.51
36 -1.29
37 -0.84
38 0.04
39 0.08
40 0.93
41 0.47
42 0.44
43 -0.25
44 -0.09
45 0.28
46 0.28
47 -0.26
48 0.34
49 0.28
50 0.29
51 0.49
52 0.14
53 0.24
54 0.96
55 0.49
56 0.28
57 1.10
58 0.49
59 -0.33
60 0.28
61 0.77
62 0.81
63 -0.10
64 -0.74
65 0.24
66 -0.41
67 -0.11
68 0.47
69 1.25
70 1.00
71 1.04
72 0.47
73 0.04
74 0.10
75 0.93
76 0.28
77 0.14
78 1.00
79 0.47
80 0.23
81 0.51
82 1.40
83 0.77
84 0.28
85 1.06
86 1.00
87 -0.33
88 -0.84
89 0.59
90 1.14
91 -0.09
92 1.04
93 0.20
94 -0.54
95 -0.41
96 0.47
97 -0.10
98 0.24
99 1.40
100 0.47
101 0.51
102 -0.54
103 0.55
104 0.28
105 0.34
106 1.00
107 0.77
108 1.25
109 0.55
110 1.06
111 -1.21
112 0.49
113 1.00
114 0.47
115 0.34
116 -1.13
117 0.93
118 0.14
119 0.24
120 -0.46
121 0.51
122 0.34
123 -0.41
134 -1.30
135 -1.14
136 0.34
137 -0.57
138 0.08
139 0.77
140 -0.68
141 0.28
142 1.00
143 0.55
144 -0.46
145 0.25
146 0.91
147 0.81
148 0.28
149 -0.09
150 0.49
151 0.28
152 -0.10
153 1.10
154 0.49
155 0.23
156 0.71
157 1.14
158 0.25
159 0.28
160 1.10
161 0.08
162 0.51
163 0.34
164 0.41
165 0.20
166 0.34
167 1.14
168 0.51
169 -1.29
170 -0.84
171 0.04
172 0.55
173 0.93
174 0.47
175 0.44
176 -0.25
177 -0.09
178 0.28
179 0.04
180 -2.61
181 0.51
182 0.28
183 0.77
184 0.49
185 0.14
186 0.24
187 0.96
188 0.49
189 0.04
190 1.10
191 0.49
192 -0.68
193 0.28
194 0.77
195 0.93
196 -0.10
197 -0.74
198 0.24
199 -0.41
200 0.44
204 0.20
205 -0.10
206 0.28
207 -0.03
208 0.93
209 0.28
210 0.14
211 0.66
212 0.08
213 0.51
214 -0.26
215 1.40
216 -0.33
217 0.28
218 0.77
219 1.00
220 -0.68
221 -0.87
222 0.59
223 1.14
224 -0.09
225 1.04
226 0.20
227 -0.54
228 -0.41
229 0.47
230 -0.10
231 0.24
232 1.40
233 0.47
234 0.51
235 0.81
236 0.55
237 -1.13
238 0.17
239 1.00
240 1.06
241 1.25
242 0.55
243 1.06
244 -0.61
245 -0.25
246 1.00
247 0.08
248 0.51
249 0.28
250 0.81
251 0.14
252 0.71
#Reported_Model_Average 0.301
#Overall_Average_Reported 0.301
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
1.000 2
2.000 3
3.000 0
4.000 4
5.000 0
6.000 0
7.000 0
8.000 1
9.000 0
10.000 0
11.000 0
12.000 0
13.000 0
14.000 0
15.000 0
16.000 0
17.000 0
18.000 0
19.000 0
20.000 0
21.000 1
22.000 0
23.000 0
24.000 0
25.000 0
26.000 0
27.000 0
28.000 0
29.000 0
30.000 0
31.000 0
32.000 0
33.000 0
34.000 0
35.000 0
36.000 0
37.000 0
38.000 0
39.000 1
40.000 0
41.000 2
42.000 2
43.000 0
44.000 0
45.000 1
46.000 0
47.000 0
48.000 0
49.000 0
50.000 0
51.000 0
52.000 0
53.000 0
54.000 1
55.000 0
56.000 1
57.000 0
58.000 0
59.000 0
60.000 1
61.000 0
62.000 3
63.000 0
64.000 3
65.000 3
66.000 4
67.000 3
68.000 0
69.000 0
70.000 2
71.000 0
72.000 0
73.000 0
74.000 1
75.000 0
76.000 0
77.000 0
78.000 0
79.000 1
80.000 0
81.000 0
82.000 0
83.000 1
84.000 0
85.000 6
86.000 0
87.000 0
88.000 0
89.000 0
90.000 0
91.000 0
92.000 0
93.000 0
94.000 0
95.000 0
96.000 0
97.000 0
98.000 0
99.000 1
100.000 1
101.000 0
102.000 0
103.000 0
104.000 1
105.000 0
106.000 0
107.000 0
108.000 0
109.000 1
110.000 0
111.000 0
112.000 0
113.000 1
114.000 0
115.000 0
116.000 2
117.000 0
118.000 0
119.000 0
120.000 0
121.000 0
122.000 1
123.000 1
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 0
137.000 2
138.000 1
139.000 0
140.000 0
141.000 1
142.000 4
143.000 0
144.000 1
145.000 1
146.000 0
147.000 1
148.000 2
149.000 1
150.000 0
151.000 2
152.000 0
153.000 0
154.000 1
155.000 0
156.000 0
157.000 0
158.000 2
159.000 0
160.000 0
161.000 0
162.000 2
163.000 0
164.000 0
165.000 0
166.000 0
167.000 0
168.000 0
169.000 0
170.000 0
171.000 0
172.000 2
173.000 0
174.000 2
175.000 3
176.000 0
177.000 0
178.000 1
179.000 0
180.000 0
181.000 0
182.000 0
183.000 1
184.000 0
185.000 0
186.000 1
187.000 1
188.000 0
189.000 0
190.000 0
191.000 1
192.000 1
193.000 2
194.000 0
195.000 2
196.000 0
197.000 2
198.000 3
199.000 0
200.000 0
201.000 0
202.000 0
203.000 0
204.000 0
205.000 0
206.000 3
207.000 0
208.000 5
209.000 0
210.000 0
211.000 2
212.000 1
213.000 0
214.000 1
215.000 1
216.000 1
217.000 0
218.000 2
219.000 0
220.000 1
221.000 4
222.000 0
223.000 0
224.000 4
225.000 0
226.000 1
227.000 3
228.000 0
229.000 2
230.000 0
231.000 1
232.000 3
233.000 1
234.000 0
235.000 2
236.000 0
237.000 1
238.000 0
239.000 0
240.000 0
241.000 0
242.000 2
243.000 0
244.000 0
245.000 0
246.000 1
247.000 0
248.000 0
249.000 0
250.000 1
251.000 0
252.000 2
#Reported_Model_Average 0.571
#Overall_Average_Reported 0.571
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 3913:M 158 GLN 2HE2 :M 162 ASN 1HD2 : -0.856: 60
: 3913:M 158 GLN 2HE2 :M 162 ASN ND2 : -0.508: 60
: 3913:M 242 THR HB :M 211 VAL 1HG1 : -0.839: 50
: 3913:M 242 THR CB :M 211 VAL 1HG1 : -0.599: 50
: 3913:M 198 ARG 2HG :M 197 VAL 3HG1 : -0.802: 79
: 3913:M 192 LEU 2HD1 :M 193 GLU N : -0.518: 58
: 3913:M 198 ARG HE :M 252 ARG NH2 : -0.512: 81
: 3913:M 252 ARG CZ :M 198 ARG HE : -0.509: 81
: 3913:M 197 VAL 2HG1 :M 193 GLU O : -0.480: 63
: 3913:M 62 ILE 2HG2 :M 67 PRO 2HG : -0.661: 56
: 3913:M 62 ILE HA :M 67 PRO 2HD : -0.559: 56
: 3913:M 62 ILE CG2 :M 67 PRO 2HG : -0.450: 56
: 3913:M 148 GLU 2HG :M 144 GLU O : -0.651: 25
: 3913:M 147 ILE O :M 151 GLU 2HG : -0.462: 28
: 3913:M 151 GLU OE1 :M 148 GLU HA : -0.404: 31
: 3913:M 214 ASN 2HB :M 235 ILE 3HG2 : -0.607: 28
: 3913:M 231 ARG O :M 235 ILE 2HG1 : -0.416: 28
: 3913:M 175 PRO 2HD :M 174 LYS 2HB : -0.598: 53
: 3913:M 174 LYS O :M 178 GLU 2HG : -0.528: 33
: 3913:M 175 PRO 1HD :M 172 THR C : -0.518: 32
: 3913:M 172 THR O :M 175 PRO 1HD : -0.413: 32
: 3913:M 85 LEU 2HD1 :M 85 LEU C : -0.587: 18
: 3913:M 85 LEU 2HD1 :M 85 LEU O : -0.576: 18
: 3913:M 85 LEU C :M 85 LEU CD1 : -0.403: 18
: 3913:M 8 GLU 2HG :M 4 GLN O : -0.581: 43
: 3913:M 141 GLU 2HG :M 138 THR OG1 : -0.581: 33
: 3913:M 4 GLN OE1 :M 2 LEU 2HB : -0.526: 35
: 3913:M 2 LEU H :M 1 MET 1HG : -0.525: 56
: 3913:M 2 LEU N :M 1 MET 1HG : -0.486: 56
: 3913:M 4 GLN H :M 4 GLN CD : -0.431: 35
: 3913:M 41 LYS O :M 45 GLU 2HG : -0.574: 26
: 3913:M 39 THR O :M 42 PRO 1HG : -0.520: 25
: 3913:M 42 PRO 1HD :M 41 LYS N : -0.427: 21
: 3913:M 195 ILE 2HG1 :M 208 ILE 1HD1 : -0.548: 48
: 3913:M 195 ILE 1HG1 :M 191 ALA O : -0.523: 48
: 3913:M 208 ILE 3HG2 :M 187 TRP CZ3 : -0.479: 38
: 3913:M 206 GLU HA :M 208 ILE 3HD1 : -0.452: 52
: 3913:M 208 ILE 2HD1 :M 208 ILE N : -0.448: 40
: 3913:M 206 GLU 1HG :M 206 GLU O : -0.424: 63
: 3913:M 186 ARG 1HB :M 142 MET CE : -0.534: 49
: 3913:M 116 GLU 2HG :M 70 VAL CG1 : -0.534: 34
: 3913:M 142 MET 1HG :M 137 GLN 2HE2 : -0.532: 34
: 3913:M 116 GLU 2HG :M 70 VAL 2HG1 : -0.525: 34
: 3913:M 142 MET CE :M 183 LEU 2HD1 : -0.516: 37
: 3913:M 142 MET 1HG :M 137 GLN NE2 : -0.402: 34
: 3913:M 79 LYS O :M 83 LEU 3HD1 : -0.524: 22
: 3913:M 233 LYS 2HE :M 237 GLU OE2 : -0.523: 34
: 3913:M 221 GLN HA :M 224 VAL CG2 : -0.521: 27
: 3913:M 227 ILE 1HD1 :M 232 PHE HD1 : -0.483: 30
: 3913:M 221 GLN HA :M 224 VAL 2HG2 : -0.467: 27
: 3913:M 221 GLN 2HG :M 227 ILE CD1 : -0.463: 30
: 3913:M 232 PHE HE2 :M 154 ALA HA : -0.459: 17
: 3913:M 215 PHE O :M 218 LEU 2HB : -0.434: 25
: 3913:M 221 GLN 2HG :M 227 ILE 3HD1 : -0.420: 30
: 3913:M 224 VAL 2HG2 :M 220 LEU O : -0.419: 27
: 3913:M 218 LEU 2HD2 :M 232 PHE CE1 : -0.404: 31
: 3913:M 226 HIS ND1 :M 224 VAL HB : -0.402: 91
: 3913:M 64 VAL 2HG2 :M 65 ARG 2HG : -0.516: 48
: 3913:M 64 VAL 3HG1 :M 65 ARG H : -0.474: 52
: 3913:M 64 VAL 3HG1 :M 65 ARG N : -0.427: 52
: 3913:M 66 ARG 1HG :M 66 ARG 1HH1 : -0.514: 65
: 3913:M 66 ARG 1HG :M 66 ARG NH1 : -0.430: 65
: 3913:M 100 LYS O :M 104 GLU 2HG : -0.477: 27
: 3913:M 212 LYS O :M 216 LEU 3HD1 : -0.471: 40
: 3913:M 56 GLU O :M 60 GLU 2HG : -0.460: 46
: 3913:M 74 GLN 1HG :M 109 THR 3HG2 : -0.459: 27
: 3913:M 123 ARG 1HB :M 122 SER O : -0.444: 46
: 3913:M 99 PHE CE2 :M 21 ALA HA : -0.441: 13
: 3913:M 229 LYS 2HE :M 229 LYS 1HB : -0.429: 60
: 3913:M 250 ILE 2HG1 :M 246 VAL O : -0.429: 35
: 3913:M 113 VAL 1HG2 :M 54 TRP CZ2 : -0.423: 15
: 3913:M 145 GLN O :M 149 VAL 3HG2 : -0.406: 23
#sum2 ::18.40 clashscore : 13.54 clashscore B<40
#summary::3913 atoms:3103 atoms B<40:440542 potential dots:27530.0 A^2:72 bumps:42 bumps B<40:1257 score
Output from PDB validation software
Summary from PDB validation
May. 10, 17:38:36 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 0.005 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 1.0 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
--------------------------------------------------------------------------------
-7.2 LEU A 2 N - CA - C 104.0 111.2
9.1 TYR A 69 N - CA - C 120.3 111.2
6.5 LYS A 72 N - CA - C 117.7 111.2
9.0 LEU A 85 CA - CB - CG 125.3 116.3
6.9 HIS A 92 N - CA - C 118.1 111.2
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 (B PRO 67 ) and Residue (B HIS 71 ) are not linked
Distance of C-N bond is 6.46
SR213_XRay_em_bcr3.pdb: Error: Z value is 8. It should be 4.
SR213_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 265) in Token 'SITE' can not be found in coordinates
SR213_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 295) in Token 'SITE' can not be found in coordinates