Detailed results of SRR115C_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 >>>----------+
| |
| SRR115C_XRay_em_bcr3_noHs_000.rin 0.0 337 residues |
| |
+| Ramachandran plot: 86.1% core 13.9% allow 0.0% gener 0.0% disall |
| |
+| All Ramachandrans: 7 labelled residues (out of 329) |
*| Chi1-chi2 plots: 8 labelled residues (out of 228) |
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
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
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
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
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
60 -0.63
61 -2.76
62 1.20
63 -0.48
64 0.67
65 0.64
66 0.82
67 -1.00
68 -0.17
69 0.74
70 0.55
71 -0.86
72 -3.77
73 1.22
74 -2.19
75 -1.12
76 -1.73
77 0.80
78 1.19
79 0.63
80 0.66
81 1.13
82 -1.02
83 0.09
84 1.22
85 1.08
86 0.19
87 0.88
88 -0.23
89 -1.05
90 -0.30
91 -1.57
92 0.45
93 -1.47
94 -1.24
95 -0.85
96 0.74
97 1.24
98 1.09
99 0.79
100 0.86
101 0.63
102 0.73
103 0.37
104 0.04
105 1.22
106 0.87
107 0.85
108 -1.48
109 -1.02
110 -2.93
111 -0.06
112 0.83
113 1.13
114 0.99
115 0.30
116 0.62
117 0.05
118 0.89
119 0.65
120 1.23
121 1.25
122 -0.41
123 0.55
124 0.73
125 0.80
126 -0.82
127 0.87
128 -2.15
129 -1.39
130 0.26
131 0.19
132 0.95
133 1.08
134 0.88
135 0.91
136 0.87
137 -0.14
138 0.85
139 1.32
140 0.76
141 0.29
142 0.50
143 0.04
144 0.66
145 1.08
146 -1.94
147 -2.11
160 -0.39
161 -0.84
162 -0.06
163 -0.06
164 0.38
165 -1.96
166 -0.17
167 0.84
168 0.80
169 0.13
170 0.82
171 1.39
172 0.82
173 1.04
174 -1.28
175 -1.21
176 -0.93
177 0.76
178 1.19
179 0.36
180 0.14
181 0.99
182 0.66
183 0.85
184 -1.28
185 -0.12
186 -3.23
187 -2.58
188 0.37
189 -0.67
190 -1.56
191 -1.18
192 0.07
193 0.19
194 -0.14
195 -0.30
196 1.08
197 -0.06
198 1.09
199 0.55
200 1.15
201 0.82
202 0.94
203 0.95
204 0.82
205 1.09
206 1.08
207 0.85
208 -2.47
209 -0.62
210 -2.51
211 0.84
212 0.40
213 0.83
214 0.76
215 0.71
216 1.01
217 0.84
218 0.79
219 0.05
220 0.75
221 -0.40
222 -1.00
223 0.55
224 -0.23
225 0.05
226 -2.93
227 -2.81
228 -1.06
229 -1.58
230 -0.57
231 -1.04
232 0.95
233 1.32
234 1.13
235 -1.38
236 0.61
237 0.65
238 1.04
239 1.14
240 0.66
241 1.08
242 1.13
243 0.85
244 0.66
245 0.68
246 0.03
247 0.24
260 -0.12
261 1.20
262 1.24
263 0.67
264 1.18
265 0.99
266 0.24
267 0.06
268 -0.55
269 0.10
270 -0.48
271 -1.33
272 -0.26
273 -0.71
274 -1.31
275 -1.82
276 -0.89
277 0.04
278 0.84
279 -1.96
280 -1.63
281 0.76
282 1.13
283 0.79
284 0.86
285 0.33
286 0.63
287 0.22
288 0.12
289 0.94
290 -0.91
291 -0.41
292 0.17
293 -0.68
294 0.30
295 -2.67
296 -0.06
297 1.18
298 0.64
299 1.39
300 1.13
301 1.25
302 0.71
303 0.29
304 -1.01
305 -1.10
306 0.33
307 -2.06
308 -2.39
309 -2.93
310 0.84
311 1.32
312 0.93
313 0.76
314 1.01
315 0.11
316 -1.19
317 1.09
318 0.05
319 0.97
320 1.02
321 0.47
322 0.87
323 0.37
324 0.99
325 0.60
326 -1.05
327 -1.91
328 -0.54
329 -0.75
330 1.23
331 1.22
332 0.40
333 -0.30
334 0.95
335 -1.03
336 -1.38
337 -0.55
338 0.27
339 0.82
340 0.85
341 0.29
342 0.95
343 0.36
344 -1.10
345 -3.49
346 -3.77
359 -1.60
360 0.58
361 -1.63
362 0.36
363 1.13
364 -0.69
365 -0.23
366 0.87
367 0.85
368 -0.69
369 -1.79
370 0.16
371 -1.47
372 -1.11
373 -1.69
374 -0.24
375 -0.15
376 0.22
377 0.84
378 -1.04
379 -2.54
380 0.16
381 0.04
382 0.48
383 -0.24
384 0.99
385 -0.68
386 -1.21
387 0.85
388 -1.81
389 -2.23
390 -0.94
391 -0.91
392 1.32
393 0.62
394 0.99
395 -3.15
396 -0.09
397 -0.10
398 -2.20
399 -1.81
400 -1.83
401 -0.62
402 1.01
403 0.61
404 -1.35
405 -0.16
406 0.60
407 -3.23
408 -0.44
409 -0.41
410 0.30
411 0.27
412 -1.95
413 -0.91
414 1.13
415 -3.76
416 -0.89
417 0.84
418 0.90
419 1.14
420 -1.67
421 -0.12
422 -0.80
423 -0.40
424 -2.67
#Reported_Model_Average -0.074
#Overall_Average_Reported -0.074
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
59 0.00
60 -0.48
61 -2.76
62 0.92
63 0.08
64 -1.10
65 -0.25
66 0.82
67 -2.19
68 -0.17
69 -0.33
70 0.58
71 -0.35
72 -2.49
73 1.19
74 -1.50
75 -0.31
76 -1.80
77 0.80
78 0.24
79 -0.39
80 0.66
81 -1.12
82 -1.02
83 0.50
84 -0.61
85 -0.65
86 0.25
87 -0.18
88 -0.65
89 -1.07
90 -0.59
91 -1.83
92 0.45
93 -2.60
94 -0.75
95 -0.96
96 0.74
97 0.18
98 0.67
99 0.14
100 1.05
101 -0.03
102 0.73
103 -0.31
104 -0.22
105 -0.70
106 0.87
107 0.96
108 -0.46
109 -1.43
110 -1.26
111 -0.47
112 -0.63
113 -0.10
114 0.99
115 -0.47
116 0.30
117 0.56
118 0.03
119 0.65
120 1.23
121 1.25
122 -0.19
123 -0.19
124 -0.18
125 0.80
126 -0.95
127 0.50
128 -1.44
129 -1.39
130 -0.31
131 -1.25
132 0.82
133 1.13
134 0.61
135 0.44
136 0.65
137 0.11
138 0.92
139 0.55
140 0.76
141 0.57
142 -0.27
143 0.44
144 0.66
145 0.20
146 -1.94
147 -1.11
148 -2.84
159 0.00
160 -0.29
161 -0.84
162 0.35
163 -0.18
164 -0.05
165 -1.13
166 -0.17
167 -1.27
168 0.80
169 -0.63
170 -0.78
171 0.63
172 -0.74
173 1.11
174 -1.65
175 -0.26
176 -0.22
177 0.76
178 0.24
179 0.12
180 0.14
181 0.58
182 0.66
183 -0.55
184 -1.81
185 0.18
186 -2.01
187 -1.64
188 0.56
189 -1.30
190 -1.22
191 -1.75
192 0.07
193 0.41
194 -0.21
195 -0.42
196 1.08
197 0.29
198 0.75
199 0.53
200 1.23
201 0.67
202 0.94
203 0.56
204 0.28
205 -1.25
206 0.46
207 0.81
208 -1.14
209 -1.16
210 -1.77
211 0.80
212 -0.90
213 0.45
214 0.76
215 0.81
216 -0.54
217 0.91
218 0.43
219 0.05
220 -0.51
221 -0.40
222 -0.60
223 0.78
224 -0.65
225 0.05
226 -2.65
227 -1.51
228 -0.90
229 -1.58
230 -0.73
231 -1.87
232 -0.28
233 0.96
234 0.65
235 -1.05
236 0.00
237 0.35
238 0.43
239 -0.35
240 0.66
241 0.80
242 0.14
243 -1.02
244 0.66
245 0.64
246 0.03
247 0.56
248 -2.84
259 -1.77
260 -0.12
261 0.13
262 0.18
263 -0.16
264 0.94
265 0.99
266 -0.58
267 0.06
268 -0.67
269 -0.54
270 -0.15
271 -0.38
272 0.40
273 -0.72
274 -1.34
275 -1.95
276 -0.89
277 0.01
278 -0.29
279 -1.96
280 -0.64
281 0.76
282 0.75
283 -0.30
284 0.86
285 0.56
286 -0.96
287 0.60
288 -0.83
289 0.96
290 -1.23
291 -0.41
292 -0.21
293 -0.09
294 -0.39
295 -2.67
296 -0.18
297 0.76
298 0.58
299 0.99
300 0.19
301 1.25
302 0.36
303 -0.37
304 -1.47
305 -0.02
306 0.22
307 -0.77
308 -2.02
309 -2.22
310 0.86
311 -0.57
312 -0.07
313 0.76
314 0.81
315 -0.05
316 -1.03
317 0.28
318 0.05
319 0.07
320 1.02
321 0.69
322 -0.75
323 -0.35
324 0.99
325 0.57
326 -1.71
327 -1.04
328 -0.54
329 -0.52
330 0.60
331 -0.61
332 0.77
333 -0.39
334 0.12
335 -0.25
336 -0.67
337 0.21
338 -0.39
339 0.82
340 0.34
341 -0.35
342 -0.61
343 0.36
344 -0.03
345 -3.49
346 -2.78
347 -2.84
358 -0.72
359 -2.23
360 0.58
361 -2.02
362 0.36
363 -0.46
364 -1.87
365 0.21
366 -0.62
367 -0.42
368 -0.88
369 -2.09
370 0.52
371 -2.60
372 -1.11
373 -1.44
374 -2.22
375 -0.09
376 0.22
377 0.66
378 -0.41
379 -1.41
380 0.67
381 -0.29
382 0.48
383 -0.28
384 0.58
385 -0.59
386 -0.16
387 -0.17
388 -2.26
389 -1.75
390 -1.14
391 0.03
392 -0.50
393 -0.85
394 0.99
395 -1.68
396 0.21
397 -0.49
398 -2.20
399 -1.81
400 -0.32
401 -0.62
402 -0.56
403 0.14
404 -1.22
405 -0.16
406 -0.24
407 -2.80
408 -0.95
409 -0.41
410 -0.29
411 -0.75
412 -0.79
413 0.00
414 0.85
415 -1.69
416 -1.87
417 -0.20
418 0.96
419 0.95
420 -1.67
421 -0.37
422 -0.54
423 -0.68
424 -2.67
425 -0.52
#Reported_Model_Average -0.315
#Overall_Average_Reported -0.315
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
59 0.00
60 0.23
61 0.44
62 -0.84
63 0.08
64 0.71
65 1.25
66 0.14
67 -0.33
68 0.49
69 -0.87
70 0.28
71 0.54
72 0.29
73 0.47
74 1.04
75 0.51
76 0.51
77 0.49
78 0.17
79 0.71
80 0.49
81 0.77
82 0.14
83 0.29
84 1.40
85 0.28
86 0.28
87 0.29
88 0.66
89 0.28
90 0.08
91 0.51
92 0.44
93 0.51
94 1.14
95 0.66
96 1.10
97 0.55
98 1.14
99 1.25
100 1.04
101 1.06
102 1.10
103 0.08
104 1.06
105 1.14
106 -1.13
107 0.71
108 1.06
109 0.23
110 0.71
111 0.08
112 0.23
113 0.51
114 0.49
115 -0.54
116 0.23
117 0.55
118 1.14
119 0.14
120 0.25
121 1.10
122 0.81
123 0.28
124 -0.09
125 0.49
126 0.24
127 0.28
128 0.28
129 1.10
130 0.08
131 0.25
132 0.08
133 0.34
134 0.29
135 0.17
136 -0.46
137 1.06
138 0.25
139 0.23
140 0.49
141 0.08
142 -0.68
143 0.47
144 0.49
145 0.28
146 1.10
147 -0.68
148 0.28
159 0.00
160 0.51
161 0.44
162 -0.84
163 0.08
164 0.71
165 1.14
166 0.14
167 -0.68
168 0.49
169 0.10
170 0.28
171 1.04
172 0.29
173 0.47
174 0.20
175 0.23
176 0.51
177 0.49
178 0.34
179 0.24
180 0.49
181 0.29
182 0.14
183 0.77
184 1.40
185 0.28
186 0.28
187 0.77
188 -0.09
189 0.28
190 0.08
191 0.34
192 0.44
193 0.51
194 1.25
195 -0.09
196 1.10
197 0.55
198 1.14
199 1.25
200 1.04
201 1.06
202 1.10
203 0.08
204 1.06
205 1.14
206 -1.13
207 0.24
208 -0.33
209 0.23
210 0.24
211 0.55
212 0.23
213 0.51
214 0.49
215 -0.28
216 0.23
217 0.55
218 1.14
219 0.14
220 0.25
221 1.10
222 0.81
223 0.28
224 -0.40
225 0.49
226 0.24
227 0.04
228 0.28
229 1.10
230 0.08
231 0.25
232 0.08
233 0.34
234 0.29
235 0.17
236 -1.13
237 1.06
238 -0.87
239 0.51
240 0.49
241 -2.12
242 0.77
243 0.47
244 0.49
245 0.28
246 1.10
247 -0.68
248 0.04
259 0.23
260 0.44
261 -0.84
262 0.08
263 0.71
264 1.14
265 0.49
266 -0.68
267 0.49
268 -0.57
269 0.28
270 1.04
271 0.29
272 0.47
273 0.20
274 0.51
275 0.51
276 -0.25
277 0.34
278 0.24
279 0.49
280 0.77
281 0.14
282 -0.33
283 1.40
284 0.28
285 0.28
286 0.77
287 -0.09
288 0.28
289 0.08
290 0.51
291 0.44
292 0.51
293 1.25
294 0.66
295 1.10
296 0.55
297 0.52
298 1.25
299 1.04
300 1.06
301 1.10
302 0.08
303 1.06
304 1.14
305 -0.46
306 0.24
307 -0.33
308 0.23
309 0.24
310 0.55
311 0.23
312 0.51
313 0.49
314 -0.54
315 0.23
316 0.55
317 1.14
318 0.49
319 0.25
320 1.10
321 0.81
322 0.28
323 -0.09
324 0.49
325 0.71
326 0.28
327 0.28
328 1.10
329 0.08
330 0.25
331 0.47
332 0.34
333 0.77
334 0.34
335 0.28
336 1.06
337 0.25
338 0.23
339 0.49
340 0.08
341 -1.14
342 0.47
343 0.49
344 -0.59
345 1.10
346 -1.14
347 0.28
358 0.34
359 -0.41
360 0.14
361 0.29
362 0.14
363 -0.68
364 1.04
365 0.28
366 0.04
367 -0.68
368 -0.09
369 0.28
370 0.08
371 0.34
372 0.44
373 0.23
374 -0.43
375 -0.09
376 1.10
377 0.55
378 1.25
379 1.25
380 0.20
381 1.06
382 1.10
383 0.08
384 0.77
385 1.14
386 -0.46
387 -0.41
388 -0.68
389 0.23
390 0.24
391 0.08
392 0.23
393 0.51
394 0.49
395 -0.54
396 0.23
397 0.08
398 0.00
399 0.49
400 0.25
401 1.10
402 -0.54
403 0.28
404 -0.09
405 0.49
406 -0.44
407 -0.46
408 0.28
409 1.10
410 0.08
411 0.25
412 -0.10
413 0.51
414 0.77
415 0.17
416 0.28
417 0.77
418 0.10
419 0.51
420 0.49
421 -0.72
422 0.29
423 0.47
424 0.49
425 0.28
#Reported_Model_Average 0.356
#Overall_Average_Reported 0.356
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
59 0.00
60 0.23
61 0.44
62 -0.84
63 0.08
64 0.71
65 1.25
66 0.14
67 -0.33
68 0.49
69 -0.87
70 0.28
71 0.54
72 0.29
73 0.47
74 1.04
75 0.51
76 0.51
77 0.49
78 0.17
79 0.71
80 0.49
81 0.77
82 0.14
83 0.29
84 1.40
85 0.28
86 0.28
87 0.29
88 0.66
89 0.28
90 0.08
91 0.51
92 0.44
93 0.51
94 1.14
95 0.66
96 1.10
97 0.55
98 1.14
99 1.25
100 1.04
101 1.06
102 1.10
103 0.08
104 1.06
105 1.14
106 -1.13
107 0.71
108 1.06
109 0.23
110 0.71
111 0.08
112 0.23
113 0.51
114 0.49
115 -0.54
116 0.23
117 0.55
118 1.14
119 0.14
120 0.25
121 1.10
122 0.81
123 0.28
124 -0.09
125 0.49
126 0.24
127 0.28
128 0.28
129 1.10
130 0.08
131 0.25
132 0.08
133 0.34
134 0.29
135 0.17
136 -0.46
137 1.06
138 0.25
139 0.23
140 0.49
141 0.08
142 -0.68
143 0.47
144 0.49
145 0.28
146 1.10
147 -0.68
148 0.28
159 0.00
160 0.51
161 0.44
162 -0.84
163 0.08
164 0.71
165 1.14
166 0.14
167 -0.68
168 0.49
169 0.10
170 0.28
171 1.04
172 0.29
173 0.47
174 0.20
175 0.23
176 0.51
177 0.49
178 0.34
179 0.24
180 0.49
181 0.29
182 0.14
183 0.77
184 1.40
185 0.28
186 0.28
187 0.77
188 -0.09
189 0.28
190 0.08
191 0.34
192 0.44
193 0.51
194 1.25
195 -0.09
196 1.10
197 0.55
198 1.14
199 1.25
200 1.04
201 1.06
202 1.10
203 0.08
204 1.06
205 1.14
206 -1.13
207 0.24
208 -0.33
209 0.23
210 0.24
211 0.55
212 0.23
213 0.51
214 0.49
215 -0.28
216 0.23
217 0.55
218 1.14
219 0.14
220 0.25
221 1.10
222 0.81
223 0.28
224 -0.40
225 0.49
226 0.24
227 0.04
228 0.28
229 1.10
230 0.08
231 0.25
232 0.08
233 0.34
234 0.29
235 0.17
236 -1.13
237 1.06
238 -0.87
239 0.51
240 0.49
241 -2.12
242 0.77
243 0.47
244 0.49
245 0.28
246 1.10
247 -0.68
248 0.04
259 0.23
260 0.44
261 -0.84
262 0.08
263 0.71
264 1.14
265 0.49
266 -0.68
267 0.49
268 -0.57
269 0.28
270 1.04
271 0.29
272 0.47
273 0.20
274 0.51
275 0.51
276 -0.25
277 0.34
278 0.24
279 0.49
280 0.77
281 0.14
282 -0.33
283 1.40
284 0.28
285 0.28
286 0.77
287 -0.09
288 0.28
289 0.08
290 0.51
291 0.44
292 0.51
293 1.25
294 0.66
295 1.10
296 0.55
297 0.52
298 1.25
299 1.04
300 1.06
301 1.10
302 0.08
303 1.06
304 1.14
305 -0.46
306 0.24
307 -0.33
308 0.23
309 0.24
310 0.55
311 0.23
312 0.51
313 0.49
314 -0.54
315 0.23
316 0.55
317 1.14
318 0.49
319 0.25
320 1.10
321 0.81
322 0.28
323 -0.09
324 0.49
325 0.71
326 0.28
327 0.28
328 1.10
329 0.08
330 0.25
331 0.47
332 0.34
333 0.77
334 0.34
335 0.28
336 1.06
337 0.25
338 0.23
339 0.49
340 0.08
341 -1.14
342 0.47
343 0.49
344 -0.59
345 1.10
346 -1.14
347 0.28
358 0.34
359 -0.41
360 0.14
361 0.29
362 0.14
363 -0.68
364 1.04
365 0.28
366 0.04
367 -0.68
368 -0.09
369 0.28
370 0.08
371 0.34
372 0.44
373 0.23
374 -0.43
375 -0.09
376 1.10
377 0.55
378 1.25
379 1.25
380 0.20
381 1.06
382 1.10
383 0.08
384 0.77
385 1.14
386 -0.46
387 -0.41
388 -0.68
389 0.23
390 0.24
391 0.08
392 0.23
393 0.51
394 0.49
395 -0.54
396 0.23
397 0.08
398 0.00
399 0.49
400 0.25
401 1.10
402 -0.54
403 0.28
404 -0.09
405 0.49
406 -0.44
407 -0.46
408 0.28
409 1.10
410 0.08
411 0.25
412 -0.10
413 0.51
414 0.77
415 0.17
416 0.28
417 0.77
418 0.10
419 0.51
420 0.49
421 -0.72
422 0.29
423 0.47
424 0.49
425 0.28
#Reported_Model_Average 0.356
#Overall_Average_Reported 0.356
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
59.000 0
60.000 2
61.000 1
62.000 0
63.000 0
64.000 6
65.000 0
66.000 1
67.000 3
68.000 0
69.000 1
70.000 3
71.000 1
72.000 3
73.000 0
74.000 3
75.000 0
76.000 1
77.000 0
78.000 0
79.000 0
80.000 0
81.000 1
82.000 0
83.000 0
84.000 2
85.000 0
86.000 0
87.000 0
88.000 2
89.000 0
90.000 0
91.000 0
92.000 1
93.000 0
94.000 0
95.000 2
96.000 0
97.000 4
98.000 1
99.000 0
100.000 0
101.000 0
102.000 1
103.000 1
104.000 0
105.000 0
106.000 0
107.000 1
108.000 1
109.000 0
110.000 1
111.000 0
112.000 0
113.000 1
114.000 0
115.000 0
116.000 1
117.000 0
118.000 2
119.000 0
120.000 1
121.000 0
122.000 3
123.000 0
124.000 2
125.000 0
126.000 2
127.000 0
128.000 0
129.000 0
130.000 2
131.000 0
132.000 3
133.000 2
134.000 1
135.000 0
136.000 0
137.000 0
138.000 1
139.000 0
140.000 0
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 6
161.000 3
162.000 1
163.000 2
164.000 2
165.000 1
166.000 0
167.000 2
168.000 0
169.000 1
170.000 0
171.000 1
172.000 0
173.000 0
174.000 1
175.000 1
176.000 1
177.000 0
178.000 0
179.000 3
180.000 0
181.000 1
182.000 0
183.000 3
184.000 1
185.000 0
186.000 2
187.000 0
188.000 0
189.000 2
190.000 0
191.000 1
192.000 0
193.000 0
194.000 1
195.000 1
196.000 0
197.000 0
198.000 0
199.000 4
200.000 0
201.000 1
202.000 0
203.000 4
204.000 0
205.000 1
206.000 0
207.000 0
208.000 0
209.000 0
210.000 1
211.000 0
212.000 0
213.000 1
214.000 0
215.000 0
216.000 0
217.000 0
218.000 0
219.000 0
220.000 1
221.000 0
222.000 0
223.000 0
224.000 2
225.000 1
226.000 0
227.000 1
228.000 0
229.000 0
230.000 1
231.000 0
232.000 5
233.000 2
234.000 0
235.000 0
236.000 0
237.000 0
238.000 0
239.000 0
240.000 0
241.000 1
242.000 0
243.000 10
244.000 0
245.000 1
246.000 0
247.000 4
248.000 0
249.000 0
250.000 0
251.000 0
252.000 0
253.000 0
254.000 0
255.000 0
256.000 0
257.000 0
258.000 0
259.000 1
260.000 1
261.000 1
262.000 0
263.000 1
264.000 1
265.000 0
266.000 2
267.000 0
268.000 0
269.000 0
270.000 0
271.000 0
272.000 0
273.000 0
274.000 1
275.000 0
276.000 1
277.000 0
278.000 2
279.000 0
280.000 0
281.000 0
282.000 0
283.000 1
284.000 0
285.000 0
286.000 1
287.000 0
288.000 2
289.000 3
290.000 0
291.000 0
292.000 0
293.000 0
294.000 1
295.000 0
296.000 0
297.000 0
298.000 1
299.000 0
300.000 2
301.000 0
302.000 1
303.000 2
304.000 0
305.000 0
306.000 0
307.000 0
308.000 0
309.000 0
310.000 0
311.000 0
312.000 0
313.000 1
314.000 0
315.000 0
316.000 1
317.000 0
318.000 0
319.000 3
320.000 0
321.000 0
322.000 1
323.000 2
324.000 1
325.000 1
326.000 0
327.000 0
328.000 1
329.000 1
330.000 2
331.000 2
332.000 1
333.000 1
334.000 0
335.000 0
336.000 0
337.000 0
338.000 0
339.000 0
340.000 0
341.000 0
342.000 2
343.000 1
344.000 0
345.000 2
346.000 0
347.000 3
348.000 0
349.000 0
350.000 0
351.000 0
352.000 0
353.000 0
354.000 0
355.000 0
356.000 0
357.000 0
358.000 1
359.000 5
360.000 0
361.000 5
362.000 0
363.000 3
364.000 9
365.000 1
366.000 0
367.000 3
368.000 1
369.000 1
370.000 0
371.000 0
372.000 3
373.000 0
374.000 1
375.000 5
376.000 0
377.000 0
378.000 1
379.000 1
380.000 0
381.000 8
382.000 3
383.000 0
384.000 7
385.000 11
386.000 1
387.000 2
388.000 6
389.000 0
390.000 2
391.000 0
392.000 0
393.000 1
394.000 7
395.000 1
396.000 1
397.000 2
398.000 4
399.000 1
400.000 1
401.000 4
402.000 0
403.000 1
404.000 4
405.000 4
406.000 0
407.000 1
408.000 1
409.000 0
410.000 2
411.000 7
412.000 0
413.000 3
414.000 0
415.000 0
416.000 2
417.000 2
418.000 0
419.000 1
420.000 1
421.000 1
422.000 5
423.000 1
424.000 1
425.000 0
#Reported_Model_Average 0.905
#Overall_Average_Reported 0.905
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 5246:M 382 GLY 2HA :M 398 TYR CB : -1.129: 152
: 5246:M 387 ARG 1HG :M 388 LEU 3HD2 : -1.002: 162
: 5246:M 385 TYR 2HB :M 390 ARG O : -0.903: 166
: 5246:M 381 LEU 2HD1 :M 384 LEU 2HB : -0.726: 151
: 5246:M 363 LEU O :M 367 LEU 1HB : -0.719: 154
: 5246:M 387 ARG 1HG :M 388 LEU CD2 : -0.714: 162
: 5246:M 381 LEU 2HD1 :M 381 LEU O : -0.699: 150
: 5246:M 364 PHE HE1 :M 363 LEU 3HD1 : -0.677: 164
: 5246:M 394 ALA 2HB :M 385 TYR 1HB : -0.666: 152
: 5246:M 385 TYR CB :M 394 ALA 2HB : -0.652: 152
: 5246:M 394 ALA HA :M 385 TYR HD2 : -0.652: 153
: 5246:M 364 PHE CE1 :M 363 LEU 3HD1 : -0.621: 164
: 5246:M 385 TYR HE2 :M 397 THR 1HG2 : -0.605: 149
: 5246:M 364 PHE HA :M 367 LEU 1HB : -0.582: 156
: 5246:M 361 LEU 1HD1 :M 385 TYR CE1 : -0.574: 147
: 5246:M 385 TYR HD2 :M 394 ALA CA : -0.561: 153
: 5246:M 364 PHE 1HB :M 381 LEU 2HD2 : -0.558: 158
: 5246:M 365 GLU OE2 :M 361 LEU 3HD2 : -0.556: 148
: 5246:M 382 GLY O :M 394 ALA 1HB : -0.513: 152
: 5246:M 381 LEU O :M 384 LEU 2HB : -0.508: 151
: 5246:M 361 LEU 2HD1 :M 384 LEU 3HD2 : -0.507: 152
: 5246:M 381 LEU 1HB :M 364 PHE HD2 : -0.500: 159
: 5246:M 385 TYR O :M 388 LEU N : -0.489: 164
: 5246:M 397 THR CG2 :M 398 TYR N : -0.487: 152
: 5246:M 384 LEU O :M 388 LEU HG : -0.460: 163
: 5246:M 394 ALA HA :M 385 TYR CD2 : -0.460: 153
: 5246:M 398 TYR CB :M 394 ALA O : -0.458: 154
: 5246:M 367 LEU CB :M 364 PHE HA : -0.454: 156
: 5246:M 385 TYR O :M 386 GLU C : -0.454: 166
: 5246:M 385 TYR HE1 :M 361 LEU 1HD1 : -0.453: 147
: 5246:M 398 TYR CB :M 382 GLY CA : -0.453: 152
: 5246:M 390 ARG 2HD :M 393 ASP 1HB : -0.438: 156
: 5246:M 388 LEU 3HD2 :M 388 LEU N : -0.437: 164
: 5246:M 381 LEU 3HD1 :M 384 LEU 3HD2 : -0.430: 152
: 5246:M 361 LEU 2HD1 :M 384 LEU CD2 : -0.429: 152
: 5246:M 364 PHE O :M 368 VAL HB : -0.420: 156
: 5246:M 364 PHE CD1 :M 364 PHE N : -0.417: 163
: 5246:M 381 LEU CD1 :M 384 LEU 3HD2 : -0.404: 152
: 5246:M 243 LYS 1HE :M 247 LEU 1HD2 : -1.051: 125
: 5246:M 243 LYS CE :M 247 LEU 1HD2 : -0.924: 125
: 5246:M 243 LYS 1HE :M 247 LEU CD2 : -0.746: 125
: 5246:M 243 LYS O :M 243 LYS 2HD : -0.621: 120
: 5246:M 243 LYS CE :M 247 LEU CD2 : -0.611: 125
: 5246:M 243 LYS 2HD :M 243 LYS C : -0.554: 120
: 5246:M 243 LYS C :M 243 LYS CD : -0.408: 120
: 5246:M 422 LEU 1HD2 :M 70 GLU CB : -0.969: 108
: 5246:M 70 GLU 2HB :M 422 LEU 1HD2 : -0.779: 108
: 5246:M 422 LEU 1HD2 :M 70 GLU 1HB : -0.712: 108
: 5246:M 74 HIS CE1 :M 422 LEU 3HD1 : -0.633: 130
: 5246:M 422 LEU CD1 :M 74 HIS CE1 : -0.517: 130
: 5246:M 76 ASN OD1 :M 74 HIS O : -0.463: 109
: 5246:M 160 ASP O :M 164 ARG 2HG : -0.963: 109
: 5246:M 160 ASP OD1 :M 161 PRO 1HD : -0.680: 119
: 5246:M 161 PRO 2HG :M 191 ASP OD1 : -0.633: 114
: 5246:M 163 THR HB :M 160 ASP 2HB : -0.595: 112
: 5246:M 160 ASP 2HB :M 163 THR CB : -0.515: 112
: 5246:M 160 ASP OD1 :M 161 PRO CD : -0.476: 119
: 5246:M 160 ASP O :M 164 ARG CG : -0.471: 109
: 5246:M 403 GLU OE1 :M 400 GLN HA : -0.931: 142
: 5246:M 116 ASP O :M 120 GLN 2HG : -0.915: 87
: 5246:M 203 LYS 2HE :M 199 TYR CZ : -0.786: 96
: 5246:M 203 LYS 2HE :M 199 TYR OH : -0.732: 101
: 5246:M 203 LYS 2HE :M 199 TYR CE2 : -0.551: 99
: 5246:M 203 LYS 2HG :M 199 TYR CE1 : -0.422: 91
: 5246:M 323 VAL 3HG1 :M 319 GLN O : -0.735: 86
: 5246:M 294 VAL 2HG2 :M 323 VAL 3HG2 : -0.611: 84
: 5246:M 319 GLN NE2 :M 319 GLN HA : -0.421: 113
: 5246:M 183 LEU 2HD1 :M 179 ARG O : -0.717: 81
: 5246:M 179 ARG 2HG :M 183 LEU CD1 : -0.672: 81
: 5246:M 179 ARG 2HG :M 183 LEU 1HD1 : -0.581: 81
: 5246:M 404 VAL 3HG1 :M 375 VAL 2HG2 : -0.705: 134
: 5246:M 405 ALA 2HB :M 375 VAL 1HG1 : -0.669: 134
: 5246:M 404 VAL 2HG1 :M 401 GLY 1HA : -0.607: 134
: 5246:M 375 VAL 2HG2 :M 404 VAL CG1 : -0.560: 134
: 5246:M 375 VAL CG1 :M 405 ALA 2HB : -0.550: 134
: 5246:M 405 ALA CB :M 375 VAL 1HG1 : -0.494: 134
: 5246:M 401 GLY O :M 405 ALA N : -0.491: 127
: 5246:M 404 VAL 2HG1 :M 401 GLY CA : -0.451: 134
: 5246:M 399 ALA C :M 401 GLY H : -0.418: 144
: 5246:M 133 ASP OD1 :M 130 THR 2HG2 : -0.695: 86
: 5246:M 133 ASP H :M 130 THR 3HG2 : -0.576: 76
: 5246:M 132 LYS HA :M 330 GLN NE2 : -0.661: 72
: 5246:M 333 LEU 2HD2 :M 132 LYS 2HG : -0.458: 77
: 5246:M 132 LYS HA :M 330 GLN 1HE2 : -0.423: 72
: 5246:M 416 GLU 1HG :M 417 LEU N : -0.659: 124
: 5246:M 417 LEU N :M 416 GLU CG : -0.530: 124
: 5246:M 424 ALA 3HB :M 421 LYS O : -0.643: 132
: 5246:M 359 ARG 1HG :M 359 ARG O : -0.637: 151
: 5246:M 359 ARG O :M 359 ARG CG : -0.574: 151
: 5246:M 358 SER OG :M 359 ARG N : -0.424: 156
: 5246:M 347 GLU 2HB :M 343 ALA O : -0.626: 134
: 5246:M 347 GLU 2HG :M 345 GLY O : -0.594: 132
: 5246:M 347 GLU H :M 345 GLY C : -0.472: 137
: 5246:M 124 VAL 3HG2 :M 95 VAL 3HG1 : -0.623: 77
: 5246:M 95 VAL 3HG1 :M 124 VAL CG2 : -0.525: 77
: 5246:M 186 GLU O :M 189 GLU 1HG : -0.622: 101
: 5246:M 298 TYR O :M 302 LYS 1HG : -0.622: 97
: 5246:M 186 GLU O :M 189 GLU N : -0.537: 99
: 5246:M 60 ASP OD1 :M 61 PRO 1HD : -0.613: 111
: 5246:M 64 ARG 1HG :M 60 ASP O : -0.465: 97
: 5246:M 64 ARG 1HG :M 64 ARG H : -0.447: 95
: 5246:M 67 LEU CB :M 64 ARG HA : -0.439: 97
: 5246:M 67 LEU 2HB :M 64 ARG O : -0.437: 97
: 5246:M 67 LEU 1HB :M 64 ARG HA : -0.405: 97
: 5246:M 289 THR OG1 :M 263 ARG NH2 : -0.598: 101
: 5246:M 289 THR N :M 288 GLU CG : -0.423: 117
: 5246:M 288 GLU 1HG :M 289 THR 3HG2 : -0.403: 117
: 5246:M 410 THR 3HG2 :M 413 ASP OD1 : -0.590: 127
: 5246:M 232 LYS 2HE :M 233 ASP OD2 : -0.553: 114
: 5246:M 411 GLN 1HG :M 232 LYS HA : -0.524: 107
: 5246:M 411 GLN HA :M 411 GLN OE1 : -0.508: 114
: 5246:M 411 GLN C :M 413 ASP N : -0.462: 120
: 5246:M 233 ASP OD1 :M 230 THR 2HG2 : -0.459: 108
: 5246:M 232 LYS 1HE :M 232 LYS 2HB : -0.453: 114
: 5246:M 232 LYS CA :M 411 GLN 1HG : -0.413: 107
: 5246:M 411 GLN C :M 413 ASP H : -0.412: 120
: 5246:M 411 GLN N :M 410 THR OG1 : -0.408: 115
: 5246:M 175 ASP 1HB :M 174 HIS O : -0.576: 94
: 5246:M 259 ASP OD1 :M 260 PRO 1HD : -0.572: 109
: 5246:M 181 LEU 1HD1 :M 205 TYR CE1 : -0.570: 80
: 5246:M 122 ILE 2HG1 :M 118 TYR O : -0.568: 76
: 5246:M 118 TYR CE1 :M 102 GLY 2HA : -0.491: 72
: 5246:M 122 ILE O :M 126 ARG CG : -0.467: 95
: 5246:M 122 ILE O :M 126 ARG 2HG : -0.446: 95
: 5246:M 329 THR OG1 :M 331 LYS 1HG : -0.564: 96
: 5246:M 332 ASP N :M 331 LYS 1HG : -0.471: 96
: 5246:M 408 GLU 1HG :M 407 GLU 2HB : -0.561: 130
: 5246:M 84 PHE HD1 :M 97 THR 3HG2 : -0.559: 81
: 5246:M 97 THR 1HG2 :M 88 VAL 3HG2 : -0.497: 82
: 5246:M 97 THR 3HG2 :M 84 PHE CD1 : -0.464: 81
: 5246:M 88 VAL 3HG2 :M 97 THR CG2 : -0.428: 82
: 5246:M 241 LYS O :M 245 GLU 2HG : -0.555: 98
: 5246:M 220 GLN O :M 224 VAL 3HG1 : -0.545: 99
: 5246:M 224 VAL CG2 :M 195 VAL 2HG2 : -0.497: 107
: 5246:M 369 GLU HA :M 372 PRO 2HG : -0.539: 161
: 5246:M 372 PRO O :M 378 TYR HE1 : -0.432: 158
: 5246:M 374 TYR H :M 372 PRO C : -0.429: 159
: 5246:M 313 ALA O :M 316 THR HB : -0.527: 98
: 5246:M 423 LYS 1HB :M 419 ASP O : -0.520: 128
: 5246:M 213 ASP OD1 :M 210 ARG NH1 : -0.509: 94
: 5246:M 138 GLN 2HG :M 134 LEU O : -0.502: 76
: 5246:M 194 TYR OH :M 162 PHE HD1 : -0.499: 110
: 5246:M 266 LEU 2HD1 :M 266 LEU HA : -0.494: 86
: 5246:M 171 HIS 2HB :M 176 ASN 1HB : -0.479: 86
: 5246:M 261 PHE O :M 264 TYR 2HB : -0.478: 84
: 5246:M 69 GLN 1HB :M 66 ALA O : -0.477: 96
: 5246:M 110 ARG O :M 113 ASP 1HB : -0.474: 84
: 5246:M 278 ARG HA :M 278 ARG 2HD : -0.471: 128
: 5246:M 342 LYS 2HB :M 342 LYS 2HE : -0.453: 119
: 5246:M 322 GLU OE1 :M 325 ARG NH1 : -0.451: 92
: 5246:M 324 ALA HA :M 328 GLY H : -0.450: 79
: 5246:M 379 TYR HE2 :M 420 ALA 2HB : -0.447: 140
: 5246:M 92 PRO O :M 98 TYR OH : -0.445: 80
: 5246:M 165 TYR CE2 :M 169 GLN NE2 : -0.439: 102
: 5246:M 167 LEU 2HD2 :M 167 LEU HA : -0.431: 100
: 5246:M 108 LEU CD1 :M 81 LEU 3HD1 : -0.425: 73
: 5246:M 303 LEU 2HD1 :M 303 LEU HA : -0.424: 103
: 5246:M 225 ALA C :M 227 GLU H : -0.421: 116
: 5246:M 300 LEU O :M 300 LEU 2HD1 : -0.414: 98
: 5246:M 71 HIS O :M 72 LEU C : -0.414: 95
: 5246:M 72 LEU HA :M 72 LEU 3HD2 : -0.411: 92
: 5246:M 103 LYS O :M 107 ARG 2HG : -0.412: 80
: 5246:M 201 LEU 3HD1 :M 184 PHE 2HB : -0.410: 79
: 5246:M 396 ASP H :M 395 ILE HB : -0.410: 154
: 5246:M 274 ASP O :M 276 ALA N : -0.408: 114
: 5246:M 283 PHE O :M 286 LEU 1HB : -0.405: 87
#sum2 ::31.64 clashscore : -1.00 clashscore B<40
#summary::5246 atoms:0 atoms B<40:592782 potential dots:37050.0 A^2:166 bumps:0 bumps B<40:1297 score
Output from PDB validation software
Summary from PDB validation
May. 11, 00:06:10 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 1.5 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
--------------------------------------------------------------------------------
-10.7 TYR A 94 N - CA - C 100.5 111.2
11.1 VAL A 95 N - CA - C 122.3 111.2
-9.2 ASP B 60 N - CA - C 102.0 111.2
9.2 ASP B 75 N - CA - C 120.4 111.2
10.0 VAL B 95 N - CA - C 121.2 111.2
12.0 ASP C 75 N - CA - C 123.2 111.2
-8.8 ASN C 76 N - CA - C 102.4 111.2
-11.4 TYR C 94 N - CA - C 99.8 111.2
10.0 TYR C 98 N - CA - C 121.2 111.2
9.6 ASP C 109 N - CA - C 120.8 111.2
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.
==> The following residues have missing atoms:
RES MOD#C SEQ ATOMS
GLU( A 59) CG CD OE1 OE2
GLU( B 59) CG CD OE1 OE2
TYR( D 118) CG CD1 CD2 CE1 CE2 CZ OH
SRR115C_XRay_em_bcr3.pdb: Error: Z value is 48. It should be 24.