Detailed results of SR478_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 >>>----------+
| |
| SR478_XRay_em_bcr3_noHs_000.rin 0.0 131 residues |
| |
| Ramachandran plot: 94.0% core 6.0% allow 0.0% gener 0.0% disall |
| |
| All Ramachandrans: 0 labelled residues (out of 119) |
+| Chi1-chi2 plots: 2 labelled residues (out of 92) |
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
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
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
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
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 -0.27
5 -1.82
6 -0.50
7 0.22
8 0.62
9 1.18
10 0.61
11 1.01
12 0.87
13 0.93
14 0.99
15 1.22
16 1.23
17 1.43
18 0.80
22 -1.06
23 -1.64
24 -0.52
25 -0.70
26 -2.30
27 0.71
28 1.43
32 0.88
33 1.18
34 1.17
35 1.01
36 0.95
37 0.56
38 0.77
39 0.91
40 0.38
41 0.50
42 -0.28
43 -0.21
44 -1.00
45 -1.32
46 -2.58
47 0.23
48 -0.37
49 0.14
50 0.99
51 1.05
52 0.81
53 0.88
54 0.95
55 0.84
56 0.47
57 1.23
58 1.43
59 0.88
60 1.32
61 1.08
62 0.76
63 0.64
64 1.11
65 0.68
66 0.57
67 0.68
68 -0.27
81 -0.34
82 -0.82
83 -1.62
84 -0.98
85 0.22
86 0.47
87 1.18
88 0.61
89 1.01
90 0.87
91 1.39
92 1.13
93 1.22
94 0.90
95 1.43
96 1.01
100 -0.84
101 -1.96
102 -0.88
103 -0.07
104 0.28
105 1.01
106 0.86
110 0.91
111 1.22
112 1.18
113 1.01
114 1.19
115 0.56
116 0.98
117 0.95
118 1.14
119 1.13
120 -0.86
121 -0.40
122 -0.11
123 -0.88
124 -2.11
125 -0.47
126 -0.25
127 0.15
128 0.99
129 0.56
130 0.77
131 1.13
132 0.95
133 0.84
134 1.01
135 1.23
136 1.39
137 1.13
138 1.32
139 0.82
140 0.99
141 1.18
142 1.39
143 1.08
144 0.77
145 1.04
146 1.14
#Reported_Model_Average 0.459
#Overall_Average_Reported 0.459
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 0.78
4 -1.82
5 -0.74
6 0.08
7 0.40
8 0.62
9 0.94
10 0.25
11 0.81
12 0.27
13 0.25
14 0.05
15 1.26
16 1.23
17 1.03
18 0.84
19 0.88
21 -0.46
22 -0.28
23 -0.63
24 0.05
25 -0.75
26 -0.97
27 -0.77
28 -0.84
29 0.00
31 0.49
32 1.42
33 0.44
34 0.24
35 -0.93
36 0.12
37 0.65
38 0.85
39 0.10
40 -0.25
41 0.69
42 -0.68
43 0.04
44 -0.76
45 -0.65
46 -2.26
47 0.14
48 0.41
49 0.68
50 0.99
51 0.96
52 0.77
53 -0.31
54 -0.44
55 0.86
56 0.69
57 1.10
58 0.92
59 0.37
60 0.16
61 1.06
62 0.76
63 -0.21
64 1.13
65 0.82
66 0.65
67 0.59
68 -0.21
69 0.00
80 -0.03
81 0.09
82 -0.11
83 -0.81
84 0.04
85 0.60
86 0.47
87 0.44
88 0.25
89 0.61
90 0.33
91 1.27
92 0.59
93 1.17
94 0.39
95 0.89
96 0.96
97 -0.08
99 -0.95
100 -0.19
101 -0.80
102 -0.69
103 0.44
104 0.45
105 -0.82
106 0.41
107 0.00
109 1.22
110 0.10
111 1.00
112 0.24
113 -0.45
114 1.03
115 0.58
116 0.56
117 0.66
118 0.42
119 1.02
120 -0.97
121 0.42
122 0.15
123 -1.14
124 -0.78
125 -0.09
126 -0.55
127 0.60
128 0.99
129 0.77
130 0.75
131 -0.54
132 0.30
133 1.01
134 0.96
135 1.10
136 0.83
137 0.43
138 0.43
139 0.83
140 0.99
141 0.45
142 1.27
143 1.10
144 0.63
145 0.88
146 1.03
147 0.00
#Reported_Model_Average 0.283
#Overall_Average_Reported 0.283
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 0.04
4 -0.68
5 0.71
6 0.59
7 -0.09
8 0.44
9 1.25
10 1.40
11 0.81
12 0.28
13 0.51
14 1.06
15 0.47
16 0.25
17 1.04
18 0.81
19 0.04
20 -1.30
21 0.51
22 -0.03
23 0.34
24 -0.46
25 0.23
26 0.47
27 -0.94
28 1.04
29 -0.25
30 0.91
31 0.09
32 0.17
33 1.14
34 0.52
35 0.71
36 0.34
37 -0.09
38 1.00
39 0.17
40 0.08
41 1.06
42 1.00
43 0.25
44 0.51
45 -0.03
46 -1.14
47 0.08
48 -0.10
49 0.51
50 0.14
51 -0.74
52 0.66
53 1.06
54 0.08
55 0.71
56 0.93
57 0.25
58 1.04
59 1.06
60 -0.83
61 0.28
62 0.49
63 1.14
64 0.51
65 0.47
66 1.00
67 0.47
68 0.24
69 1.10
80 0.34
81 0.04
82 -1.14
83 0.71
84 0.59
85 -0.09
86 0.44
87 1.25
88 1.40
89 0.81
90 0.28
91 0.51
92 1.06
93 0.47
94 0.25
95 1.04
96 0.93
97 0.04
98 -0.83
99 0.51
100 0.25
101 0.34
102 0.28
103 0.23
104 0.47
105 -0.94
106 1.04
107 0.49
108 0.91
109 -0.56
110 0.17
111 1.25
112 0.52
113 0.71
114 0.34
115 -0.09
116 1.00
117 0.17
118 0.08
119 0.77
120 1.00
121 0.25
122 0.51
123 -0.03
124 -1.14
125 0.08
126 -0.10
127 0.51
128 0.14
129 -0.74
130 0.66
131 0.77
132 0.47
133 -0.44
134 0.93
135 -0.57
136 1.04
137 1.06
138 0.51
139 0.28
140 0.49
141 1.25
142 0.51
143 0.47
144 1.00
145 0.47
146 -0.41
147 1.10
#Reported_Model_Average 0.384
#Overall_Average_Reported 0.384
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 0.04
4 -0.68
5 0.71
6 0.59
7 -0.09
8 0.44
9 1.25
10 1.40
11 0.81
12 0.28
13 0.51
14 1.06
15 0.47
16 0.25
17 1.04
18 0.81
19 0.04
20 -1.30
21 0.51
22 -0.03
23 0.34
24 -0.46
25 0.23
26 0.47
27 -0.94
28 1.04
29 -0.25
30 0.91
31 0.09
32 0.17
33 1.14
34 0.52
35 0.71
36 0.34
37 -0.09
38 1.00
39 0.17
40 0.08
41 1.06
42 1.00
43 0.25
44 0.51
45 -0.03
46 -1.14
47 0.08
48 -0.10
49 0.51
50 0.14
51 -0.74
52 0.66
53 1.06
54 0.08
55 0.71
56 0.93
57 0.25
58 1.04
59 1.06
60 -0.83
61 0.28
62 0.49
63 1.14
64 0.51
65 0.47
66 1.00
67 0.47
68 0.24
69 1.10
80 0.34
81 0.04
82 -1.14
83 0.71
84 0.59
85 -0.09
86 0.44
87 1.25
88 1.40
89 0.81
90 0.28
91 0.51
92 1.06
93 0.47
94 0.25
95 1.04
96 0.93
97 0.04
98 -0.83
99 0.51
100 0.25
101 0.34
102 0.28
103 0.23
104 0.47
105 -0.94
106 1.04
107 0.49
108 0.91
109 -0.56
110 0.17
111 1.25
112 0.52
113 0.71
114 0.34
115 -0.09
116 1.00
117 0.17
118 0.08
119 0.77
120 1.00
121 0.25
122 0.51
123 -0.03
124 -1.14
125 0.08
126 -0.10
127 0.51
128 0.14
129 -0.74
130 0.66
131 0.77
132 0.47
133 -0.44
134 0.93
135 -0.57
136 1.04
137 1.06
138 0.51
139 0.28
140 0.49
141 1.25
142 0.51
143 0.47
144 1.00
145 0.47
146 -0.41
147 1.10
#Reported_Model_Average 0.384
#Overall_Average_Reported 0.384
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 0
5.000 0
6.000 1
7.000 1
8.000 1
9.000 1
10.000 0
11.000 0
12.000 0
13.000 0
14.000 2
15.000 1
16.000 0
17.000 1
18.000 1
19.000 1
20.000 0
21.000 0
22.000 0
23.000 0
24.000 1
25.000 0
26.000 0
27.000 5
28.000 2
29.000 0
30.000 1
31.000 1
32.000 0
33.000 1
34.000 1
35.000 2
36.000 0
37.000 0
38.000 0
39.000 1
40.000 0
41.000 0
42.000 4
43.000 1
44.000 0
45.000 0
46.000 2
47.000 1
48.000 0
49.000 0
50.000 0
51.000 1
52.000 0
53.000 5
54.000 5
55.000 0
56.000 0
57.000 3
58.000 1
59.000 0
60.000 0
61.000 1
62.000 0
63.000 1
64.000 2
65.000 0
66.000 0
67.000 0
68.000 2
69.000 0
70.000 0
71.000 0
72.000 0
73.000 0
74.000 0
75.000 0
76.000 0
77.000 0
78.000 0
79.000 0
80.000 0
81.000 0
82.000 0
83.000 0
84.000 1
85.000 0
86.000 0
87.000 1
88.000 0
89.000 0
90.000 0
91.000 0
92.000 0
93.000 0
94.000 3
95.000 0
96.000 0
97.000 0
98.000 1
99.000 0
100.000 0
101.000 0
102.000 1
103.000 0
104.000 0
105.000 4
106.000 1
107.000 0
108.000 0
109.000 1
110.000 0
111.000 0
112.000 0
113.000 2
114.000 0
115.000 0
116.000 0
117.000 1
118.000 0
119.000 0
120.000 2
121.000 1
122.000 0
123.000 0
124.000 0
125.000 1
126.000 4
127.000 0
128.000 0
129.000 1
130.000 1
131.000 8
132.000 0
133.000 0
134.000 1
135.000 3
136.000 0
137.000 0
138.000 0
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
#Reported_Model_Average 0.634
#Overall_Average_Reported 0.634
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 2233:M 53 LEU 1HD2 :M 131 LEU 1HB : -0.907: 43
: 2233:M 53 LEU 2HD2 :M 131 LEU 3HD2 : -0.569: 43
: 2233:M 53 LEU 1HD2 :M 131 LEU CB : -0.561: 43
: 2233:M 53 LEU CD2 :M 131 LEU 3HD2 : -0.545: 43
: 2233:M 131 LEU 3HD1 :M 131 LEU C : -0.514: 46
: 2233:M 131 LEU 3HD1 :M 131 LEU O : -0.492: 46
: 2233:M 53 LEU 1HD1 :M 130 VAL 2HG1 : -0.419: 43
: 2233:M 42 VAL 3HG1 :M 135 GLN 1HG : -0.839: 46
: 2233:M 135 GLN 1HG :M 42 VAL CG1 : -0.759: 46
: 2233:M 42 VAL 3HG1 :M 135 GLN CG : -0.574: 46
: 2233:M 134 ILE 2HG2 :M 42 VAL 1HG2 : -0.520: 46
: 2233:M 43 GLN 1HG :M 39 SER O : -0.775: 55
: 2233:M 27 ILE 3HD1 :M 27 ILE O : -0.743: 34
: 2233:M 102 GLU OE1 :M 28 HIS HE1 : -0.613: 39
: 2233:M 27 ILE 3HD1 :M 27 ILE C : -0.454: 34
: 2233:M 28 HIS N :M 27 ILE CG2 : -0.411: 27
: 2233:M 105 ILE 3HD1 :M 105 ILE O : -0.732: 39
: 2233:M 105 ILE 3HD1 :M 105 ILE C : -0.475: 39
: 2233:M 58 HIS CE1 :M 54 LYS 2HD : -0.647: 41
: 2233:M 54 LYS 1HD :M 54 LYS C : -0.469: 41
: 2233:M 54 LYS 2HE :M 54 LYS 2HB : -0.411: 41
: 2233:M 126 LYS NZ :M 126 LYS HA : -0.631: 54
: 2233:M 126 LYS 3HZ :M 126 LYS HA : -0.507: 54
: 2233:M 68 ARG 1HG :M 64 ASN O : -0.598: 54
: 2233:M 68 ARG 2HH2 :M 64 ASN 2HB : -0.430: 58
: 2233:M 120 VAL 2HG2 :M 57 GLN CG : -0.589: 40
: 2233:M 57 GLN 2HG :M 120 VAL 2HG2 : -0.579: 40
: 2233:M 61 GLU 2HG :M 57 GLN O : -0.452: 41
: 2233:M 8 PRO 1HD :M 7 VAL N : -0.512: 38
: 2233:M 33 TYR 1HB :M 17 HIS CD2 : -0.502: 28
: 2233:M 6 SER O :M 9 TYR 2HB : -0.497: 35
: 2233:M 18 ILE 2HG1 :M 14 LEU O : -0.493: 32
: 2233:M 31 ASN 2HB :M 109 ASN 2HB : -0.493: 24
: 2233:M 30 MET 1HG :M 14 LEU 2HD2 : -0.415: 34
: 2233:M 84 SER O :M 87 TYR 2HB : -0.478: 30
: 2233:M 117 SER O :M 121 GLN 2HG : -0.470: 52
: 2233:M 15 LYS O :M 19 GLU 2HG : -0.470: 46
: 2233:M 46 LEU 2HD1 :M 46 LEU C : -0.460: 50
: 2233:M 94 GLN 2HE2 :M 94 GLN 1HB : -0.454: 35
: 2233:M 98 MET 2HG :M 94 GLN O : -0.454: 60
: 2233:M 129 VAL HB :M 125 THR 2HG2 : -0.454: 41
: 2233:M 24 GLU OE2 :M 106 HIS HE1 : -0.448: 38
: 2233:M 51 VAL HB :M 47 THR 2HG2 : -0.425: 39
: 2233:M 113 ARG 2HG :M 63 TYR CE2 : -0.410: 27
: 2233:M 113 ARG 1HG :M 34 TYR CG : -0.404: 24
: 2233:M 35 ARG HE :M 35 ARG 2HB : -0.400: 34
#sum2 ::20.60 clashscore : 12.52 clashscore B<40
#summary::2233 atoms:1677 atoms B<40:250350 potential dots:15650.0 A^2:46 bumps:21 bumps B<40:758.7 score
Output from PDB validation software
Summary from PDB validation
May. 10, 19:12:26 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 0.9 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
--------------------------------------------------------------------------------
5.7 LYS A 26 N - CA - C 116.9 111.2
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.
SR478_XRay_em_bcr3.pdb: Error: Z value is 4. It should be 2.