Detailed results of SPR104_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 >>>----------+
| |
| SPR104_XRay_em_bcr3_noHs_000.rin 0.0 129 residues |
| |
+| Ramachandran plot: 89.7% core 10.3% allow 0.0% gener 0.0% disall |
| |
| All Ramachandrans: 0 labelled residues (out of 117) |
+| Chi1-chi2 plots: 2 labelled residues (out of 84) |
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
13 0.13
14 -1.00
15 -0.87
16 -1.43
17 -0.69
18 -0.92
19 -0.51
20 -1.40
21 -1.16
22 0.42
23 -0.96
24 -1.78
25 -0.65
26 -1.07
27 0.44
28 -0.26
29 1.00
30 -0.42
31 0.35
32 -0.42
33 -0.35
34 -0.23
35 -0.87
36 -0.49
37 0.57
38 -0.21
39 -0.02
40 0.44
41 1.14
42 -0.61
43 0.40
44 -0.66
45 -0.23
46 -0.39
47 -1.52
48 0.34
49 -1.43
50 -0.76
51 0.07
52 -0.49
53 0.07
54 0.24
55 -1.05
56 0.12
60 -0.21
61 0.06
62 -0.68
63 0.45
64 -0.36
65 -0.02
66 1.11
67 0.68
68 0.55
69 1.20
70 0.74
74 1.13
75 0.21
76 -0.81
89 -0.62
90 -1.46
91 0.40
92 0.22
93 -1.05
94 -1.43
95 0.82
96 -0.87
97 -0.55
98 -1.44
99 -1.77
100 0.42
101 -0.96
102 -1.26
103 -0.65
104 -1.28
105 0.87
106 -0.29
107 0.68
108 0.09
109 0.35
110 -0.33
111 -0.43
112 -0.09
113 -1.07
114 -0.69
115 0.31
116 -0.33
117 -0.02
118 0.58
119 0.82
120 -0.61
121 0.37
122 -0.46
123 -0.34
124 -0.43
125 -1.39
126 0.34
127 -1.38
128 -0.68
129 -0.39
130 -0.02
131 0.00
132 0.29
133 -1.77
134 -0.33
138 -0.49
139 0.14
140 -0.12
141 0.45
142 -0.17
143 0.25
144 1.11
145 0.87
146 0.87
147 1.22
148 1.23
152 0.62
153 -0.43
#Reported_Model_Average -0.217
#Overall_Average_Reported -0.217
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
12 -0.74
13 0.30
14 -0.78
15 -0.79
16 -0.27
17 -0.48
18 -0.19
19 0.15
20 -0.58
21 -0.42
22 0.45
23 -0.04
24 -0.91
25 -0.07
26 -0.73
27 0.50
28 -0.65
29 1.00
30 -0.86
31 0.42
32 -0.29
33 0.35
34 -0.10
35 -0.07
36 -0.43
37 0.72
38 -0.46
39 0.12
40 0.71
41 1.14
42 -0.61
43 0.40
44 -0.66
45 0.47
46 -0.13
47 -1.29
48 -0.01
49 -1.66
50 -0.76
51 0.66
52 0.09
53 0.07
54 0.08
55 -0.05
56 -0.09
57 -0.61
59 0.00
60 -0.26
61 0.06
62 -1.86
63 0.54
64 -0.08
65 0.52
66 0.92
67 -0.71
68 0.79
69 0.27
70 0.42
71 1.15
73 -1.08
74 1.20
75 0.21
76 0.01
77 -0.30
88 0.00
89 -0.18
90 -2.88
91 0.52
92 0.15
93 -1.15
94 -0.26
95 0.04
96 -0.26
97 0.26
98 -0.45
99 -0.72
100 -0.23
101 -0.04
102 -0.99
103 0.07
104 -0.83
105 -0.02
106 -0.27
107 0.68
108 0.07
109 0.49
110 0.22
111 0.30
112 -0.16
113 -0.17
114 -0.60
115 0.56
116 -0.52
117 0.40
118 0.92
119 0.82
120 -0.61
121 0.37
122 -0.46
123 0.26
124 -0.08
125 -0.92
126 0.31
127 -1.12
128 -0.68
129 0.43
130 0.32
131 0.00
132 0.18
133 -0.43
134 -0.31
135 0.70
137 0.00
138 0.14
139 0.14
140 -0.58
141 0.54
142 0.36
143 0.56
144 0.80
145 0.03
146 0.90
147 0.85
148 0.10
149 -0.29
151 -1.08
152 0.86
153 -0.43
154 0.84
#Reported_Model_Average -0.061
#Overall_Average_Reported -0.061
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
12 -0.84
13 0.08
14 1.04
15 0.28
16 0.81
17 0.28
18 0.28
19 0.20
20 0.77
21 0.77
22 0.08
23 1.06
24 0.17
25 0.28
26 0.41
27 0.04
28 -0.10
29 1.10
30 1.12
31 0.08
32 0.08
33 -0.46
34 0.93
35 0.09
36 0.71
37 0.66
38 0.17
39 0.71
40 0.51
41 1.10
42 0.14
43 0.25
44 0.49
45 0.47
46 1.04
47 -1.97
48 0.93
49 0.71
50 0.49
51 1.62
52 0.59
53 0.44
54 0.23
55 1.04
56 0.08
57 0.47
58 0.91
59 1.10
60 -0.10
61 1.10
62 0.81
63 0.55
64 1.06
65 0.59
66 0.51
67 0.04
68 -0.46
69 1.40
70 0.25
71 0.08
72 0.91
73 -0.74
74 0.23
75 0.49
76 1.40
77 -0.10
88 0.14
89 0.04
90 -0.84
91 0.08
92 0.71
93 0.28
94 0.81
95 0.28
96 0.28
97 0.20
98 0.77
99 -0.33
100 0.08
101 1.06
102 0.17
103 0.28
104 0.51
105 0.04
106 -0.10
107 1.10
108 1.12
109 0.08
110 0.08
111 -0.46
112 0.93
113 -0.56
114 0.71
115 0.66
116 0.17
117 0.71
118 0.51
119 1.10
120 0.14
121 0.25
122 0.49
123 0.47
124 1.40
125 -1.97
126 0.93
127 0.71
128 0.49
129 1.62
130 0.59
131 0.44
132 0.23
133 0.20
134 0.08
135 -0.10
136 0.91
137 1.10
138 -0.10
139 1.10
140 0.93
141 0.55
142 1.06
143 0.59
144 0.51
145 0.04
146 -0.46
147 1.40
148 0.25
149 0.08
150 0.91
151 -0.09
152 0.23
153 0.49
154 1.04
#Reported_Model_Average 0.425
#Overall_Average_Reported 0.425
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
12 -0.84
13 0.08
14 1.04
15 0.28
16 0.81
17 0.28
18 0.28
19 0.20
20 0.77
21 0.77
22 0.08
23 1.06
24 0.17
25 0.28
26 0.41
27 0.04
28 -0.10
29 1.10
30 1.12
31 0.08
32 0.08
33 -0.46
34 0.93
35 0.09
36 0.71
37 0.66
38 0.17
39 0.71
40 0.51
41 1.10
42 0.14
43 0.25
44 0.49
45 0.47
46 1.04
47 -1.97
48 0.93
49 0.71
50 0.49
51 1.62
52 0.59
53 0.44
54 0.23
55 1.04
56 0.08
57 0.47
58 0.91
59 1.10
60 -0.10
61 1.10
62 0.81
63 0.55
64 1.06
65 0.59
66 0.51
67 0.04
68 -0.46
69 1.40
70 0.25
71 0.08
72 0.91
73 -0.74
74 0.23
75 0.49
76 1.40
77 -0.10
88 0.14
89 0.04
90 -0.84
91 0.08
92 0.71
93 0.28
94 0.81
95 0.28
96 0.28
97 0.20
98 0.77
99 -0.33
100 0.08
101 1.06
102 0.17
103 0.28
104 0.51
105 0.04
106 -0.10
107 1.10
108 1.12
109 0.08
110 0.08
111 -0.46
112 0.93
113 -0.56
114 0.71
115 0.66
116 0.17
117 0.71
118 0.51
119 1.10
120 0.14
121 0.25
122 0.49
123 0.47
124 1.40
125 -1.97
126 0.93
127 0.71
128 0.49
129 1.62
130 0.59
131 0.44
132 0.23
133 0.20
134 0.08
135 -0.10
136 0.91
137 1.10
138 -0.10
139 1.10
140 0.93
141 0.55
142 1.06
143 0.59
144 0.51
145 0.04
146 -0.46
147 1.40
148 0.25
149 0.08
150 0.91
151 -0.09
152 0.23
153 0.49
154 1.04
#Reported_Model_Average 0.425
#Overall_Average_Reported 0.425
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
12.000 0
13.000 0
14.000 1
15.000 0
16.000 0
17.000 0
18.000 0
19.000 2
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 0
30.000 3
31.000 0
32.000 1
33.000 0
34.000 4
35.000 2
36.000 3
37.000 0
38.000 1
39.000 0
40.000 0
41.000 0
42.000 1
43.000 1
44.000 0
45.000 0
46.000 1
47.000 1
48.000 1
49.000 2
50.000 0
51.000 1
52.000 0
53.000 1
54.000 0
55.000 0
56.000 0
57.000 2
58.000 0
59.000 0
60.000 2
61.000 0
62.000 7
63.000 0
64.000 2
65.000 0
66.000 3
67.000 0
68.000 1
69.000 0
70.000 2
71.000 0
72.000 5
73.000 1
74.000 0
75.000 2
76.000 1
77.000 0
78.000 0
79.000 0
80.000 0
81.000 0
82.000 0
83.000 0
84.000 0
85.000 0
86.000 0
87.000 0
88.000 0
89.000 0
90.000 0
91.000 0
92.000 1
93.000 0
94.000 0
95.000 1
96.000 0
97.000 3
98.000 0
99.000 2
100.000 0
101.000 0
102.000 0
103.000 0
104.000 2
105.000 0
106.000 0
107.000 0
108.000 0
109.000 0
110.000 3
111.000 0
112.000 3
113.000 3
114.000 2
115.000 0
116.000 1
117.000 0
118.000 0
119.000 0
120.000 0
121.000 0
122.000 1
123.000 0
124.000 0
125.000 0
126.000 1
127.000 2
128.000 0
129.000 0
130.000 1
131.000 1
132.000 1
133.000 0
134.000 1
135.000 0
136.000 0
137.000 0
138.000 2
139.000 7
140.000 1
141.000 0
142.000 1
143.000 0
144.000 2
145.000 0
146.000 0
147.000 2
148.000 0
149.000 0
150.000 5
151.000 1
152.000 0
153.000 0
154.000 0
#Reported_Model_Average 0.727
#Overall_Average_Reported 0.727
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 2103:M 113 ASN 2HD2 :M 97 HIS HA : -0.955: 14
: 2103:M 113 ASN ND2 :M 97 HIS HA : -0.707: 14
: 2103:M 97 HIS ND1 :M 113 ASN ND2 : -0.452: 18
: 2103:M 36 ARG 2HH1 :M 66 ASN ND2 : -0.874: 39
: 2103:M 66 ASN 1HD2 :M 36 ARG 2HH1 : -0.758: 39
: 2103:M 66 ASN O :M 70 GLN 1HG : -0.748: 37
: 2103:M 70 GLN HA :M 73 VAL 2HG1 : -0.562: 74
: 2103:M 46 PHE CE2 :M 36 ARG NH1 : -0.484: 39
: 2103:M 144 ASN 1HD2 :M 114 ARG 2HH1 : -0.873: 33
: 2103:M 144 ASN 1HD2 :M 114 ARG NH1 : -0.659: 33
: 2103:M 139 GLY 1HA :M 62 ILE 1HG1 : -0.870: 22
: 2103:M 62 ILE 3HG2 :M 138 LYS C : -0.625: 32
: 2103:M 139 GLY 2HA :M 127 ARG CB : -0.606: 21
: 2103:M 139 GLY 2HA :M 127 ARG 2HB : -0.597: 21
: 2103:M 62 ILE 1HG1 :M 139 GLY CA : -0.519: 22
: 2103:M 62 ILE CG2 :M 139 GLY 1HA : -0.514: 32
: 2103:M 139 GLY 1HA :M 62 ILE 3HG2 : -0.431: 32
: 2103:M 62 ILE CG2 :M 138 LYS O : -0.404: 32
: 2103:M 139 GLY 1HA :M 62 ILE CG1 : -0.402: 22
: 2103:M 49 ARG 1HD :M 47 ASP OD1 : -0.866: 16
: 2103:M 51 TRP CZ2 :M 49 ARG 2HD : -0.693: 19
: 2103:M 35 ASN 2HD2 :M 19 HIS HA : -0.805: 19
: 2103:M 19 HIS HA :M 35 ASN ND2 : -0.592: 19
: 2103:M 151 VAL 3HG1 :M 147 PHE O : -0.795: 37
: 2103:M 147 PHE HZ :M 76 PHE CE2 : -0.425: 31
: 2103:M 34 ILE 1HD1 :M 150 MET 2HE A: -0.695: 69
: 2103:M 150 MET CE A:M 34 ILE 1HD1 : -0.622: 69
: 2103:M 112 ILE CD1 :M 72 MET 2HG : -0.584: 19
: 2103:M 150 MET 1HE A:M 142 LEU 1HD1 : -0.555: 69
: 2103:M 34 ILE CD1 :M 150 MET 2HE A: -0.541: 69
: 2103:M 34 ILE 1HG1 :M 48 ILE 1HG1 : -0.521: 20
: 2103:M 126 ILE 1HD1 :M 72 MET CE : -0.469: 98
: 2103:M 72 MET CG :M 112 ILE 1HD1 : -0.464: 19
: 2103:M 72 MET 1HE :M 150 MET SD A: -0.418: 142
: 2103:M 72 MET 2HG :M 112 ILE 1HD1 : -0.401: 19
: 2103:M 122 ALA 2HB :M 95 GLU 2HG : -0.680: 26
: 2103:M 75 ALA CB :M 99 LEU 2HD2 : -0.668: 28
: 2103:M 99 LEU 2HD2 :M 75 ALA 3HB : -0.450: 28
: 2103:M 64 LEU CD2 :M 110 LYS 2HD : -0.598: 16
: 2103:M 64 LEU 3HD2 :M 110 LYS 2HD : -0.553: 16
: 2103:M 68 GLU OE1 :M 110 LYS NZ : -0.498: 20
: 2103:M 130 SER 2HB :M 131 PRO 1HD : -0.549: 23
: 2103:M 30 TRP HH2 :M 57 LYS 2HG : -0.542: 37
: 2103:M 30 TRP CH2 :M 57 LYS 2HG : -0.492: 37
: 2103:M 53 PRO 2HD :M 30 TRP CD1 : -0.405: 19
: 2103:M 140 ILE 1HD1 :M 32 LYS 2HD : -0.501: 17
: 2103:M 14 PHE HA :M 38 SER O : -0.460: 15
: 2103:M 43 PRO 1HD :M 42 ALA 1HB : -0.428: 24
: 2103:M 134 THR 3HG2 :M 132 ASP OD1 : -0.424: 29
: 2103:M 92 PHE HA :M 116 SER O : -0.405: 16
: 2103:M 60 LYS 1HB :M 60 LYS 2HE : -0.405: 49
: 2103:M 104 ASN OD1 :M 104 ASN C : -0.401: 24
#sum2 ::24.73 clashscore : 23.43 clashscore B<40
#summary::2103 atoms:1878 atoms B<40:237218 potential dots:14830.0 A^2:52 bumps:44 bumps B<40:491.6 score
Output from PDB validation software
Summary from PDB validation
May. 10, 23:18:00 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 0.007 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.
All covalent bond angles lie within a 6.0*RMSD range about the
standard dictionary values.
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.
SPR104_XRay_em_bcr3.pdb: Error: Z value is 8. It should be 4.
SPR104_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 5) in Token 'SITE' can not be found in coordinates
SPR104_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 101) in Token 'SITE' can not be found in coordinates
SPR104_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 96) in Token 'SITE' can not be found in coordinates