Detailed results of DHR8C_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 >>>----------+
| |
| DHR8C_XRay_em_bcr3_noHs_000.rin 0.0 134 residues |
| |
| Ramachandran plot: 91.2% core 8.8% allow 0.0% gener 0.0% disall |
| |
| All Ramachandrans: 0 labelled residues (out of 130) |
| Chi1-chi2 plots: 0 labelled residues (out of 88) |
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
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
23 -0.51
24 -0.56
25 -0.02
26 -0.36
27 0.22
28 -0.82
29 -0.75
30 0.89
31 0.05
32 -0.79
33 -1.89
34 -0.38
35 0.10
36 -1.24
37 -0.39
38 -0.91
39 -0.33
40 -1.14
41 -1.46
42 0.29
43 -0.05
44 -0.17
45 -0.43
46 -1.52
47 -0.40
48 -0.45
49 -1.64
50 0.10
51 0.10
52 -0.53
53 0.34
54 -0.30
55 -1.19
56 -0.97
57 -1.33
58 -0.44
59 -1.16
60 0.00
61 -0.56
62 -0.81
63 -2.31
64 -0.73
65 0.29
66 0.85
67 -0.53
68 0.89
69 -0.21
70 0.08
71 -0.75
72 -0.19
73 -0.65
74 -0.87
75 -0.71
76 0.00
77 -0.41
78 -0.55
79 -0.58
80 0.38
81 -0.80
82 -0.72
83 -0.43
84 -0.34
85 0.49
86 -0.44
87 0.04
88 -1.12
89 -0.48
102 -0.44
103 -0.67
104 -0.02
105 -0.36
106 0.04
107 -0.82
108 -0.75
109 1.05
110 -0.15
111 -0.76
112 -1.89
113 -0.38
114 0.10
115 -2.30
116 -0.57
117 -0.63
118 -0.33
119 -0.93
120 -1.25
121 0.52
122 -0.05
123 -0.17
124 -0.56
125 -2.43
126 0.27
127 -0.45
128 -1.64
129 0.10
130 0.10
131 -0.45
132 0.34
133 -0.23
134 -1.19
135 -0.91
136 -1.02
137 -0.43
138 -0.56
139 -0.16
140 -0.37
141 -0.63
142 -1.53
143 -1.28
144 0.85
145 1.22
146 -0.57
147 0.53
148 -0.21
149 -0.05
150 -0.75
151 -0.19
152 -0.43
153 -0.73
154 -0.71
155 -0.16
156 -0.49
157 -0.39
158 -0.97
159 0.38
160 -1.24
161 -0.72
162 -0.16
163 0.05
164 0.04
#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
22 0.00
23 -0.49
24 0.31
25 0.27
26 -0.88
27 0.10
28 -0.93
29 -0.06
30 0.89
31 0.39
32 0.05
33 -0.68
34 0.24
35 -0.23
36 -0.29
37 -0.19
38 -0.58
39 -0.33
40 0.08
41 -0.58
42 0.29
43 0.41
44 0.17
45 -0.01
46 -1.20
47 -0.95
48 -0.55
49 -1.64
50 0.30
51 -0.59
52 -0.62
53 0.58
54 0.20
55 -1.19
56 -0.62
57 -0.27
58 0.24
59 -1.16
60 0.31
61 -0.18
62 -0.27
63 -0.88
64 -0.35
65 -0.16
66 0.71
67 -0.53
68 0.89
69 -0.37
70 -0.50
71 0.14
72 0.11
73 -0.89
74 -0.87
75 -0.88
76 0.25
77 0.36
78 -0.55
79 0.15
80 0.48
81 -0.03
82 -0.72
83 -0.05
84 -0.33
85 0.55
86 -0.22
87 -0.57
88 -0.73
89 0.13
90 1.11
101 -0.10
102 -0.44
103 0.15
104 0.27
105 -0.88
106 -0.34
107 -0.13
108 -0.35
109 1.05
110 0.39
111 -0.74
112 -0.59
113 -0.05
114 0.17
115 -1.51
116 -0.88
117 -1.14
118 -0.33
119 0.19
120 -0.22
121 0.57
122 0.43
123 0.18
124 -0.42
125 -1.65
126 -0.24
127 -1.21
128 -1.64
129 0.39
130 -0.48
131 -0.58
132 0.58
133 0.46
134 -1.19
135 -0.58
136 -1.19
137 0.22
138 -0.56
139 0.33
140 0.19
141 -0.18
142 -0.50
143 -0.75
144 -0.33
145 1.19
146 -0.57
147 0.53
148 -1.46
149 -0.56
150 0.25
151 -0.11
152 -0.38
153 -0.73
154 0.09
155 0.36
156 0.22
157 -0.39
158 -0.88
159 0.48
160 -0.35
161 -0.72
162 0.07
163 -0.86
164 -0.02
165 -1.17
#Reported_Model_Average -0.239
#Overall_Average_Reported -0.239
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
22 0.00
23 0.71
24 0.10
25 -0.84
26 1.06
27 0.59
28 1.06
29 0.08
30 1.10
31 1.00
32 0.34
33 0.47
34 -0.09
35 -0.87
36 0.59
37 0.71
38 0.51
39 0.44
40 0.47
41 0.28
42 0.93
43 0.29
44 1.06
45 -0.59
46 0.55
47 -0.54
48 0.25
49 1.10
50 0.66
51 1.06
52 0.59
53 0.93
54 0.47
55 1.10
56 0.28
57 0.47
58 0.77
59 1.10
60 0.93
61 0.47
62 0.20
63 -0.33
64 0.51
65 -0.68
66 -0.10
67 0.14
68 1.10
69 -0.57
70 1.00
71 0.28
72 1.00
73 -0.46
74 1.10
75 0.29
76 0.93
77 0.51
78 0.49
79 1.06
80 -0.74
81 1.14
82 0.44
83 0.77
84 0.28
85 0.20
86 0.20
87 0.20
88 1.04
89 0.20
90 0.00
101 0.41
102 0.00
103 0.10
104 -0.84
105 1.06
106 0.17
107 1.06
108 0.55
109 1.10
110 0.66
111 0.34
112 0.47
113 -0.09
114 -0.57
115 0.34
116 1.04
117 0.51
118 0.44
119 0.47
120 0.28
121 0.93
122 0.29
123 1.06
124 0.28
125 0.55
126 -0.94
127 0.25
128 1.10
129 -0.09
130 1.06
131 0.59
132 0.93
133 0.47
134 1.10
135 0.28
136 0.47
137 0.77
138 1.10
139 0.93
140 0.47
141 0.20
142 -0.33
143 0.51
144 -0.68
145 -0.10
146 0.14
147 1.10
148 -0.57
149 1.00
150 0.28
151 1.00
152 -0.59
153 1.10
154 -0.68
155 0.93
156 0.51
157 0.49
158 1.06
159 -0.09
160 1.14
161 0.64
162 -0.33
163 0.04
164 0.20
165 -1.21
#Reported_Model_Average 0.408
#Overall_Average_Reported 0.408
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
22 0.00
23 0.71
24 0.10
25 -0.84
26 1.06
27 0.59
28 1.06
29 0.08
30 1.10
31 1.00
32 0.34
33 0.47
34 -0.09
35 -0.87
36 0.59
37 0.71
38 0.51
39 0.44
40 0.47
41 0.28
42 0.93
43 0.29
44 1.06
45 -0.59
46 0.55
47 -0.54
48 0.25
49 1.10
50 0.66
51 1.06
52 0.59
53 0.93
54 0.47
55 1.10
56 0.28
57 0.47
58 0.77
59 1.10
60 0.93
61 0.47
62 0.20
63 -0.33
64 0.51
65 -0.68
66 -0.10
67 0.14
68 1.10
69 -0.57
70 1.00
71 0.28
72 1.00
73 -0.46
74 1.10
75 0.29
76 0.93
77 0.51
78 0.49
79 1.06
80 -0.74
81 1.14
82 0.44
83 0.77
84 0.28
85 0.20
86 0.20
87 0.20
88 1.04
89 0.20
90 0.00
101 0.41
102 0.00
103 0.10
104 -0.84
105 1.06
106 0.17
107 1.06
108 0.55
109 1.10
110 0.66
111 0.34
112 0.47
113 -0.09
114 -0.57
115 0.34
116 1.04
117 0.51
118 0.44
119 0.47
120 0.28
121 0.93
122 0.29
123 1.06
124 0.28
125 0.55
126 -0.94
127 0.25
128 1.10
129 -0.09
130 1.06
131 0.59
132 0.93
133 0.47
134 1.10
135 0.28
136 0.47
137 0.77
138 1.10
139 0.93
140 0.47
141 0.20
142 -0.33
143 0.51
144 -0.68
145 -0.10
146 0.14
147 1.10
148 -0.57
149 1.00
150 0.28
151 1.00
152 -0.59
153 1.10
154 -0.68
155 0.93
156 0.51
157 0.49
158 1.06
159 -0.09
160 1.14
161 0.64
162 -0.33
163 0.04
164 0.20
165 -1.21
#Reported_Model_Average 0.408
#Overall_Average_Reported 0.408
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
22.000 0
23.000 3
24.000 0
25.000 0
26.000 4
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 2
38.000 0
39.000 0
40.000 0
41.000 0
42.000 2
43.000 0
44.000 0
45.000 0
46.000 0
47.000 2
48.000 0
49.000 0
50.000 0
51.000 0
52.000 0
53.000 0
54.000 0
55.000 1
56.000 0
57.000 0
58.000 0
59.000 0
60.000 0
61.000 1
62.000 1
63.000 0
64.000 0
65.000 0
66.000 0
67.000 0
68.000 0
69.000 0
70.000 0
71.000 1
72.000 0
73.000 2
74.000 0
75.000 1
76.000 0
77.000 0
78.000 0
79.000 0
80.000 0
81.000 1
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 0
93.000 0
94.000 0
95.000 0
96.000 0
97.000 0
98.000 0
99.000 0
100.000 0
101.000 0
102.000 0
103.000 0
104.000 0
105.000 2
106.000 0
107.000 0
108.000 1
109.000 0
110.000 0
111.000 0
112.000 2
113.000 0
114.000 0
115.000 0
116.000 1
117.000 0
118.000 0
119.000 0
120.000 0
121.000 1
122.000 0
123.000 2
124.000 0
125.000 1
126.000 0
127.000 0
128.000 0
129.000 0
130.000 1
131.000 0
132.000 0
133.000 0
134.000 0
135.000 1
136.000 0
137.000 0
138.000 0
139.000 0
140.000 0
141.000 1
142.000 1
143.000 0
144.000 1
145.000 0
146.000 0
147.000 0
148.000 2
149.000 1
150.000 2
151.000 0
152.000 0
153.000 0
154.000 1
155.000 0
156.000 0
157.000 0
158.000 1
159.000 1
160.000 1
161.000 0
162.000 0
163.000 0
164.000 0
165.000 1
#Reported_Model_Average 0.319
#Overall_Average_Reported 0.319
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 2109:M 121 ILE 1HG1 :M 116 PHE HD1 : -0.759: 37
: 2109:M 108 THR 2HG2 :M 148 GLN 1HG : -0.722: 69
: 2109:M 148 GLN 1HE2 :M 150 GLU 2HG : -0.588: 64
: 2109:M 150 GLU 1HB :M 141 HIS 2HB : -0.426: 37
: 2109:M 81 TYR 2HB :M 158 LEU 1HB : -0.616: 38
: 2109:M 23 ARG 2HD :M 73 GLU OE1 : -0.604: 99
: 2109:M 61 LYS CG :M 73 GLU 1HG : -0.504: 69
: 2109:M 23 ARG HE :M 23 ARG 1HB : -0.424: 82
: 2109:M 26 LEU C :M 26 LEU 3HD2 : -0.563: 49
: 2109:M 26 LEU C :M 26 LEU CD2 : -0.412: 49
: 2109:M 135 GLU 2HG :M 154 LEU 2HD1 : -0.515: 58
: 2109:M 144 LEU CD1 :M 142 LEU 1HD1 : -0.513: 49
: 2109:M 42 ILE 1HG1 :M 37 PHE HD1 : -0.509: 31
: 2109:M 42 ILE 1HG1 :M 37 PHE CD1 : -0.406: 31
: 2109:M 105 LEU C :M 105 LEU 3HD2 : -0.499: 38
: 2109:M 71 GLU 1HB :M 62 HIS 2HB : -0.494: 33
: 2109:M 55 GLY 2HA :M 75 LEU O : -0.472: 36
: 2109:M 159 VAL 3HG1 :M 165 HIS CD2 : -0.458: 67
: 2109:M 125 THR 3HG2 :M 160 TYR CE1 : -0.417: 52
: 2109:M 123 LEU 3HD1 :M 149 VAL 1HG1 : -0.413: 34
: 2109:M 130 LEU 3HD2 :M 123 LEU 2HD1 : -0.413: 36
: 2109:M 112 LYS 1HB :M 112 LYS 2HE : -0.413: 62
: 2109:M 47 ILE H :M 47 ILE 1HG1 : -0.409: 48
#sum2 ::10.91 clashscore : 7.36 clashscore B<40
#summary::2109 atoms:1359 atoms B<40:236357 potential dots:14770.0 A^2:23 bumps:10 bumps B<40:652.4 score
Output from PDB validation software
Summary from PDB validation
May. 10, 02:20:51 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
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
------------------------------------------------------------------------
0.051 PRO A 82 CB - CG 1.543 1.492
-0.053 GLU A 84 CB - CG 1.467 1.520
*** 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
--------------------------------------------------------------------------------
-9.5 VAL A 34 N - CA - C 101.7 111.2
9.2 ILE A 47 N - CA - C 120.4 111.2
-11.2 HIS A 89 N - CA - C 100.0 111.2
-10.4 VAL B 34 N - CA - C 100.8 111.2
-9.4 ASP B 38 N - CA - C 101.8 111.2
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
ASN( A 22) CG OD1 ND2
ARG( B 23) CG CD NE CZ NH1 NH2
==> The following residues have extra atoms:
RES MOD#C SEQ ATOMS
HIS( A 90) O2
DHR8C_XRay_em_bcr3.pdb: Error: Z value is 24. It should be 12.