Detailed results of CCR55_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 >>>----------+
| |
| CCR55_XRay_em_bcr3_noHs_000.rin 0.0 114 residues |
| |
+| Ramachandran plot: 92.9% core 6.1% allow 1.0% gener 0.0% disall |
| |
+| All Ramachandrans: 2 labelled residues (out of 112) |
| Chi1-chi2 plots: 0 labelled residues (out of 67) |
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
Model Secondary Structures from Procheck
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
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 -0.08
4 -0.63
5 0.58
6 -0.17
7 0.49
8 -1.50
9 0.25
10 1.14
11 0.66
12 1.08
13 0.84
14 1.32
15 0.99
16 0.99
17 0.95
18 -0.11
19 -0.93
20 0.91
21 -0.92
22 -0.26
23 -0.44
24 -1.19
25 -0.63
26 0.66
27 1.05
28 1.08
29 0.85
30 0.36
31 0.26
32 0.63
33 -0.64
34 -0.09
35 -0.44
36 -1.30
37 0.20
38 -0.52
39 1.08
40 0.05
41 -1.16
42 0.66
43 1.23
44 1.08
45 1.24
46 0.76
47 0.80
48 0.68
49 -1.21
50 -1.14
51 -0.49
52 0.67
53 -0.33
54 -0.88
55 0.29
56 -0.44
57 0.08
58 0.10
59 0.10
60 -0.78
61 0.31
62 -0.62
63 0.36
64 0.09
65 -0.70
66 0.65
67 -0.31
68 0.44
69 0.01
70 -0.18
71 -0.21
72 -0.52
73 -0.46
74 -2.00
75 -3.76
76 -1.54
77 -0.13
78 1.03
79 -0.40
80 -0.49
81 0.09
82 -2.08
83 -0.27
84 -0.41
85 -2.36
86 -1.34
87 0.54
88 -0.28
89 -0.36
90 0.57
91 0.70
92 -0.49
93 -0.27
94 0.05
95 -0.92
96 -1.11
97 -0.93
98 -0.60
99 -0.44
100 -0.81
101 -0.37
102 -0.75
103 0.58
104 0.34
105 1.03
106 -0.15
107 0.40
108 -0.33
109 -1.10
110 -3.49
111 1.13
112 1.08
113 0.65
114 0.36
#Reported_Model_Average -0.107
#Overall_Average_Reported -0.107
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 1.15
3 0.24
4 -0.42
5 0.12
6 -0.07
7 0.68
8 -1.96
9 0.73
10 -0.06
11 0.66
12 1.06
13 -0.53
14 1.21
15 0.99
16 0.99
17 0.90
18 -0.11
19 -0.20
20 0.91
21 -1.89
22 -0.54
23 -0.01
24 -1.19
25 0.12
26 0.66
27 0.25
28 1.13
29 0.73
30 0.36
31 0.70
32 0.63
33 -0.42
34 0.41
35 -0.34
36 -1.92
37 0.29
38 -0.52
39 1.08
40 -0.67
41 -1.46
42 0.66
43 0.68
44 0.81
45 0.86
46 0.76
47 0.80
48 0.77
49 -1.93
50 -0.16
51 0.03
52 0.67
53 0.33
54 -0.88
55 0.51
56 0.22
57 -0.50
58 -0.98
59 0.30
60 -0.78
61 0.59
62 -0.72
63 0.36
64 0.09
65 -0.70
66 0.61
67 -0.31
68 -0.06
69 0.15
70 -0.97
71 0.47
72 0.20
73 0.08
74 -2.00
75 -2.24
76 -0.94
77 -0.13
78 1.03
79 -0.40
80 0.34
81 -0.42
82 -2.08
83 -0.89
84 -0.05
85 -1.52
86 -0.79
87 0.54
88 0.06
89 -0.48
90 0.53
91 1.02
92 0.39
93 0.33
94 0.34
95 -0.75
96 -0.86
97 -0.93
98 -0.01
99 0.21
100 -0.16
101 -0.49
102 -0.34
103 0.58
104 0.15
105 1.03
106 0.30
107 0.40
108 0.28
109 -0.94
110 -3.49
111 1.16
112 0.73
113 0.77
114 0.36
115 0.87
#Reported_Model_Average -0.025
#Overall_Average_Reported -0.025
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
2 0.08
3 0.14
4 1.50
5 0.17
6 -0.83
7 1.50
8 1.07
9 0.49
10 1.10
11 0.44
12 -0.43
13 1.11
14 0.29
15 0.44
16 0.76
17 0.66
18 0.44
19 0.62
20 1.10
21 0.19
22 0.96
23 0.28
24 1.10
25 0.17
26 0.44
27 -0.62
28 -0.43
29 -0.46
30 0.44
31 0.29
32 1.10
33 0.71
34 1.07
35 -0.49
36 1.06
37 0.49
38 0.59
39 0.63
40 0.60
41 0.16
42 0.76
43 0.62
44 0.60
45 0.39
46 0.76
47 0.76
48 0.66
49 -1.09
50 0.71
51 0.24
52 1.10
53 0.25
54 0.14
55 0.41
56 1.07
57 0.71
58 1.07
59 1.07
60 0.59
61 1.18
62 -0.68
63 0.49
64 0.00
65 0.44
66 1.06
67 1.10
68 0.04
69 0.51
70 0.36
71 0.55
72 0.07
73 0.41
74 0.14
75 0.17
76 0.71
77 1.10
78 1.10
79 0.14
80 0.19
81 0.37
82 -0.77
83 -0.05
84 0.36
85 1.25
86 0.71
87 0.64
88 1.07
89 -1.33
90 -0.09
91 0.34
92 -0.46
93 0.71
94 0.79
95 0.84
96 0.41
97 0.59
98 -0.03
99 1.06
100 0.23
101 -0.33
102 0.51
103 0.14
104 0.23
105 1.10
106 -0.74
107 0.59
108 0.25
109 1.06
110 0.63
111 0.44
112 0.61
113 0.16
114 0.44
115 0.00
#Reported_Model_Average 0.444
#Overall_Average_Reported 0.444
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
2 0.08
3 0.14
4 1.50
5 0.17
6 -0.83
7 1.50
8 1.07
9 0.49
10 1.10
11 0.44
12 -0.43
13 1.11
14 0.29
15 0.44
16 0.76
17 0.66
18 0.44
19 0.62
20 1.10
21 0.19
22 0.96
23 0.28
24 1.10
25 0.17
26 0.44
27 -0.62
28 -0.43
29 -0.46
30 0.44
31 0.29
32 1.10
33 0.71
34 1.07
35 -0.49
36 1.06
37 0.49
38 0.59
39 0.63
40 0.60
41 0.16
42 0.76
43 0.62
44 0.60
45 0.39
46 0.76
47 0.76
48 0.66
49 -1.09
50 0.71
51 0.24
52 1.10
53 0.25
54 0.14
55 0.41
56 1.07
57 0.71
58 1.07
59 1.07
60 0.59
61 1.18
62 -0.68
63 0.49
64 0.00
65 0.44
66 1.06
67 1.10
68 0.04
69 0.51
70 0.36
71 0.55
72 0.07
73 0.41
74 0.14
75 0.17
76 0.71
77 1.10
78 1.10
79 0.14
80 0.19
81 0.37
82 -0.77
83 -0.05
84 0.36
85 1.25
86 0.71
87 0.64
88 1.07
89 -1.33
90 -0.09
91 0.34
92 -0.46
93 0.71
94 0.79
95 0.84
96 0.41
97 0.59
98 -0.03
99 1.06
100 0.23
101 -0.33
102 0.51
103 0.14
104 0.23
105 1.10
106 -0.74
107 0.59
108 0.25
109 1.06
110 0.63
111 0.44
112 0.61
113 0.16
114 0.44
115 0.00
#Reported_Model_Average 0.444
#Overall_Average_Reported 0.444
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
2.000 0
3.000 0
4.000 0
5.000 3
6.000 0
7.000 1
8.000 2
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 1
18.000 0
19.000 0
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 0
31.000 2
32.000 0
33.000 0
34.000 0
35.000 2
36.000 0
37.000 0
38.000 0
39.000 0
40.000 2
41.000 0
42.000 0
43.000 2
44.000 0
45.000 0
46.000 0
47.000 0
48.000 0
49.000 0
50.000 1
51.000 0
52.000 0
53.000 0
54.000 0
55.000 0
56.000 1
57.000 2
58.000 7
59.000 0
60.000 0
61.000 0
62.000 0
63.000 0
64.000 0
65.000 0
66.000 2
67.000 0
68.000 0
69.000 1
70.000 0
71.000 1
72.000 0
73.000 1
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 1
84.000 0
85.000 1
86.000 1
87.000 0
88.000 0
89.000 0
90.000 1
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 0
106.000 0
107.000 0
108.000 0
109.000 3
110.000 0
111.000 0
112.000 0
113.000 0
114.000 0
115.000 0
#Reported_Model_Average 0.333
#Overall_Average_Reported 0.333
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 1726:A 43 GLN 1HE2 :A 109 LEU H : -0.928: 13
: 1726:A 109 LEU H :A 43 GLN NE2 : -0.498: 13
: 1726:A 109 LEU 1HD1 :A 7 ILE 1HD1 : -0.425: 18
: 1726:A 8 LEU 3HD2 :A 57 VAL 3HG1 : -0.824: 21
: 1726:A 57 VAL 3HG1 :A 8 LEU CD2 : -0.665: 21
: 1726:A 58 LEU 1HD1 :A 5 TYR HD2 : -0.805: 20
: 1726:A 5 TYR CD2 :A 58 LEU 1HD1 : -0.694: 20
: 1726:A 58 LEU C :A 58 LEU 3HD1 : -0.532: 20
: 1726:A 5 TYR HD2 :A 58 LEU CD1 : -0.484: 20
: 1726:A 58 LEU C :A 58 LEU CD1 : -0.400: 20
: 1726:A 83 HIS HD2 :A 73 GLU OE1 : -0.734: 18
: 1726:A 40 GLU CD :A 40 GLU H : -0.708: 38
: 1726:A 31 ASP OD2 :A 35 HIS HE1 : -0.573: 12
: 1726:A 31 ASP OD2 :A 35 HIS CE1 : -0.418: 12
: 1726:A 85 TYR CE1 :A 71 LYS 1HD : -0.512: 30
: 1726:A 50 PHE 2HB :A 56 LEU 1HD1 : -0.461: 16
: 1726:A 66 LEU 3HD2 :A 66 LEU HA : -0.439: 26
: 1726:A 86 ARG 2HD :A 69 ASP OD2 : -0.428: 32
: 1726:A 90 VAL 1HG2 :A 17 LYS HA : -0.411: 20
#sum2 ::11.01 clashscore : 11.12 clashscore B<40
#summary::1726 atoms:1708 atoms B<40:194215 potential dots:12140.0 A^2:19 bumps:19 bumps B<40:592.7 score
Output from PDB validation software
Summary from PDB validation
May. 9, 22:14:00 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 0.005 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 1.3 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
--------------------------------------------------------------------------------
8.7 TRP A 49 N - CA - C 119.9 111.2
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.
==> The following residues are missing:
(Note: The SEQ number starts from 1 for each chain according to SEQRES
sequence record.)
RES MOD#C SEQ
MET( A-113 )
THR( A-112 )
LEU( A-111 )
ILE( A-110 )
TYR( A-109 )
LYS( A-108 )
ILE( A-107 )
LEU( A-106 )
SER( A-105 )
ARG( A-104 )
ALA( A-103 )
GLU( A-102 )
TRP( A-101 )
ASP( A-100 )
ALA( A -99 )
ALA( A -98 )
LYS( A -97 )
ALA( A -96 )
GLN( A -95 )
GLY( A -94 )
ARG( A -93 )
PHE( A -92 )
GLU( A -91 )
GLY( A -90 )
SER( A -89 )
ALA( A -88 )
VAL( A -87 )
ASP( A -86 )
LEU( A -85 )
ALA( A -84 )
ASP( A -83 )
GLY( A -82 )
PHE( A -81 )
ILE( A -80 )
HIS( A -79 )
LEU( A -78 )
SER( A -77 )
ALA( A -76 )
GLY( A -75 )
GLU( A -74 )
GLN( A -73 )
ALA( A -72 )
GLN( A -71 )
GLU( A -70 )
THR( A -69 )
ALA( A -68 )
ALA( A -67 )
LYS( A -66 )
TRP( A -65 )
PHE( A -64 )
ARG( A -63 )
GLY( A -62 )
GLN( A -61 )
ALA( A -60 )
ASN( A -59 )
LEU( A -58 )
VAL( A -57 )
LEU( A -56 )
LEU( A -55 )
ALA( A -54 )
VAL( A -53 )
GLU( A -52 )
ALA( A -51 )
GLU( A -50 )
PRO( A -49 )
LEU( A -48 )
GLY( A -47 )
GLU( A -46 )
ASP( A -45 )
LEU( A -44 )
LYS( A -43 )
TRP( A -42 )
GLU( A -41 )
ALA( A -40 )
SER( A -39 )
ARG( A -38 )
GLY( A -37 )
GLY( A -36 )
ALA( A -35 )
ARG( A -34 )
PHE( A -33 )
PRO( A -32 )
HIS( A -31 )
LEU( A -30 )
TYR( A -29 )
ARG( A -28 )
PRO( A -27 )
LEU( A -26 )
LEU( A -25 )
VAL( A -24 )
SER( A -23 )
GLU( A -22 )
VAL( A -21 )
THR( A -20 )
ARG( A -19 )
GLU( A -18 )
ALA( A -17 )
ASP( A -16 )
LEU( A -15 )
ASP( A -14 )
LEU( A -13 )
ASP( A -12 )
ALA( A -11 )
ASP( A -10 )
GLY( A -9 )
VAL( A -8 )
PRO( A -7 )
GLN( A -6 )
LEU( A -5 )
GLY( A -4 )
ASP( A -3 )
HIS( A -2 )
LEU( A -1 )
ALA( A 0 )
LEU( A 1 )
PDB Chain_ID: A
1 15
SEQRES: MET THR LEU ILE TYR LYS ILE LEU SER ARG ALA GLU TRP ASP ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 30
SEQRES: ALA LYS ALA GLN GLY ARG PHE GLU GLY SER ALA VAL ASP LEU ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
31 45
SEQRES: ASP GLY PHE ILE HIS LEU SER ALA GLY GLU GLN ALA GLN GLU THR
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
46 60
SEQRES: ALA ALA LYS TRP PHE ARG GLY GLN ALA ASN LEU VAL LEU LEU ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
61 75
SEQRES: VAL GLU ALA GLU PRO LEU GLY GLU ASP LEU LYS TRP GLU ALA SER
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
76 90
SEQRES: ARG GLY GLY ALA ARG PHE PRO HIS LEU TYR ARG PRO LEU LEU VAL
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
91 105
SEQRES: SER GLU VAL THR ARG GLU ALA ASP LEU ASP LEU ASP ALA ASP GLY
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
106 120
SEQRES: VAL PRO GLN LEU GLY ASP HIS LEU ALA LEU THR LEU ILE TYR LYS
COORDS: ... ... ... ... ... ... ... ... ... ... THR LEU ILE TYR LYS
2 6
121 135
SEQRES: ILE LEU SER ARG ALA GLU TRP ASP ALA ALA LYS ALA GLN GLY ARG
COORDS: ILE LEU SER ARG ALA GLU TRP ASP ALA ALA LYS ALA GLN GLY ARG
7 21
136 150
SEQRES: PHE GLU GLY SER ALA VAL ASP LEU ALA ASP GLY PHE ILE HIS LEU
COORDS: PHE GLU GLY SER ALA VAL ASP LEU ALA ASP GLY PHE ILE HIS LEU
22 36
151 165
SEQRES: SER ALA GLY GLU GLN ALA GLN GLU THR ALA ALA LYS TRP PHE ARG
COORDS: SER ALA GLY GLU GLN ALA GLN GLU THR ALA ALA LYS TRP PHE ARG
37 51
166 180
SEQRES: GLY GLN ALA ASN LEU VAL LEU LEU ALA VAL GLU ALA GLU PRO LEU
COORDS: GLY GLN ALA ASN LEU VAL LEU LEU ALA VAL GLU ALA GLU PRO LEU
52 66
181 195
SEQRES: GLY GLU ASP LEU LYS TRP GLU ALA SER ARG GLY GLY ALA ARG PHE
COORDS: GLY GLU ASP LEU LYS TRP GLU ALA SER ARG GLY GLY ALA ARG PHE
67 81
196 210
SEQRES: PRO HIS LEU TYR ARG PRO LEU LEU VAL SER GLU VAL THR ARG GLU
COORDS: PRO HIS LEU TYR ARG PRO LEU LEU VAL SER GLU VAL THR ARG GLU
82 96
211 225
SEQRES: ALA ASP LEU ASP LEU ASP ALA ASP GLY VAL PRO GLN LEU GLY ASP
COORDS: ALA ASP LEU ASP LEU ASP ALA ASP GLY VAL PRO GLN LEU GLY ASP
97 111
226 229
SEQRES: HIS LEU ALA LEU
COORDS: HIS LEU ALA LEU
112 115
==> The following residues have missing atoms:
RES MOD#C SEQ ATOMS
GLU( A 64) CG CD OE1 OE2
==> The following residues have extra atoms:
RES MOD#C SEQ ATOMS
LEU( A 115) O2