Detailed results of MBR242E_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 >>>----------+
| |
| MBR242E_XRay_em_bcr3_noHs_000.rin 0.0 92 residues |
| |
| Ramachandran plot: 96.3% core 3.7% allow 0.0% gener 0.0% disall |
| |
+| All Ramachandrans: 1 labelled residues (out of 88) |
| Chi1-chi2 plots: 0 labelled residues (out of 51) |
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
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
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
8 -0.37
9 -0.52
10 -2.84
11 0.65
12 0.65
13 1.13
14 0.13
15 1.05
16 0.82
17 1.14
18 0.81
19 0.94
20 0.95
21 0.82
22 -0.35
23 -3.46
24 -1.44
25 1.25
26 0.84
27 0.60
28 0.29
29 1.01
30 0.71
31 1.13
32 1.32
33 1.13
34 -0.41
35 -1.92
36 -0.67
37 -2.16
38 -0.68
39 -0.07
40 -0.22
41 -0.04
42 0.72
43 0.99
44 1.01
45 0.76
46 1.14
47 0.80
48 0.08
52 0.88
53 1.14
54 0.87
55 0.66
56 1.19
57 0.66
58 1.39
59 1.13
60 1.01
61 0.76
62 1.13
63 1.22
64 0.88
65 -0.24
66 0.93
67 -0.82
68 -0.05
69 -0.79
70 -0.76
71 -0.07
72 -0.41
73 -1.27
74 -0.47
75 -0.67
76 -0.57
77 -0.45
78 0.26
79 0.40
80 -0.15
81 -1.54
82 0.80
83 0.14
84 0.72
85 1.14
86 1.05
87 0.76
88 1.14
89 0.99
90 0.61
91 0.76
92 0.85
93 0.37
94 0.74
95 0.98
96 0.98
97 0.76
98 -0.03
#Reported_Model_Average 0.304
#Overall_Average_Reported 0.304
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
7 -0.89
8 -0.83
9 -0.52
10 -2.84
11 0.49
12 0.60
13 0.54
14 0.19
15 0.66
16 0.82
17 1.10
18 0.89
19 0.94
20 0.70
21 0.82
22 0.14
23 -3.46
24 -1.08
25 1.25
26 0.38
27 0.15
28 -0.39
29 1.07
30 0.81
31 1.01
32 -0.19
33 0.73
34 0.23
35 -1.92
36 -0.73
37 -2.16
38 -1.00
39 -0.33
40 -0.22
41 0.27
42 -0.14
43 0.99
44 0.95
45 0.76
46 0.89
47 0.80
48 0.42
49 0.00
51 -2.08
52 0.08
53 0.71
54 1.24
55 0.66
56 0.24
57 0.66
58 0.84
59 0.44
60 -0.48
61 0.76
62 1.02
63 0.60
64 0.62
65 -0.24
66 0.93
67 -0.14
68 0.04
69 -0.96
70 -0.76
71 -0.04
72 -0.67
73 -0.33
74 -0.47
75 -0.78
76 -0.52
77 -0.77
78 0.40
79 -0.08
80 -0.34
81 -0.50
82 0.80
83 0.14
84 -0.53
85 1.14
86 0.86
87 0.76
88 1.15
89 0.70
90 0.09
91 0.76
92 0.69
93 -0.35
94 0.99
95 0.86
96 0.37
97 0.76
98 -0.82
99 -1.55
#Reported_Model_Average 0.096
#Overall_Average_Reported 0.096
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
7 -0.41
8 0.47
9 0.14
10 0.14
11 -1.37
12 -0.46
13 0.29
14 0.62
15 -0.62
16 0.44
17 0.56
18 0.30
19 0.63
20 0.07
21 0.76
22 1.30
23 0.14
24 0.51
25 1.10
26 0.24
27 1.10
28 -0.30
29 0.62
30 1.11
31 1.30
32 0.29
33 -0.30
34 1.30
35 0.49
36 0.25
37 1.10
38 -0.46
39 0.19
40 0.59
41 0.30
42 0.62
43 0.44
44 1.11
45 0.76
46 -0.20
47 0.44
48 0.39
49 1.10
51 0.41
52 -0.46
53 -0.20
54 -0.13
55 0.76
56 -0.38
57 0.44
58 -0.58
59 1.30
60 0.62
61 -0.02
62 1.30
63 0.66
64 0.16
65 1.10
66 1.10
67 1.06
68 1.18
69 0.41
70 0.59
71 0.19
72 0.19
73 0.41
74 1.10
75 0.08
76 0.19
77 0.52
78 1.09
79 0.17
80 0.19
81 1.07
82 -0.25
83 1.10
84 0.60
85 0.44
86 0.30
87 -0.02
88 0.56
89 -0.30
90 0.87
91 0.44
92 -0.46
93 0.30
94 0.62
95 -1.25
96 -1.25
97 0.44
98 0.44
99 0.04
#Reported_Model_Average 0.372
#Overall_Average_Reported 0.372
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
7 -0.41
8 0.47
9 0.14
10 0.14
11 -1.37
12 -0.46
13 0.29
14 0.62
15 -0.62
16 0.44
17 0.56
18 0.30
19 0.63
20 0.07
21 0.76
22 1.30
23 0.14
24 0.51
25 1.10
26 0.24
27 1.10
28 -0.30
29 0.62
30 1.11
31 1.30
32 0.29
33 -0.30
34 1.30
35 0.49
36 0.25
37 1.10
38 -0.46
39 0.19
40 0.59
41 0.30
42 0.62
43 0.44
44 1.11
45 0.76
46 -0.20
47 0.44
48 0.39
49 1.10
51 0.41
52 -0.46
53 -0.20
54 -0.13
55 0.76
56 -0.38
57 0.44
58 -0.58
59 1.30
60 0.62
61 -0.02
62 1.30
63 0.66
64 0.16
65 1.10
66 1.10
67 1.06
68 1.18
69 0.41
70 0.59
71 0.19
72 0.19
73 0.41
74 1.10
75 0.08
76 0.19
77 0.52
78 1.09
79 0.17
80 0.19
81 1.07
82 -0.25
83 1.10
84 0.60
85 0.44
86 0.30
87 -0.02
88 0.56
89 -0.30
90 0.87
91 0.44
92 -0.46
93 0.30
94 0.62
95 -1.25
96 -1.25
97 0.44
98 0.44
99 0.04
#Reported_Model_Average 0.372
#Overall_Average_Reported 0.372
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
7.000 0
8.000 2
9.000 2
10.000 2
11.000 0
12.000 0
13.000 0
14.000 1
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 1
25.000 0
26.000 0
27.000 1
28.000 0
29.000 0
30.000 0
31.000 0
32.000 0
33.000 0
34.000 1
35.000 2
36.000 2
37.000 0
38.000 2
39.000 1
40.000 0
41.000 0
42.000 0
43.000 0
44.000 0
45.000 0
46.000 0
47.000 0
48.000 0
49.000 0
50.000 0
51.000 1
52.000 0
53.000 0
54.000 1
55.000 0
56.000 0
57.000 0
58.000 0
59.000 0
60.000 0
61.000 0
62.000 0
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 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 1
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
#Reported_Model_Average 0.237
#Overall_Average_Reported 0.237
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 1408:A 80 ARG 2HB :A 38 GLU 1HB : -0.722: 38
: 1408:A 39 ARG 1HG :A 38 GLU O : -0.450: 39
: 1408:A 36 GLN HA :A 34 LEU O : -0.659: 48
: 1408:A 9 ALA 1HB :A 10 ALA HA : -0.659: 52
: 1408:A 81 ILE CD1 :A 35 ALA 2HB : -0.600: 47
: 1408:A 10 ALA HA :A 9 ALA CB : -0.480: 52
: 1408:A 35 ALA HA :A 36 GLN HA : -0.402: 48
: 1408:A 24 ASN 2HB :A 27 ARG 2HB : -0.465: 40
: 1408:A 8 LYS 1HB :A 8 LYS 1HE : -0.457: 55
: 1408:A 17 ARG 1HD :A 14 GLN OE1 : -0.414: 43
: 1408:A 54 THR OG1 :A 51 ASN ND2 : -0.411: 30
#sum2 ::7.81 clashscore : 2.99 clashscore B<40
#summary::1408 atoms:1002 atoms B<40:157774 potential dots:9861.0 A^2:11 bumps:3 bumps B<40:459.8 score
Output from PDB validation software
Summary from PDB validation
May. 10, 12:42:07 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 0.010 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 1.1 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.
==> The following residues are missing:
(Note: The SEQ number starts from 1 for each chain according to SEQRES
sequence record.)
RES MOD#C SEQ
MSE( A-101 )
ALA( A-100 )
GLY( A -99 )
GLN( A -98 )
SER( A -97 )
ASP( A -96 )
ARG( A -95 )
LYS( A -94 )
ALA( A -93 )
ALA( A -92 )
LEU( A -91 )
LEU( A -90 )
ASP( A -89 )
GLN( A -88 )
VAL( A -87 )
ALA( A -86 )
ARG( A -85 )
VAL( A -84 )
GLY( A -83 )
LYS( A -82 )
ALA( A -81 )
LEU( A -80 )
ALA( A -79 )
ASN( A -78 )
GLY( A -77 )
ARG( A -76 )
ARG( A -75 )
LEU( A -74 )
GLN( A -73 )
ILE( A -72 )
LEU( A -71 )
ASP( A -70 )
LEU( A -69 )
LEU( A -68 )
ALA( A -67 )
GLN( A -66 )
GLY( A -65 )
GLU( A -64 )
ARG( A -63 )
ALA( A -62 )
VAL( A -61 )
GLU( A -60 )
ALA( A -59 )
ILE( A -58 )
ALA( A -57 )
THR( A -56 )
ALA( A -55 )
THR( A -54 )
GLY( A -53 )
MSE( A -52 )
ASN( A -51 )
LEU( A -50 )
THR( A -49 )
THR( A -48 )
ALA( A -47 )
SER( A -46 )
ALA( A -45 )
ASN( A -44 )
LEU( A -43 )
GLN( A -42 )
ALA( A -41 )
LEU( A -40 )
LYS( A -39 )
SER( A -38 )
GLY( A -37 )
GLY( A -36 )
LEU( A -35 )
VAL( A -34 )
GLU( A -33 )
ALA( A -32 )
ARG( A -31 )
ARG( A -30 )
GLU( A -29 )
GLY( A -28 )
THR( A -27 )
ARG( A -26 )
GLN( A -25 )
TYR( A -24 )
TYR( A -23 )
ARG( A -22 )
ILE( A -21 )
ALA( A -20 )
GLY( A -19 )
GLU( A -18 )
ASP( A -17 )
VAL( A -16 )
ALA( A -15 )
ARG( A -14 )
LEU( A -13 )
PHE( A -12 )
ALA( A -11 )
LEU( A -10 )
VAL( A -9 )
GLN( A -8 )
VAL( A -7 )
VAL( A -6 )
ALA( A -5 )
ASP( A -4 )
GLU( A -3 )
HIS( A -2 )
LEU( A -1 )
GLU( A 0 )
HIS( A 1 )
HIS( A 2 )
HIS( A 3 )
HIS( A 4 )
HIS( A 5 )
HIS( A 6 )
PDB Chain_ID: A
1 15
SEQRES: MSE ALA GLY GLN SER ASP ARG LYS ALA ALA LEU LEU ASP GLN VAL
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 30
SEQRES: ALA ARG VAL GLY LYS ALA LEU ALA ASN GLY ARG ARG LEU GLN ILE
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
31 45
SEQRES: LEU ASP LEU LEU ALA GLN GLY GLU ARG ALA VAL GLU ALA ILE ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
46 60
SEQRES: THR ALA THR GLY MSE ASN LEU THR THR ALA SER ALA ASN LEU GLN
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
61 75
SEQRES: ALA LEU LYS SER GLY GLY LEU VAL GLU ALA ARG ARG GLU GLY THR
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
76 90
SEQRES: ARG GLN TYR TYR ARG ILE ALA GLY GLU ASP VAL ALA ARG LEU PHE
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
91 105
SEQRES: ALA LEU VAL GLN VAL VAL ALA ASP GLU HIS LEU GLU HIS HIS HIS
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
106 120
SEQRES: HIS HIS HIS ARG LYS ALA ALA LEU LEU ASP GLN VAL ALA ARG VAL
COORDS: ... ... ... ARG LYS ALA ALA LEU LEU ASP GLN VAL ALA ARG VAL
7 18
121 135
SEQRES: GLY LYS ALA LEU ALA ASN GLY ARG ARG LEU GLN ILE LEU ASP LEU
COORDS: GLY LYS ALA LEU ALA ASN GLY ARG ARG LEU GLN ILE LEU ASP LEU
19 33
136 150
SEQRES: LEU ALA GLN GLY GLU ARG ALA VAL GLU ALA ILE ALA THR ALA THR
COORDS: LEU ALA GLN GLY GLU ARG ALA VAL GLU ALA ILE ALA THR ALA THR
34 48
151 165
SEQRES: GLY MSE ASN LEU THR THR ALA SER ALA ASN LEU GLN ALA LEU LYS
COORDS: GLY MSE ASN LEU THR THR ALA SER ALA ASN LEU GLN ALA LEU LYS
49 63
166 180
SEQRES: SER GLY GLY LEU VAL GLU ALA ARG ARG GLU GLY THR ARG GLN TYR
COORDS: SER GLY GLY LEU VAL GLU ALA ARG ARG GLU GLY THR ARG GLN TYR
64 78
181 195
SEQRES: TYR ARG ILE ALA GLY GLU ASP VAL ALA ARG LEU PHE ALA LEU VAL
COORDS: TYR ARG ILE ALA GLY GLU ASP VAL ALA ARG LEU PHE ALA LEU VAL
79 93
196 201
SEQRES: GLN VAL VAL ALA ASP GLU
COORDS: GLN VAL VAL ALA ASP GLU
94 99