Detailed results of MRR110B_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 >>>----------+
| |
| MRR110B_XRay_em_bcr3_noHs_000.rin 0.0 89 residues |
| |
+| Ramachandran plot: 94.5% core 4.1% allow 1.4% gener 0.0% disall |
| |
+| All Ramachandrans: 1 labelled residues (out of 81) |
+| Chi1-chi2 plots: 1 labelled residues (out of 52) |
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
2 0.23
3 -0.42
4 0.06
5 0.70
6 -0.44
10 0.25
11 -0.12
12 -0.33
13 -0.31
14 0.30
15 -0.34
16 -0.02
17 -0.55
18 -0.31
19 -1.21
20 -0.30
21 -0.56
22 -1.63
23 -0.66
24 0.40
25 -0.25
26 -0.17
27 -0.44
28 -2.22
35 -1.08
36 -0.71
37 -0.39
38 -0.80
39 -0.70
40 -0.48
41 -0.51
42 -0.23
43 -0.19
44 -0.32
45 -1.57
46 -0.45
47 -0.60
48 -0.65
49 0.29
50 -2.06
51 -0.35
52 -0.92
53 0.17
54 -0.18
55 -0.36
56 -3.43
57 0.61
58 -0.35
59 -0.11
60 0.05
61 -0.27
62 -1.85
63 0.08
64 -0.32
65 -0.23
66 -0.16
67 -0.17
68 0.16
69 -0.99
70 -0.84
71 0.41
72 -0.35
73 -0.01
74 0.07
75 0.05
76 -0.96
77 -0.25
82 -0.37
83 -0.65
84 0.34
85 -1.24
86 -0.48
87 -0.49
88 -1.33
89 -0.68
90 -0.65
91 0.00
92 -1.31
93 -0.87
94 -0.42
95 0.13
#Reported_Model_Average -0.461
#Overall_Average_Reported -0.461
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
1 1.25
2 0.30
3 -0.34
4 0.48
5 1.02
6 0.09
7 0.87
9 0.00
10 0.72
11 -0.20
12 0.17
13 -0.31
14 0.39
15 -0.12
16 0.52
17 -0.55
18 -0.30
19 -0.12
20 0.15
21 0.16
22 -1.63
23 0.08
24 0.40
25 0.29
26 0.40
27 0.11
28 -1.29
29 1.06
34 0.00
35 -1.08
36 -0.71
37 0.25
38 -1.88
39 -1.57
40 -0.60
41 0.18
42 -0.21
43 0.01
44 0.19
45 -0.83
46 -0.16
47 -0.74
48 -0.65
49 0.33
50 -1.23
51 -0.01
52 -0.92
53 -0.35
54 0.37
55 0.35
56 -1.49
57 -0.07
58 0.27
59 -0.11
60 0.35
61 0.11
62 -1.20
63 -0.50
64 -0.32
65 0.10
66 -0.16
67 0.46
68 0.39
69 -0.99
70 -0.01
71 0.50
72 0.27
73 -0.01
74 0.28
75 0.32
76 -0.96
77 -0.25
78 0.00
81 0.00
82 0.25
83 -0.12
84 -0.09
85 -0.09
86 -0.36
87 0.38
88 -0.81
89 -0.60
90 -0.65
91 0.44
92 -0.71
93 -0.03
94 0.11
95 -0.29
96 -3.38
#Reported_Model_Average -0.164
#Overall_Average_Reported -0.164
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
1 0.01
2 1.09
3 0.47
4 0.81
5 0.17
6 0.28
7 1.06
9 0.44
10 0.41
11 0.14
12 0.65
13 1.75
14 0.79
15 1.50
16 0.00
17 0.59
18 0.41
19 1.18
20 0.08
21 0.95
22 0.59
23 -0.43
24 0.25
25 0.08
26 0.55
27 0.41
28 -0.56
29 0.34
34 0.00
35 0.00
36 1.75
37 0.52
38 0.36
39 0.35
40 0.49
41 1.07
42 -0.56
43 1.07
44 0.55
45 -0.03
46 0.23
47 0.08
48 1.75
49 0.49
50 1.50
51 0.19
52 1.75
53 0.95
54 1.07
55 0.07
56 0.51
57 0.28
58 -0.33
59 0.49
60 0.51
61 0.71
62 0.04
63 1.00
64 0.47
65 0.47
66 1.10
67 -2.63
68 -0.35
69 0.59
70 0.41
71 1.18
72 0.49
73 1.75
74 -0.30
75 1.18
76 0.00
77 0.00
78 1.10
81 1.10
82 -0.81
83 0.41
84 1.07
85 0.49
86 1.18
87 -0.30
88 0.01
89 1.50
90 1.75
91 0.26
92 -0.35
93 0.41
94 0.47
95 0.17
96 0.00
#Reported_Model_Average 0.491
#Overall_Average_Reported 0.491
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
1 0.01
2 1.09
3 0.47
4 0.81
5 0.17
6 0.28
7 1.06
9 0.44
10 0.41
11 0.14
12 0.65
13 1.75
14 0.79
15 1.50
16 0.00
17 0.59
18 0.41
19 1.18
20 0.08
21 0.95
22 0.59
23 -0.43
24 0.25
25 0.08
26 0.55
27 0.41
28 -0.56
29 0.34
34 0.00
35 0.00
36 1.75
37 0.52
38 0.36
39 0.35
40 0.49
41 1.07
42 -0.56
43 1.07
44 0.55
45 -0.03
46 0.23
47 0.08
48 1.75
49 0.49
50 1.50
51 0.19
52 1.75
53 0.95
54 1.07
55 0.07
56 0.51
57 0.28
58 -0.33
59 0.49
60 0.51
61 0.71
62 0.04
63 1.00
64 0.47
65 0.47
66 1.10
67 -2.63
68 -0.35
69 0.59
70 0.41
71 1.18
72 0.49
73 1.75
74 -0.30
75 1.18
76 0.00
77 0.00
78 1.10
81 1.10
82 -0.81
83 0.41
84 1.07
85 0.49
86 1.18
87 -0.30
88 0.01
89 1.50
90 1.75
91 0.26
92 -0.35
93 0.41
94 0.47
95 0.17
96 0.00
#Reported_Model_Average 0.491
#Overall_Average_Reported 0.491
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
1.000 0
2.000 0
3.000 0
4.000 0
5.000 0
6.000 0
7.000 0
8.000 0
9.000 2
10.000 1
11.000 0
12.000 2
13.000 0
14.000 0
15.000 0
16.000 0
17.000 0
18.000 0
19.000 0
20.000 0
21.000 0
22.000 0
23.000 0
24.000 0
25.000 2
26.000 0
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 6
39.000 2
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 0
52.000 0
53.000 0
54.000 0
55.000 0
56.000 0
57.000 0
58.000 0
59.000 0
60.000 0
61.000 3
62.000 2
63.000 3
64.000 0
65.000 0
66.000 0
67.000 0
68.000 0
69.000 0
70.000 1
71.000 0
72.000 0
73.000 0
74.000 3
75.000 0
76.000 0
77.000 0
78.000 0
79.000 0
80.000 0
81.000 0
82.000 2
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 0
96.000 6
#Reported_Model_Average 0.396
#Overall_Average_Reported 0.396
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 1335:A 96 LEU 2HD2 :A 96 LEU H : -0.810: 34
: 1335:A 96 LEU CD2 :A 96 LEU H : -0.643: 34
: 1335:A 96 LEU N :A 96 LEU 2HD2 : -0.588: 34
: 1335:A 70 GLU 1HB :A 92 ILE 1HD1 : -0.771: 19
: 1335:A 63 VAL 3HG2 :A 61 PHE CD2 : -0.722: 23
: 1335:A 61 PHE HD2 :A 63 VAL 3HG2 : -0.696: 23
: 1335:A 63 VAL 3HG2 :A 61 PHE CE2 : -0.426: 23
: 1335:A 38 LEU 3HD1 :A 38 LEU C : -0.709: 15
: 1335:A 38 LEU C :A 38 LEU CD1 : -0.503: 15
: 1335:A 39 LYS N :A 38 LEU 2HD2 : -0.436: 11
: 1335:A 38 LEU 3HD1 :A 39 LYS N : -0.424: 15
: 1335:A 9 PRO 2HG :A 82 LEU 1HD2 : -0.693: 24
: 1335:A 9 PRO 2HG :A 82 LEU CD2 : -0.542: 24
: 1335:A 74 TYR CZ :A 10 ASN HA : -0.605: 23
: 1335:A 74 TYR HD1 :A 12 SER HG : -0.520: 21
: 1335:A 12 SER OG :A 74 TYR HD1 : -0.481: 21
: 1335:A 25 LYS NZ :A 37 GLN 1HE2 : -0.528: 17
: 1335:A 37 GLN 1HE2 :A 25 LYS 1HZ : -0.424: 17
: 1335:A 62 GLU O :A 62 GLU 2HG : -0.470: 29
#sum2 ::14.23 clashscore : 14.23 clashscore B<40
#summary::1335 atoms:1335 atoms B<40:150710 potential dots:9419.0 A^2:19 bumps:19 bumps B<40:385.7 score
Output from PDB validation software
Summary from PDB validation
May. 10, 13:29:58 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 1.4 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
--------------------------------------------------------------------------------
-11.6 LYS A 3 N - CA - C 99.6 111.2
-9.3 ASN A 16 N - CA - C 101.9 111.2
-9.1 PHE A 42 N - CA - C 102.1 111.2
-8.7 ILE A 68 N - CA - C 102.5 111.2
-8.9 GLU A 70 N - CA - C 102.3 111.2
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
MSE( A -97 )
ASN( A -96 )
TYR( A -95 )
LYS( A -94 )
ILE( A -93 )
SER( A -92 )
GLU( A -91 )
LEU( A -90 )
MSE( A -89 )
PRO( A -88 )
ASN( A -87 )
LEU( A -86 )
SER( A -85 )
GLY( A -84 )
THR( A -83 )
ILE( A -82 )
ASN( A -81 )
ALA( A -80 )
GLU( A -79 )
VAL( A -78 )
VAL( A -77 )
THR( A -76 )
ALA( A -75 )
TYR( A -74 )
PRO( A -73 )
LYS( A -72 )
LYS( A -71 )
GLU( A -70 )
PHE( A -69 )
SER( A -68 )
ARG( A -67 )
LYS( A -66 )
ASP( A -65 )
GLY( A -64 )
THR( A -63 )
LYS( A -62 )
GLY( A -61 )
GLN( A -60 )
LEU( A -59 )
LYS( A -58 )
SER( A -57 )
LEU( A -56 )
PHE( A -55 )
LEU( A -54 )
LYS( A -53 )
ASP( A -52 )
ASP( A -51 )
THR( A -50 )
GLY( A -49 )
SER( A -48 )
ILE( A -47 )
ARG( A -46 )
GLY( A -45 )
THR( A -44 )
LEU( A -43 )
TRP( A -42 )
ASN( A -41 )
GLU( A -40 )
LEU( A -39 )
ALA( A -38 )
ASP( A -37 )
PHE( A -36 )
GLU( A -35 )
VAL( A -34 )
LYS( A -33 )
LYS( A -32 )
GLY( A -31 )
ASP( A -30 )
ILE( A -29 )
ALA( A -28 )
GLU( A -27 )
VAL( A -26 )
SER( A -25 )
GLY( A -24 )
TYR( A -23 )
VAL( A -22 )
LYS( A -21 )
GLN( A -20 )
GLY( A -19 )
TYR( A -18 )
SER( A -17 )
GLY( A -16 )
LEU( A -15 )
GLU( A -14 )
ILE( A -13 )
SER( A -12 )
VAL( A -11 )
ASP( A -10 )
ASN( A -9 )
ILE( A -8 )
GLY( A -7 )
ILE( A -6 )
ILE( A -5 )
GLU( A -4 )
LYS( A -3 )
SER( A -2 )
LEU( A -1 )
SEQUENCE WARNING: Residue (A SER 29 ) and Residue (A THR 34 ) are not linked
Distance of C-N bond is 5.87
SEQUENCE WARNING: Residue (A GLY 78 ) and Residue (A GLY 81 ) are not linked
Distance of C-N bond is 4.96
PDB Chain_ID: A
1 15
SEQRES: MSE ASN TYR LYS ILE SER GLU LEU MSE PRO ASN LEU SER GLY THR
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 30
SEQRES: ILE ASN ALA GLU VAL VAL THR ALA TYR PRO LYS LYS GLU PHE SER
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
31 45
SEQRES: ARG LYS ASP GLY THR LYS GLY GLN LEU LYS SER LEU PHE LEU LYS
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
46 60
SEQRES: ASP ASP THR GLY SER ILE ARG GLY THR LEU TRP ASN GLU LEU ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
61 75
SEQRES: ASP PHE GLU VAL LYS LYS GLY ASP ILE ALA GLU VAL SER GLY TYR
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
76 90
SEQRES: VAL LYS GLN GLY TYR SER GLY LEU GLU ILE SER VAL ASP ASN ILE
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
91 105
SEQRES: GLY ILE ILE GLU LYS SER LEU MSE ASN TYR LYS ILE SER GLU LEU
COORDS: ... ... ... ... ... ... ... MSE ASN TYR LYS ILE SER GLU LEU
0 7
106 120
SEQRES: MSE PRO ASN LEU SER GLY THR ILE ASN ALA GLU VAL VAL THR ALA
COORDS: MSE PRO ASN LEU SER GLY THR ILE ASN ALA GLU VAL VAL THR ALA
8 22
121 135
SEQRES: TYR PRO LYS LYS GLU PHE SER THR LYS GLY GLN LEU LYS SER LEU
COORDS: TYR PRO LYS LYS GLU PHE SER THR LYS GLY GLN LEU LYS SER LEU
23 41
136 150
SEQRES: PHE LEU LYS ASP ASP THR GLY SER ILE ARG GLY THR LEU TRP ASN
COORDS: PHE LEU LYS ASP ASP THR GLY SER ILE ARG GLY THR LEU TRP ASN
42 56
151 165
SEQRES: GLU LEU ALA ASP PHE GLU VAL LYS LYS GLY ASP ILE ALA GLU VAL
COORDS: GLU LEU ALA ASP PHE GLU VAL LYS LYS GLY ASP ILE ALA GLU VAL
57 71
166 180
SEQRES: SER GLY TYR VAL LYS GLN GLY GLY LEU GLU ILE SER VAL ASP ASN
COORDS: SER GLY TYR VAL LYS GLN GLY GLY LEU GLU ILE SER VAL ASP ASN
72 88
181 188
SEQRES: ILE GLY ILE ILE GLU LYS SER LEU
COORDS: ILE GLY ILE ILE GLU LYS SER LEU
89 96
==> The following residues have missing atoms:
RES MOD#C SEQ ATOMS
THR( A 34) OG1 CG2
LYS( A 35) CB CG CD CE NZ
LYS( A 76) CG CD CE NZ
GLN( A 77) CG CD OE1 NE2
==> The following residues have extra atoms:
RES MOD#C SEQ ATOMS
LEU( A 96) O2