Detailed results of STR65_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 >>>----------+
| |
| STR65_XRay_em_bcr3_noHs_000.rin 0.0 97 residues |
| |
| Ramachandran plot: 96.1% core 3.9% allow 0.0% gener 0.0% disall |
| |
+| All Ramachandrans: 1 labelled residues (out of 89) |
| Chi1-chi2 plots: 0 labelled residues (out of 55) |
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
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
12 0.82
13 1.01
14 1.08
15 1.22
16 0.76
17 0.85
18 1.08
19 0.54
20 1.01
21 0.25
25 0.37
26 0.75
27 -0.39
28 0.88
29 -0.14
30 0.40
31 -0.32
35 0.19
36 0.95
37 0.94
38 0.76
39 1.22
40 1.02
41 0.80
42 0.99
43 1.22
44 1.18
45 1.13
46 1.43
47 1.13
48 -0.72
49 0.77
50 -3.27
51 0.62
52 -0.85
53 0.11
54 0.47
55 0.82
56 -0.28
57 0.56
58 1.05
59 0.66
60 1.14
61 1.25
62 0.82
63 -1.32
64 -0.27
65 -0.44
66 -1.57
67 -0.55
68 0.02
69 0.68
70 0.63
71 0.84
72 1.04
73 0.68
74 1.05
75 0.54
76 0.57
77 -0.15
78 0.36
79 0.82
80 1.22
81 0.98
82 -0.11
83 0.75
84 0.91
85 -0.53
86 -0.49
87 -0.14
88 -0.18
89 -0.85
90 -0.21
91 -1.03
92 0.35
93 0.14
94 0.40
95 -1.02
96 -0.07
97 0.87
101 0.87
102 1.04
103 1.13
104 1.04
105 0.87
106 1.13
107 0.98
108 0.85
109 -1.37
#Reported_Model_Average 0.413
#Overall_Average_Reported 0.413
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
11 -0.88
12 0.82
13 0.92
14 1.15
15 0.23
16 0.76
17 0.88
18 0.69
19 -0.25
20 0.50
21 0.25
22 0.00
24 -1.88
25 0.43
26 0.02
27 -0.39
28 0.88
29 0.33
30 0.40
31 -0.16
32 -0.72
34 1.18
35 0.48
36 0.46
37 0.85
38 0.76
39 1.26
40 1.02
41 0.84
42 0.93
43 0.76
44 0.80
45 0.67
46 1.09
47 1.20
48 -0.81
49 0.77
50 -1.56
51 0.62
52 -0.13
53 0.49
54 0.47
55 -0.78
56 -0.07
57 0.69
58 0.98
59 0.66
60 0.19
61 1.25
62 1.04
63 -0.60
64 0.30
65 -0.44
66 -0.78
67 -0.90
68 0.02
69 -0.01
70 0.60
71 0.57
72 0.68
73 -0.88
74 0.89
75 0.54
76 0.57
77 -0.59
78 0.36
79 0.81
80 1.09
81 0.83
82 -0.11
83 0.36
84 0.91
85 0.22
86 0.12
87 -0.66
88 -0.02
89 -1.64
90 0.33
91 -0.12
92 0.35
93 -0.28
94 0.00
95 -1.32
96 0.64
97 0.82
98 0.56
100 0.74
101 0.62
102 0.89
103 1.02
104 0.94
105 0.65
106 0.04
107 0.95
108 0.87
109 -1.28
110 -1.73
#Reported_Model_Average 0.279
#Overall_Average_Reported 0.279
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
11 0.08
12 0.76
13 -0.06
14 0.62
15 -0.50
16 0.76
17 0.71
18 0.29
19 -0.22
20 1.11
21 0.63
22 1.10
24 0.51
25 0.55
26 0.34
27 -0.25
28 0.34
29 -0.80
30 0.59
31 0.20
32 0.16
34 0.29
35 0.62
36 0.47
37 0.39
38 0.76
39 -0.94
40 0.63
41 1.11
42 1.30
43 0.66
44 0.86
45 1.30
46 0.61
47 0.29
48 -0.33
49 1.10
50 -0.09
51 0.44
52 1.00
53 0.59
54 -0.41
55 0.60
56 0.30
57 0.74
58 -0.62
59 0.44
60 1.10
61 0.63
62 0.60
63 0.29
64 0.28
65 1.10
66 1.62
67 0.51
68 0.05
69 0.62
70 0.87
71 0.39
72 0.66
73 0.66
74 0.74
75 0.76
76 0.63
77 1.01
78 0.76
79 0.62
80 0.66
81 0.41
82 0.44
83 0.17
84 1.10
85 0.41
86 -0.41
87 0.81
88 -1.14
89 0.81
90 0.47
91 0.51
92 0.44
93 0.28
94 -0.43
95 1.04
96 0.34
97 -0.20
98 -1.70
100 -0.32
101 0.62
102 -0.32
103 1.30
104 0.66
105 0.62
106 0.16
107 0.30
108 -0.46
109 0.04
110 0.20
#Reported_Model_Average 0.410
#Overall_Average_Reported 0.410
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
11 0.08
12 0.76
13 -0.06
14 0.62
15 -0.50
16 0.76
17 0.71
18 0.29
19 -0.22
20 1.11
21 0.63
22 1.10
24 0.51
25 0.55
26 0.34
27 -0.25
28 0.34
29 -0.80
30 0.59
31 0.20
32 0.16
34 0.29
35 0.62
36 0.47
37 0.39
38 0.76
39 -0.94
40 0.63
41 1.11
42 1.30
43 0.66
44 0.86
45 1.30
46 0.61
47 0.29
48 -0.33
49 1.10
50 -0.09
51 0.44
52 1.00
53 0.59
54 -0.41
55 0.60
56 0.30
57 0.74
58 -0.62
59 0.44
60 1.10
61 0.63
62 0.60
63 0.29
64 0.28
65 1.10
66 1.62
67 0.51
68 0.05
69 0.62
70 0.87
71 0.39
72 0.66
73 0.66
74 0.74
75 0.76
76 0.63
77 1.01
78 0.76
79 0.62
80 0.66
81 0.41
82 0.44
83 0.17
84 1.10
85 0.41
86 -0.41
87 0.81
88 -1.14
89 0.81
90 0.47
91 0.51
92 0.44
93 0.28
94 -0.43
95 1.04
96 0.34
97 -0.20
98 -1.70
100 -0.32
101 0.62
102 -0.32
103 1.30
104 0.66
105 0.62
106 0.16
107 0.30
108 -0.46
109 0.04
110 0.20
#Reported_Model_Average 0.410
#Overall_Average_Reported 0.410
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
11.000 3
12.000 0
13.000 0
14.000 3
15.000 4
16.000 0
17.000 1
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 1
28.000 0
29.000 0
30.000 1
31.000 0
32.000 0
33.000 0
34.000 0
35.000 1
36.000 0
37.000 0
38.000 0
39.000 0
40.000 0
41.000 0
42.000 0
43.000 0
44.000 1
45.000 1
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 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 6
68.000 1
69.000 2
70.000 3
71.000 0
72.000 0
73.000 0
74.000 0
75.000 0
76.000 0
77.000 2
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 5
88.000 0
89.000 7
90.000 1
91.000 1
92.000 1
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 1
103.000 0
104.000 1
105.000 0
106.000 1
107.000 0
108.000 0
109.000 0
110.000 0
#Reported_Model_Average 0.540
#Overall_Average_Reported 0.540
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 1491:A 87 ILE 3HG2 :A 89 ILE 1HD1 : -1.001: 36
: 1491:A 87 ILE 3HG2 :A 89 ILE CD1 : -0.622: 36
: 1491:A 89 ILE 1HD1 :A 87 ILE CG2 : -0.497: 36
: 1491:A 89 ILE N :A 89 ILE 2HD1 : -0.492: 36
: 1491:A 87 ILE O :A 89 ILE 2HD1 : -0.471: 36
: 1491:A 80 LYS CD :A 87 ILE 3HD1 : -0.463: 44
: 1491:A 89 ILE O :A 92 PRO 2HD : -0.421: 25
: 1491:A 67 ASN C :A 67 ASN 2HD2 : -0.711: 51
: 1491:A 67 ASN ND2 :A 69 GLU H : -0.702: 50
: 1491:A 69 GLU H :A 67 ASN 2HD2 : -0.660: 50
: 1491:A 70 PHE 1HB :A 27 ALA O : -0.529: 47
: 1491:A 70 PHE CD1 :A 30 PRO 2HG : -0.524: 44
: 1491:A 67 ASN 2HD2 :A 68 PRO N : -0.483: 51
: 1491:A 67 ASN O :A 70 PHE 2HB : -0.407: 51
: 1491:A 14 GLU 2HG :A 11 THR 2HG2 : -0.684: 44
: 1491:A 14 GLU CG :A 11 THR 2HG2 : -0.573: 44
: 1491:A 14 GLU 2HG :A 11 THR CG2 : -0.410: 44
: 1491:A 102 GLN O :A 106 LEU 3HD1 : -0.598: 41
: 1491:A 19 PHE CE2 :A 15 LYS 2HE : -0.592: 49
: 1491:A 15 LYS 2HE :A 19 PHE HE2 : -0.485: 49
: 1491:A 15 LYS HA :A 15 LYS 1HD : -0.459: 46
: 1491:A 35 GLU 2HG :A 77 TRP CZ2 : -0.527: 35
: 1491:A 81 VAL 3HG2 :A 77 TRP O : -0.449: 29
: 1491:A 90 LYS NZ :A 91 ASN 1HD2 : -0.513: 46
: 1491:A 44 TYR OH :A 104 LYS 1HB : -0.466: 31
: 1491:A 17 LEU 1HD1 :A 56 VAL CG1 : -0.462: 44
: 1491:A 50 VAL O :A 45 LEU 2HB : -0.426: 38
#sum2 ::18.11 clashscore : 10.56 clashscore B<40
#summary::1491 atoms:947 atoms B<40:168136 potential dots:10510.0 A^2:27 bumps:10 bumps B<40:455.2 score
Output from PDB validation software
Summary from PDB validation
May. 11, 01:43:25 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 0.006 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.
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
--------------------------------------------------------------------------------
-7.5 VAL A 52 N - CA - C 103.7 111.2
-9.4 ASN A 67 N - CA - C 101.8 111.2
6.9 LYS A 90 N - CA - C 118.1 111.2
-11.6 PHE A 95 N - CA - C 99.6 111.2
6.9 SER A 96 N - CA - C 118.1 111.2
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-104 )
VAL( A-103 )
ASN( A-102 )
PHE( A-101 )
LYS( A-100 )
ASP( A -99 )
LYS( A -98 )
SER( A -97 )
MSE( A -96 )
PRO( A -95 )
THR( A -94 )
ALA( A -93 )
ILE( A -92 )
GLU( A -91 )
LYS( A -90 )
ALA( A -89 )
LEU( A -88 )
ASP( A -87 )
PHE( A -86 )
ILE( A -85 )
GLY( A -84 )
GLY( A -83 )
MSE( A -82 )
ASN( A -81 )
THR( A -80 )
SER( A -79 )
ALA( A -78 )
SER( A -77 )
VAL( A -76 )
PRO( A -75 )
HIS( A -74 )
SER( A -73 )
MSE( A -72 )
ASP( A -71 )
GLU( A -70 )
SER( A -69 )
THR( A -68 )
ALA( A -67 )
LYS( A -66 )
GLY( A -65 )
ILE( A -64 )
LEU( A -63 )
LYS( A -62 )
TYR( A -61 )
LEU( A -60 )
HIS( A -59 )
ASP( A -58 )
LEU( A -57 )
GLY( A -56 )
VAL( A -55 )
PRO( A -54 )
VAL( A -53 )
SER( A -52 )
PRO( A -51 )
GLU( A -50 )
VAL( A -49 )
VAL( A -48 )
VAL( A -47 )
ALA( A -46 )
ARG( A -45 )
GLY( A -44 )
GLU( A -43 )
GLN( A -42 )
GLU( A -41 )
GLY( A -40 )
TRP( A -39 )
ASN( A -38 )
PRO( A -37 )
GLU( A -36 )
PHE( A -35 )
THR( A -34 )
LYS( A -33 )
LYS( A -32 )
VAL( A -31 )
ALA( A -30 )
GLY( A -29 )
TRP( A -28 )
ALA( A -27 )
GLU( A -26 )
LYS( A -25 )
VAL( A -24 )
ALA( A -23 )
SER( A -22 )
GLY( A -21 )
ASN( A -20 )
ARG( A -19 )
ILE( A -18 )
LEU( A -17 )
ILE( A -16 )
LYS( A -15 )
ASN( A -14 )
PRO( A -13 )
GLU( A -12 )
TYR( A -11 )
PHE( A -10 )
SER( A -9 )
THR( A -8 )
TYR( A -7 )
MSE( A -6 )
GLN( A -5 )
GLU( A -4 )
GLN( A -3 )
LEU( A -2 )
LYS( A -1 )
GLU( A 0 )
LEU( A 1 )
VAL( A 2 )
LEU( A 3 )
GLU( A 4 )
HIS( A 5 )
HIS( A 6 )
HIS( A 7 )
HIS( A 8 )
HIS( A 9 )
HIS( A 10 )
PDB Chain_ID: A
1 15
SEQRES: MSE VAL ASN PHE LYS ASP LYS SER MSE PRO THR ALA ILE GLU LYS
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 30
SEQRES: ALA LEU ASP PHE ILE GLY GLY MSE ASN THR SER ALA SER VAL PRO
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
31 45
SEQRES: HIS SER MSE ASP GLU SER THR ALA LYS GLY ILE LEU LYS TYR LEU
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
46 60
SEQRES: HIS ASP LEU GLY VAL PRO VAL SER PRO GLU VAL VAL VAL ALA ARG
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
61 75
SEQRES: GLY GLU GLN GLU GLY TRP ASN PRO GLU PHE THR LYS LYS VAL ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
76 90
SEQRES: GLY TRP ALA GLU LYS VAL ALA SER GLY ASN ARG ILE LEU ILE LYS
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
91 105
SEQRES: ASN PRO GLU TYR PHE SER THR TYR MSE GLN GLU GLN LEU LYS GLU
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
106 120
SEQRES: LEU VAL LEU GLU HIS HIS HIS HIS HIS HIS THR ALA ILE GLU LYS
COORDS: ... ... ... ... ... ... ... ... ... ... THR ALA ILE GLU LYS
11 15
121 135
SEQRES: ALA LEU ASP PHE ILE GLY GLY MSE ASN THR SER ALA SER VAL PRO
COORDS: ALA LEU ASP PHE ILE GLY GLY MSE ASN THR SER ALA SER VAL PRO
16 30
136 150
SEQRES: HIS SER MSE ASP GLU SER THR ALA LYS GLY ILE LEU LYS TYR LEU
COORDS: HIS SER MSE ASP GLU SER THR ALA LYS GLY ILE LEU LYS TYR LEU
31 45
151 165
SEQRES: HIS ASP LEU GLY VAL PRO VAL SER PRO GLU VAL VAL VAL ALA ARG
COORDS: HIS ASP LEU GLY VAL PRO VAL SER PRO GLU VAL VAL VAL ALA ARG
46 60
166 180
SEQRES: GLY GLU GLN GLU GLY TRP ASN PRO GLU PHE THR LYS LYS VAL ALA
COORDS: GLY GLU GLN GLU GLY TRP ASN PRO GLU PHE THR LYS LYS VAL ALA
61 75
181 195
SEQRES: GLY TRP ALA GLU LYS VAL ALA SER GLY ASN ARG ILE LEU ILE LYS
COORDS: GLY TRP ALA GLU LYS VAL ALA SER GLY ASN ARG ILE LEU ILE LYS
76 90
196 210
SEQRES: ASN PRO GLU TYR PHE SER THR TYR MSE GLN GLU GLN LEU LYS GLU
COORDS: ASN PRO GLU TYR PHE SER THR TYR MSE GLN GLU GLN LEU LYS GLU
91 105
211 215
SEQRES: LEU VAL LEU GLU HIS
COORDS: LEU VAL LEU GLU HIS
106 110