Detailed results of DHR29B_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 >>>----------+
| |
| DHR29B_XRay_em_bcr3_noHs_000.rin 0.0 84 residues |
| |
+| Ramachandran plot: 91.2% core 7.4% allow 1.5% gener 0.0% disall |
| |
+| All Ramachandrans: 2 labelled residues (out of 79) |
+| Chi1-chi2 plots: 1 labelled residues (out of 47) |
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
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 -1.35
3 0.62
4 0.19
5 -0.49
6 -1.03
7 -0.49
8 0.20
9 -0.04
10 -0.15
11 -0.76
12 -0.30
13 0.58
14 -0.27
15 -0.40
16 -0.26
17 0.45
23 -0.48
24 -0.27
25 -0.30
26 -0.24
27 0.31
28 -0.41
29 0.38
30 -0.30
31 0.30
32 -0.77
33 -0.87
34 0.33
35 -1.73
36 -5.13
37 -3.76
38 -0.86
39 -1.73
40 1.05
41 0.37
42 -0.49
43 -0.12
44 0.26
45 -1.20
46 0.08
47 0.08
48 -0.03
49 -1.71
50 -1.16
51 0.57
52 -0.14
53 -1.27
54 -0.47
55 -1.07
56 -0.59
57 -0.02
58 -0.63
59 0.55
60 -0.39
61 -0.32
62 -0.63
63 0.42
64 -0.39
65 0.37
66 0.34
67 0.37
68 0.05
69 -0.12
70 -0.19
71 -0.50
72 -1.18
73 -1.25
74 -0.21
75 -0.41
76 -0.24
77 0.15
78 0.08
79 0.31
80 0.24
81 -0.74
82 -0.18
83 -0.17
84 -0.59
85 -0.06
#Reported_Model_Average -0.382
#Overall_Average_Reported -0.382
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 0.55
2 -1.04
3 0.62
4 -0.05
5 -0.34
6 -0.95
7 0.01
8 0.08
9 0.13
10 -0.26
11 -0.76
12 0.03
13 0.66
14 0.18
15 -0.40
16 -0.26
17 0.82
18 0.66
20 0.88
22 -0.88
23 0.19
24 0.30
25 -0.30
26 0.41
27 0.71
28 -0.69
29 0.62
30 0.44
31 -0.29
32 -0.45
33 -0.87
34 0.39
35 -1.11
36 -5.13
37 -2.24
38 -1.44
39 -1.20
40 0.82
41 0.02
42 -0.49
43 0.38
44 0.59
45 -1.20
46 -0.10
47 -0.50
48 -0.02
49 -1.42
50 -0.60
51 0.57
52 -0.09
53 -0.81
54 -0.47
55 -1.07
56 0.12
57 0.15
58 -0.33
59 0.69
60 -0.04
61 0.18
62 -0.06
63 0.41
64 0.01
65 0.37
66 0.61
67 0.37
68 -0.52
69 -0.35
70 0.48
71 -0.36
72 -1.13
73 -0.22
74 0.10
75 -0.22
76 -0.24
77 -0.14
78 0.41
79 0.14
80 0.44
81 0.07
82 0.36
83 -0.41
84 -0.43
85 -1.58
86 0.06
#Reported_Model_Average -0.196
#Overall_Average_Reported -0.196
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 0.24
2 0.51
3 0.64
4 0.79
5 1.07
6 0.79
7 1.07
8 0.65
9 1.07
10 -0.35
11 0.59
12 0.55
13 0.41
14 0.55
15 0.64
16 0.14
17 0.41
18 0.49
20 1.07
22 0.08
23 -0.10
24 0.77
25 0.44
26 0.49
27 1.18
28 0.19
29 1.18
30 0.55
31 0.95
32 0.41
33 1.75
34 -0.43
35 -0.26
36 0.44
37 0.34
38 0.81
39 0.41
40 -0.74
41 0.41
42 0.00
43 0.77
44 0.37
45 0.59
46 1.09
47 1.18
48 -0.03
49 1.06
50 0.17
51 1.10
52 0.59
53 0.04
54 0.44
55 1.75
56 0.41
57 0.80
58 -0.03
59 1.30
60 0.41
61 1.00
62 0.55
63 1.18
64 -0.59
65 0.25
66 0.93
67 0.44
68 0.41
69 1.07
70 -1.54
71 1.07
72 0.08
73 0.41
74 1.07
75 0.65
76 0.44
77 0.24
78 0.08
79 1.18
80 0.79
81 1.07
82 0.10
83 0.36
84 -0.37
85 -0.49
86 0.20
#Reported_Model_Average 0.509
#Overall_Average_Reported 0.509
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 0.24
2 0.51
3 0.64
4 0.79
5 1.07
6 0.79
7 1.07
8 0.65
9 1.07
10 -0.35
11 0.59
12 0.55
13 0.41
14 0.55
15 0.64
16 0.14
17 0.41
18 0.49
20 1.07
22 0.08
23 -0.10
24 0.77
25 0.44
26 0.49
27 1.18
28 0.19
29 1.18
30 0.55
31 0.95
32 0.41
33 1.75
34 -0.43
35 -0.26
36 0.44
37 0.34
38 0.81
39 0.41
40 -0.74
41 0.41
42 0.00
43 0.77
44 0.37
45 0.59
46 1.09
47 1.18
48 -0.03
49 1.06
50 0.17
51 1.10
52 0.59
53 0.04
54 0.44
55 1.75
56 0.41
57 0.80
58 -0.03
59 1.30
60 0.41
61 1.00
62 0.55
63 1.18
64 -0.59
65 0.25
66 0.93
67 0.44
68 0.41
69 1.07
70 -1.54
71 1.07
72 0.08
73 0.41
74 1.07
75 0.65
76 0.44
77 0.24
78 0.08
79 1.18
80 0.79
81 1.07
82 0.10
83 0.36
84 -0.37
85 -0.49
86 0.20
#Reported_Model_Average 0.509
#Overall_Average_Reported 0.509
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 1
2.000 1
3.000 0
4.000 0
5.000 0
6.000 0
7.000 0
8.000 0
9.000 1
10.000 0
11.000 0
12.000 0
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 0
26.000 0
27.000 0
28.000 0
29.000 3
30.000 1
31.000 1
32.000 3
33.000 0
34.000 5
35.000 6
36.000 7
37.000 2
38.000 7
39.000 1
40.000 0
41.000 0
42.000 0
43.000 1
44.000 1
45.000 0
46.000 0
47.000 1
48.000 0
49.000 0
50.000 0
51.000 0
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 1
64.000 2
65.000 0
66.000 0
67.000 1
68.000 0
69.000 1
70.000 0
71.000 3
72.000 3
73.000 1
74.000 1
75.000 0
76.000 0
77.000 1
78.000 0
79.000 0
80.000 0
81.000 0
82.000 0
83.000 0
84.000 0
85.000 1
86.000 0
#Reported_Model_Average 0.674
#Overall_Average_Reported 0.674
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 1313:A 37 SER 1HB :A 36 PRO O : -0.955: 42
: 1313:A 36 PRO 2HD :A 34 TYR CE2 : -0.635: 33
: 1313:A 36 PRO O :A 37 SER CB : -0.550: 42
: 1313:A 34 TYR CE2 :A 36 PRO 2HG : -0.493: 32
: 1313:A 36 PRO 2HD :A 34 TYR CZ : -0.430: 35
: 1313:A 36 PRO CD :A 34 TYR CE2 : -0.427: 33
: 1313:A 36 PRO 2HD :A 34 TYR CD2 : -0.400: 33
: 1313:A 38 ILE 3HG2 :A 35 ASN OD1 : -0.899: 51
: 1313:A 38 ILE 3HG2 :A 35 ASN CG : -0.588: 51
: 1313:A 35 ASN CG :A 38 ILE CG2 : -0.583: 51
: 1313:A 35 ASN ND2 :A 38 ILE 1HG2 : -0.549: 51
: 1313:A 35 ASN ND2 :A 38 ILE CG2 : -0.493: 51
: 1313:A 67 PRO O :A 35 ASN ND2 : -0.444: 23
: 1313:A 38 ILE 2HD1 :A 38 ILE O : -0.412: 39
: 1313:A 32 GLU 2HG :A 72 VAL 1HG1 : -0.823: 50
: 1313:A 32 GLU 2HG :A 72 VAL CG1 : -0.707: 50
: 1313:A 72 VAL 1HG1 :A 32 GLU CG : -0.519: 50
: 1313:A 39 ASN O :A 43 LEU HG : -0.702: 50
: 1313:A 71 ILE 2HD1 :A 29 VAL 1HG1 : -0.653: 27
: 1313:A 71 ILE 3HG2 :A 29 VAL 3HG1 : -0.517: 27
: 1313:A 71 ILE 3HG2 :A 29 VAL CG1 : -0.440: 27
: 1313:A 30 LYS 1HB :A 73 GLU 2HB : -0.635: 26
: 1313:A 64 GLU 2HG :A 44 PHE O : -0.595: 30
: 1313:A 64 GLU O :A 63 VAL 2HG1 : -0.415: 22
: 1313:A 77 ARG 2HG :A 74 ILE O : -0.582: 34
: 1313:A 1 ARG O :A 2 ASP C : -0.435: 37
: 1313:A 54 PRO 1HG :A 85 HIS CD2 : -0.433: 47
: 1313:A 9 LEU 1HD1 :A 47 VAL 3HG1 : -0.405: 19
: 1313:A 69 ILE 3HG2 :A 31 THR HB : -0.404: 23
#sum2 ::22.09 clashscore : 14.94 clashscore B<40
#summary::1313 atoms:1138 atoms B<40:146452 potential dots:9153.0 A^2:29 bumps:17 bumps B<40:254 score
Output from PDB validation software
Summary from PDB validation
May. 10, 01:32:53 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
--------------------------------------------------------------------------------
-9.3 THR A 4 N - CA - C 101.9 111.2
-12.1 ALA A 45 N - CA - C 99.1 111.2
-7.9 VAL A 47 N - CA - C 103.3 111.2
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
ARG( A -89 )
ASP( A -88 )
PRO( A -87 )
THR( A -86 )
LEU( A -85 )
THR( A -84 )
LEU( A -83 )
SER( A -82 )
LEU( A -81 )
ILE( A -80 )
ALA( A -79 )
LYS( A -78 )
ASN( A -77 )
THR( A -76 )
PRO( A -75 )
ALA( A -74 )
ASN( A -73 )
SER( A -72 )
MSE( A -71 )
ILE( A -70 )
MSE( A -69 )
THR( A -68 )
LYS( A -67 )
LEU( A -66 )
PRO( A -65 )
SER( A -64 )
VAL( A -63 )
ARG( A -62 )
VAL( A -61 )
LYS( A -60 )
THR( A -59 )
GLU( A -58 )
GLY( A -57 )
TYR( A -56 )
ASN( A -55 )
PRO( A -54 )
SER( A -53 )
ILE( A -52 )
ASN( A -51 )
VAL( A -50 )
ASN( A -49 )
GLU( A -48 )
LEU( A -47 )
PHE( A -46 )
ALA( A -45 )
TYR( A -44 )
VAL( A -43 )
ASP( A -42 )
LEU( A -41 )
SER( A -40 )
GLY( A -39 )
SER( A -38 )
GLU( A -37 )
PRO( A -36 )
GLY( A -35 )
GLU( A -34 )
HIS( A -33 )
ASP( A -32 )
TYR( A -31 )
GLU( A -30 )
VAL( A -29 )
LYS( A -28 )
VAL( A -27 )
GLU( A -26 )
PRO( A -25 )
ILE( A -24 )
PRO( A -23 )
ASN( A -22 )
ILE( A -21 )
LYS( A -20 )
ILE( A -19 )
VAL( A -18 )
GLU( A -17 )
ILE( A -16 )
SER( A -15 )
PRO( A -14 )
ARG( A -13 )
VAL( A -12 )
VAL( A -11 )
THR( A -10 )
LEU( A -9 )
GLN( A -8 )
LEU( A -7 )
GLU( A -6 )
HIS( A -5 )
HIS( A -4 )
HIS( A -3 )
HIS( A -2 )
HIS( A -1 )
HIS( A 0 )
PDB Chain_ID: A
1 15
SEQRES: ARG ASP PRO THR LEU THR LEU SER LEU ILE ALA LYS ASN THR PRO
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 30
SEQRES: ALA ASN SER MSE ILE MSE THR LYS LEU PRO SER VAL ARG VAL LYS
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
31 45
SEQRES: THR GLU GLY TYR ASN PRO SER ILE ASN VAL ASN GLU LEU PHE ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
46 60
SEQRES: TYR VAL ASP LEU SER GLY SER GLU PRO GLY GLU HIS ASP TYR GLU
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
61 75
SEQRES: VAL LYS VAL GLU PRO ILE PRO ASN ILE LYS ILE VAL GLU ILE SER
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
76 90
SEQRES: PRO ARG VAL VAL THR LEU GLN LEU GLU HIS HIS HIS HIS HIS HIS
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
91 105
SEQRES: ARG ASP PRO THR LEU THR LEU SER LEU ILE ALA LYS ASN THR PRO
COORDS: ARG ASP PRO THR LEU THR LEU SER LEU ILE ALA LYS ASN THR PRO
1 15
106 120
SEQRES: ALA ASN SER MSE ILE MSE THR LYS LEU PRO SER VAL ARG VAL LYS
COORDS: ALA ASN SER MSE ILE MSE THR LYS LEU PRO SER VAL ARG VAL LYS
16 30
121 135
SEQRES: THR GLU GLY TYR ASN PRO SER ILE ASN VAL ASN GLU LEU PHE ALA
COORDS: THR GLU GLY TYR ASN PRO SER ILE ASN VAL ASN GLU LEU PHE ALA
31 45
136 150
SEQRES: TYR VAL ASP LEU SER GLY SER GLU PRO GLY GLU HIS ASP TYR GLU
COORDS: TYR VAL ASP LEU SER GLY SER GLU PRO GLY GLU HIS ASP TYR GLU
46 60
151 165
SEQRES: VAL LYS VAL GLU PRO ILE PRO ASN ILE LYS ILE VAL GLU ILE SER
COORDS: VAL LYS VAL GLU PRO ILE PRO ASN ILE LYS ILE VAL GLU ILE SER
61 75
166 176
SEQRES: PRO ARG VAL VAL THR LEU GLN LEU GLU HIS HIS
COORDS: PRO ARG VAL VAL THR LEU GLN LEU GLU HIS HIS
76 86
==> The following residues have missing atoms:
RES MOD#C SEQ ATOMS
GLU( A 42) CB CG CD OE1 OE2