Detailed results of HR3102A_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 >>>----------+
| |
| HR3102A_XRay_em_bcr3_noHs_000.rin 0.0 70 residues |
| |
| Ramachandran plot: 98.1% core 1.9% allow 0.0% gener 0.0% disall |
| |
+| All Ramachandrans: 1 labelled residues (out of 59) |
| Chi1-chi2 plots: 0 labelled residues (out of 40) |
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
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
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 -5.13
3 0.03
4 -0.84
5 0.72
6 0.87
7 0.54
8 0.63
9 0.88
10 1.13
11 0.30
12 0.84
13 0.85
14 1.01
15 0.27
16 -0.35
17 0.28
21 -0.27
22 -0.73
23 -0.49
24 0.89
25 -1.60
26 -0.59
27 0.65
28 1.14
29 0.49
30 0.69
31 0.82
32 0.14
36 1.03
37 -0.68
38 0.18
39 0.74
40 0.99
41 0.87
42 1.05
43 1.22
44 1.25
45 0.57
46 0.83
47 1.24
48 0.87
49 0.65
53 -0.43
54 0.88
55 0.04
56 -1.15
57 -1.16
58 -0.23
59 -1.23
60 -0.55
61 -0.18
62 -0.40
63 0.75
64 1.08
65 1.01
66 1.22
70 0.81
71 0.80
72 0.68
#Reported_Model_Average 0.270
#Overall_Average_Reported 0.270
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 0.00
2 -5.13
3 0.03
4 -0.84
5 0.63
6 0.75
7 0.54
8 0.77
9 0.52
10 1.13
11 0.45
12 0.72
13 1.08
14 0.96
15 0.70
16 0.01
17 -0.43
18 -0.59
20 0.79
21 0.30
22 -0.22
23 -0.03
24 0.89
25 -1.14
26 -0.68
27 0.77
28 0.92
29 0.72
30 0.01
31 0.82
32 0.60
33 0.55
35 0.00
36 1.03
37 -0.68
38 -0.27
39 0.74
40 0.99
41 1.07
42 0.66
43 1.03
44 1.25
45 0.35
46 1.06
47 0.18
48 0.36
49 0.65
50 0.00
52 -1.20
53 -0.43
54 0.89
55 0.03
56 -0.76
57 -0.85
58 0.47
59 -0.89
60 -0.48
61 -0.02
62 -0.06
63 0.45
64 0.95
65 0.98
66 0.38
67 0.92
69 0.00
70 0.77
71 0.80
72 0.75
73 0.50
75 0.00
#Reported_Model_Average 0.246
#Overall_Average_Reported 0.246
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 0.00
2 0.00
3 0.64
4 0.41
5 0.62
6 0.62
7 -0.02
8 -0.11
9 0.16
10 0.29
11 -0.02
12 1.30
13 0.66
14 -0.59
15 0.82
16 0.47
17 -0.41
18 -0.10
20 0.00
21 0.36
22 0.08
23 -0.41
24 1.10
25 0.81
26 0.51
27 1.30
28 0.56
29 0.66
30 1.11
31 0.76
32 0.62
33 -0.68
35 0.44
36 1.10
37 0.49
38 0.17
39 0.63
40 0.44
41 0.62
42 0.74
43 0.66
44 0.63
45 0.74
46 0.95
47 -0.13
48 0.62
49 0.76
50 0.63
52 0.50
53 -0.02
54 -1.37
55 0.56
56 0.28
57 0.24
58 0.71
59 -0.80
60 -0.49
61 0.71
62 0.08
63 -0.32
64 0.60
65 -0.43
66 1.28
67 -0.43
69 0.76
70 0.30
71 0.44
72 0.66
73 0.30
75 0.00
#Reported_Model_Average 0.351
#Overall_Average_Reported 0.351
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 0.00
2 0.00
3 0.64
4 0.41
5 0.62
6 0.62
7 -0.02
8 -0.11
9 0.16
10 0.29
11 -0.02
12 1.30
13 0.66
14 -0.59
15 0.82
16 0.47
17 -0.41
18 -0.10
20 0.00
21 0.36
22 0.08
23 -0.41
24 1.10
25 0.81
26 0.51
27 1.30
28 0.56
29 0.66
30 1.11
31 0.76
32 0.62
33 -0.68
35 0.44
36 1.10
37 0.49
38 0.17
39 0.63
40 0.44
41 0.62
42 0.74
43 0.66
44 0.63
45 0.74
46 0.95
47 -0.13
48 0.62
49 0.76
50 0.63
52 0.50
53 -0.02
54 -1.37
55 0.56
56 0.28
57 0.24
58 0.71
59 -0.80
60 -0.49
61 0.71
62 0.08
63 -0.32
64 0.60
65 -0.43
66 1.28
67 -0.43
69 0.76
70 0.30
71 0.44
72 0.66
73 0.30
75 0.00
#Reported_Model_Average 0.351
#Overall_Average_Reported 0.351
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 2
3.000 2
4.000 0
5.000 0
6.000 0
7.000 0
8.000 0
9.000 1
10.000 1
11.000 0
12.000 1
13.000 1
14.000 1
15.000 1
16.000 1
17.000 0
18.000 2
19.000 0
20.000 2
21.000 2
22.000 0
23.000 0
24.000 0
25.000 2
26.000 0
27.000 0
28.000 1
29.000 0
30.000 0
31.000 0
32.000 1
33.000 0
34.000 0
35.000 0
36.000 0
37.000 0
38.000 0
39.000 0
40.000 0
41.000 0
42.000 0
43.000 1
44.000 0
45.000 0
46.000 1
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 1
59.000 2
60.000 1
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 0
70.000 1
71.000 0
72.000 0
73.000 0
74.000 0
75.000 0
#Reported_Model_Average 0.400
#Overall_Average_Reported 0.400
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 1073:A 21 LEU 1HD1 :A 16 SER 1HB : -0.749: 45
: 1073:A 21 LEU 2HD2 :A 25 ILE 3HD1 : -0.544: 43
: 1073:A 70 VAL 3HG2 :A 66 PHE O : -0.497: 36
: 1073:A 25 ILE 1HD1 :A 66 PHE CD1 : -0.402: 39
: 1073:A 3 PRO 1HD :A 2 PRO N : -0.636: 52
: 1073:A 2 PRO N :A 3 PRO CD : -0.493: 52
: 1073:A 18 LYS HA :A 18 LYS 2HE : -0.634: 51
: 1073:A 20 ASN 2HD2 :A 59 VAL 2HG2 : -0.542: 48
: 1073:A 20 ASN ND2 :A 59 VAL 2HG2 : -0.536: 48
: 1073:A 9 LEU HG :A 13 LYS 2HE : -0.482: 53
: 1073:A 60 HIS CE1 :A 58 ARG 1HD : -0.456: 40
: 1073:A 28 ARG O :A 32 GLU 2HG : -0.446: 35
: 1073:A 15 HIS CE1 :A 43 LYS 1HE : -0.436: 52
: 1073:A 12 LEU 3HD2 :A 46 CYS SG : -0.434: 44
: 1073:A 10 ASP O :A 14 ILE 2HG1 : -0.427: 45
#sum2 ::13.98 clashscore : 7.26 clashscore B<40
#summary::1073 atoms:551 atoms B<40:122355 potential dots:7647.0 A^2:15 bumps:4 bumps B<40:358.5 score
Output from PDB validation software
Summary from PDB validation
May. 10, 06:12:05 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 1.2 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
PRO( A -77 )
PRO( A -76 )
PRO( A -75 )
ASN( A -74 )
GLU( A -73 )
GLU( A -72 )
ALA( A -71 )
ARG( A -70 )
LEU( A -69 )
ASP( A -68 )
ILE( A -67 )
LEU( A -66 )
LYS( A -65 )
ILE( A -64 )
HIS( A -63 )
SER( A -62 )
ARG( A -61 )
LYS( A -60 )
MSE( A -59 )
ASN( A -58 )
LEU( A -57 )
THR( A -56 )
ARG( A -55 )
GLY( A -54 )
ILE( A -53 )
ASN( A -52 )
LEU( A -51 )
ARG( A -50 )
LYS( A -49 )
ILE( A -48 )
ALA( A -47 )
GLU( A -46 )
LEU( A -45 )
MSE( A -44 )
PRO( A -43 )
GLY( A -42 )
ALA( A -41 )
SER( A -40 )
GLY( A -39 )
ALA( A -38 )
GLU( A -37 )
VAL( A -36 )
LYS( A -35 )
GLY( A -34 )
VAL( A -33 )
CYS( A -32 )
THR( A -31 )
GLU( A -30 )
ALA( A -29 )
GLY( A -28 )
MSE( A -27 )
TYR( A -26 )
ALA( A -25 )
LEU( A -24 )
ARG( A -23 )
GLU( A -22 )
ARG( A -21 )
ARG( A -20 )
VAL( A -19 )
HIS( A -18 )
VAL( A -17 )
THR( A -16 )
GLN( A -15 )
GLU( A -14 )
ASP( A -13 )
PHE( A -12 )
GLU( A -11 )
MSE( A -10 )
ALA( A -9 )
VAL( A -8 )
ALA( A -7 )
LYS( A -6 )
VAL( A -5 )
MSE( A -4 )
GLN( A -3 )
LYS( A -2 )
ASP( A -1 )
SER( A 0 )
PDB Chain_ID: A
1 15
SEQRES: PRO PRO PRO ASN GLU GLU ALA ARG LEU ASP ILE LEU LYS ILE HIS
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 30
SEQRES: SER ARG LYS MSE ASN LEU THR ARG GLY ILE ASN LEU ARG LYS ILE
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
31 45
SEQRES: ALA GLU LEU MSE PRO GLY ALA SER GLY ALA GLU VAL LYS GLY VAL
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
46 60
SEQRES: CYS THR GLU ALA GLY MSE TYR ALA LEU ARG GLU ARG ARG VAL HIS
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
61 75
SEQRES: VAL THR GLN GLU ASP PHE GLU MSE ALA VAL ALA LYS VAL MSE GLN
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
76 90
SEQRES: LYS ASP SER PRO PRO PRO ASN GLU GLU ALA ARG LEU ASP ILE LEU
COORDS: ... ... ... PRO PRO PRO ASN GLU GLU ALA ARG LEU ASP ILE LEU
1 12
91 105
SEQRES: LYS ILE HIS SER ARG LYS MSE ASN LEU THR ARG GLY ILE ASN LEU
COORDS: LYS ILE HIS SER ARG LYS MSE ASN LEU THR ARG GLY ILE ASN LEU
13 27
106 120
SEQRES: ARG LYS ILE ALA GLU LEU MSE PRO GLY ALA SER GLY ALA GLU VAL
COORDS: ARG LYS ILE ALA GLU LEU MSE PRO GLY ALA SER GLY ALA GLU VAL
28 42
121 135
SEQRES: LYS GLY VAL CYS THR GLU ALA GLY MSE TYR ALA LEU ARG GLU ARG
COORDS: LYS GLY VAL CYS THR GLU ALA GLY MSE TYR ALA LEU ARG GLU ARG
43 57
136 150
SEQRES: ARG VAL HIS VAL THR GLN GLU ASP PHE GLU MSE ALA VAL ALA LYS
COORDS: ARG VAL HIS VAL THR GLN GLU ASP PHE GLU MSE ALA VAL ALA LYS
58 72
151 153
SEQRES: VAL MSE GLN
COORDS: VAL MSE GLN
73 75
==> The following residues have missing atoms:
RES MOD#C SEQ ATOMS
PRO( A 1) CG CD
PRO( A 2) CG CD
GLN( A 75) CG CD OE1 NE2
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: ASN CHNID: A SSEQ: 2) in Token 'HELIX' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: ARG CHNID: A SSEQ: 15) in Token 'HELIX' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: ASN CHNID: A SSEQ: 24) in Token 'HELIX' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: LEU CHNID: A SSEQ: 31) in Token 'HELIX' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: SER CHNID: A SSEQ: 36) in Token 'HELIX' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: GLU CHNID: A SSEQ: 54) in Token 'HELIX' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: THR CHNID: A SSEQ: 60) in Token 'HELIX' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: GLN CHNID: A SSEQ: 73) in Token 'HELIX' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 17) in Token 'MODRES' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 32) in Token 'MODRES' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 49) in Token 'MODRES' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 66) in Token 'MODRES' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 72) in Token 'MODRES' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: ASN CHNID: A SSEQ: 18) in Token 'SHEET' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: LEU CHNID: A SSEQ: 19) in Token 'SHEET' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (RES: HIS CHNID: A SSEQ: 58) in Token 'SHEET' can not be found in coordinates
HR3102A_XRay_em_bcr3.pdb: Error: Record (ATOM: N RES: ASN CHNID: A SSEQ: 18) in Token 'SHEET' can not be found in coordinates