Detailed results of GMR137_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 >>>----------+
| |
| GMR137_XRay_em_bcr3_noHs_000.rin 0.0 69 residues |
| |
| Ramachandran plot: 93.3% core 6.7% allow 0.0% gener 0.0% disall |
| |
| All Ramachandrans: 0 labelled residues (out of 67) |
| Chi1-chi2 plots: 0 labelled residues (out of 34) |
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
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 -0.31
3 -1.53
4 0.42
5 0.12
6 0.58
7 0.67
8 -0.30
9 0.40
10 0.21
11 0.13
12 -1.67
13 -0.60
14 0.45
15 -0.54
16 -0.89
17 -0.83
18 -1.35
19 -0.65
20 0.77
21 0.87
22 1.08
23 0.99
24 0.82
25 0.91
26 0.66
27 -1.13
28 -2.10
29 -0.69
30 -0.16
31 -0.90
32 0.06
33 0.87
34 -1.96
35 -0.01
36 0.23
37 0.53
38 -0.46
39 -0.62
40 0.44
41 1.14
42 -0.75
43 -0.48
44 -0.37
45 -0.56
46 -0.12
47 0.44
48 -1.65
49 1.05
50 0.93
51 -1.34
52 -0.10
53 0.21
54 0.31
55 -1.48
56 -1.04
57 1.00
58 -0.33
59 -1.22
60 -0.10
61 -0.59
62 -0.23
63 -0.51
64 -0.13
65 -0.08
66 -0.29
67 -0.65
68 -1.94
#Reported_Model_Average -0.214
#Overall_Average_Reported -0.214
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 0.19
2 -0.70
3 -1.97
4 0.35
5 0.59
6 0.87
7 0.67
8 0.03
9 0.40
10 -0.25
11 0.38
12 -0.96
13 -0.01
14 0.45
15 -0.54
16 -0.77
17 -0.43
18 -0.65
19 -0.54
20 0.72
21 -0.01
22 1.06
23 -0.24
24 -0.15
25 0.64
26 0.66
27 -0.30
28 -1.19
29 -0.10
30 -0.16
31 0.06
32 0.06
33 -0.13
34 -2.02
35 -0.55
36 0.50
37 0.56
38 -0.04
39 -0.34
40 0.85
41 1.14
42 -0.12
43 -0.10
44 -0.71
45 0.23
46 0.16
47 -0.20
48 -1.65
49 -0.22
50 0.81
51 -1.34
52 0.09
53 -0.34
54 0.56
55 -0.41
56 -0.77
57 1.00
58 0.38
59 -1.22
60 -0.32
61 0.23
62 0.06
63 -0.33
64 0.14
65 -0.61
66 0.44
67 -0.65
68 -1.94
69 0.00
#Reported_Model_Average -0.126
#Overall_Average_Reported -0.126
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 1.00
2 0.00
3 1.07
4 0.79
5 0.44
6 0.51
7 1.10
8 -1.54
9 -0.88
10 0.49
11 0.79
12 -0.09
13 0.23
14 1.10
15 0.49
16 0.04
17 0.49
18 0.36
19 0.00
20 0.74
21 -0.13
22 0.62
23 1.30
24 1.30
25 0.16
26 0.44
27 -0.33
28 -0.10
29 0.66
30 0.14
31 -0.03
32 0.49
33 0.04
34 -1.04
35 0.66
36 0.95
37 1.18
38 -0.20
39 0.36
40 0.51
41 1.10
42 0.41
43 0.08
44 0.77
45 0.04
46 0.71
47 0.04
48 0.14
49 0.71
50 0.23
51 0.14
52 0.55
53 0.79
54 1.18
55 0.55
56 0.51
57 1.10
58 0.34
59 0.14
60 1.18
61 0.41
62 0.96
63 -1.33
64 1.25
65 -0.84
66 -1.30
67 1.10
68 1.10
69 1.10
#Reported_Model_Average 0.395
#Overall_Average_Reported 0.395
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 1.00
2 0.00
3 1.07
4 0.79
5 0.44
6 0.51
7 1.10
8 -1.54
9 -0.88
10 0.49
11 0.79
12 -0.09
13 0.23
14 1.10
15 0.49
16 0.04
17 0.49
18 0.36
19 0.00
20 0.74
21 -0.13
22 0.62
23 1.30
24 1.30
25 0.16
26 0.44
27 -0.33
28 -0.10
29 0.66
30 0.14
31 -0.03
32 0.49
33 0.04
34 -1.04
35 0.66
36 0.95
37 1.18
38 -0.20
39 0.36
40 0.51
41 1.10
42 0.41
43 0.08
44 0.77
45 0.04
46 0.71
47 0.04
48 0.14
49 0.71
50 0.23
51 0.14
52 0.55
53 0.79
54 1.18
55 0.55
56 0.51
57 1.10
58 0.34
59 0.14
60 1.18
61 0.41
62 0.96
63 -1.33
64 1.25
65 -0.84
66 -1.30
67 1.10
68 1.10
69 1.10
#Reported_Model_Average 0.395
#Overall_Average_Reported 0.395
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 1
6.000 0
7.000 0
8.000 0
9.000 0
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 1
21.000 0
22.000 0
23.000 1
24.000 1
25.000 0
26.000 0
27.000 0
28.000 6
29.000 0
30.000 0
31.000 0
32.000 1
33.000 0
34.000 0
35.000 1
36.000 0
37.000 0
38.000 1
39.000 2
40.000 0
41.000 0
42.000 0
43.000 0
44.000 1
45.000 0
46.000 1
47.000 0
48.000 0
49.000 1
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 2
61.000 1
62.000 0
63.000 0
64.000 0
65.000 0
66.000 0
67.000 0
68.000 0
69.000 0
#Reported_Model_Average 0.319
#Overall_Average_Reported 0.319
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 1005:A 44 LEU 1HD1 :A 39 LEU 2HB : -0.681: 42
: 1005:A 60 VAL CG2 :A 5 VAL 2HG2 : -0.428: 27
: 1005:A 39 LEU 3HD1 :A 60 VAL 2HG1 : -0.425: 22
: 1005:A 28 LYS 2HB :A 28 LYS NZ : -0.606: 66
: 1005:A 28 LYS NZ :A 28 LYS CB : -0.450: 66
: 1005:A 28 LYS 2HB :A 28 LYS 3HZ : -0.411: 66
: 1005:A 49 PHE CE1 :A 46 ARG HA : -0.516: 33
: 1005:A 61 GLU 1HB :A 38 GLU 1HB : -0.504: 22
: 1005:A 32 ALA O :A 35 VAL 2HG1 : -0.485: 42
: 1005:A 20 VAL O :A 24 LEU 3HD1 : -0.470: 47
: 1005:A 54 VAL 1HG2 :A 23 LEU 2HD1 : -0.433: 24
#sum2 ::10.95 clashscore : 6.11 clashscore B<40
#summary::1005 atoms:818 atoms B<40:114373 potential dots:7148.0 A^2:11 bumps:5 bumps B<40:299.1 score
Output from PDB validation software
Summary from PDB validation
May. 10, 04:38:08 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 1.1 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 -77 )
ASN( A -76 )
LEU( A -75 )
THR( A -74 )
VAL( A -73 )
ASN( A -72 )
GLY( A -71 )
LYS( A -70 )
PRO( A -69 )
SER( A -68 )
THR( A -67 )
VAL( A -66 )
ASP( A -65 )
GLY( A -64 )
ALA( A -63 )
GLU( A -62 )
SER( A -61 )
LEU( A -60 )
ASN( A -59 )
VAL( A -58 )
THR( A -57 )
GLU( A -56 )
LEU( A -55 )
LEU( A -54 )
SER( A -53 )
ALA( A -52 )
LEU( A -51 )
LYS( A -50 )
VAL( A -49 )
ALA( A -48 )
GLN( A -47 )
ALA( A -46 )
GLU( A -45 )
TYR( A -44 )
VAL( A -43 )
THR( A -42 )
VAL( A -41 )
GLU( A -40 )
LEU( A -39 )
ASN( A -38 )
GLY( A -37 )
GLU( A -36 )
VAL( A -35 )
LEU( A -34 )
GLU( A -33 )
ARG( A -32 )
GLU( A -31 )
ALA( A -30 )
PHE( A -29 )
ASP( A -28 )
ALA( A -27 )
THR( A -26 )
THR( A -25 )
VAL( A -24 )
LYS( A -23 )
ASP( A -22 )
GLY( A -21 )
ASP( A -20 )
ALA( A -19 )
VAL( A -18 )
GLU( A -17 )
PHE( A -16 )
LEU( A -15 )
TYR( A -14 )
PHE( A -13 )
MSE( A -12 )
GLY( A -11 )
GLY( A -10 )
GLY( A -9 )
LYS( 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: MSE ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL ASP GLY ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 30
SEQRES: GLU SER LEU ASN VAL THR GLU LEU LEU SER ALA LEU LYS VAL ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
31 45
SEQRES: GLN ALA GLU TYR VAL THR VAL GLU LEU ASN GLY GLU VAL LEU GLU
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
46 60
SEQRES: ARG GLU ALA PHE ASP ALA THR THR VAL LYS ASP GLY ASP ALA VAL
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
61 75
SEQRES: GLU PHE LEU TYR PHE MSE GLY GLY GLY LYS LEU GLU HIS HIS HIS
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
76 90
SEQRES: HIS HIS HIS MET ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL
COORDS: ... ... ... MET ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL
1 12
91 105
SEQRES: ASP GLY ALA GLU SER LEU ASN VAL THR GLU LEU LEU SER ALA LEU
COORDS: ASP GLY ALA GLU SER LEU ASN VAL THR GLU LEU LEU SER ALA LEU
13 27
106 120
SEQRES: LYS VAL ALA GLN ALA GLU TYR VAL THR VAL GLU LEU ASN GLY GLU
COORDS: LYS VAL ALA GLN ALA GLU TYR VAL THR VAL GLU LEU ASN GLY GLU
28 42
121 135
SEQRES: VAL LEU GLU ARG GLU ALA PHE ASP ALA THR THR VAL LYS ASP GLY
COORDS: VAL LEU GLU ARG GLU ALA PHE ASP ALA THR THR VAL LYS ASP GLY
43 57
136 147
SEQRES: ASP ALA VAL GLU PHE LEU TYR PHE MET GLY GLY GLY
COORDS: ASP ALA VAL GLU PHE LEU TYR PHE MET GLY GLY GLY
58 69
==> The following residues have missing atoms:
RES MOD#C SEQ ATOMS
MET( A 1) SD
MET( A 66) SD
==> The following residues have extra atoms:
RES MOD#C SEQ ATOMS
MET( A 1) SE
MET( A 66) SE
GMR137_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 1) in Token 'MODRES' can not be found in coordinates
GMR137_XRay_em_bcr3.pdb: Error: Record (RES: MSE CHNID: A SSEQ: 66) in Token 'MODRES' can not be found in coordinates