Detailed results of RPR324_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 >>>----------+
| |
| RPR324_XRay_em_bcr3_noHs_000.rin 0.0 94 residues |
| |
| Ramachandran plot: 92.9% core 7.1% allow 0.0% gener 0.0% disall |
| |
| All Ramachandrans: 0 labelled residues (out of 92) |
| Chi1-chi2 plots: 0 labelled residues (out of 58) |
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
3 0.11
4 1.24
5 1.22
6 1.14
7 1.14
8 0.98
9 0.66
10 1.14
11 0.80
12 0.80
13 0.66
14 -0.13
15 0.94
16 -1.15
17 -0.87
18 0.26
19 -0.72
20 0.28
21 0.14
22 -0.20
23 0.00
24 -0.17
25 0.45
26 -0.44
27 -0.49
28 -0.41
29 -0.70
30 -0.27
31 -0.41
32 -2.23
33 -2.47
34 0.93
35 -0.95
36 -0.73
37 0.74
38 1.13
39 1.08
40 1.05
41 0.85
42 0.99
43 1.01
44 0.99
45 0.66
46 0.82
47 1.01
48 0.40
49 1.22
50 0.99
51 -0.50
52 0.16
53 -2.71
54 -0.70
55 -1.13
56 -2.24
57 0.88
58 0.87
59 1.22
60 1.09
61 0.84
62 1.23
63 0.82
64 0.57
65 0.12
66 -0.28
67 0.36
68 -0.26
69 -0.51
70 -0.11
71 0.87
72 0.61
73 -0.27
74 -1.44
75 -0.51
76 -0.32
77 0.09
78 1.22
79 0.12
80 0.88
81 0.99
82 0.80
83 1.14
84 1.01
85 1.14
86 0.87
87 0.85
88 0.98
89 0.66
90 0.76
91 1.22
92 1.02
93 0.66
94 0.88
#Reported_Model_Average 0.298
#Overall_Average_Reported 0.298
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
2 0.29
3 0.24
4 1.19
5 0.61
6 1.12
7 -0.86
8 0.98
9 0.66
10 0.81
11 0.85
12 0.70
13 0.66
14 -1.25
15 0.49
16 -0.51
17 -0.57
18 0.44
19 -0.72
20 0.16
21 -0.43
22 0.39
23 0.14
24 0.16
25 0.45
26 -0.19
27 0.09
28 -1.21
29 -0.70
30 -1.10
31 -0.84
32 -1.30
33 -0.96
34 0.93
35 -0.04
36 -0.41
37 0.35
38 1.02
39 1.02
40 0.47
41 0.87
42 0.64
43 0.96
44 0.99
45 0.11
46 0.82
47 0.96
48 0.57
49 0.56
50 0.99
51 0.03
52 0.16
53 -1.43
54 -0.36
55 -0.13
56 -2.24
57 0.71
58 0.69
59 0.76
60 0.42
61 0.86
62 0.84
63 0.73
64 0.35
65 -0.13
66 0.32
67 0.36
68 0.35
69 -0.51
70 0.33
71 0.29
72 0.09
73 -0.41
74 -0.87
75 0.16
76 0.09
77 0.01
78 1.04
79 0.59
80 0.41
81 0.99
82 0.80
83 0.74
84 0.96
85 1.12
86 1.05
87 0.73
88 0.95
89 0.66
90 0.76
91 0.30
92 1.02
93 0.66
94 0.60
95 0.62
#Reported_Model_Average 0.277
#Overall_Average_Reported 0.277
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
2 0.08
3 0.34
4 0.39
5 -0.22
6 0.29
7 0.56
8 0.74
9 0.76
10 -0.20
11 0.55
12 1.11
13 0.76
14 0.62
15 0.39
16 1.29
17 0.23
18 0.81
19 0.44
20 0.71
21 0.04
22 0.08
23 0.93
24 0.08
25 0.64
26 0.28
27 0.17
28 0.20
29 0.49
30 0.81
31 0.23
32 0.51
33 0.77
34 1.10
35 0.81
36 0.23
37 0.16
38 -1.37
39 -0.28
40 1.28
41 -0.46
42 0.29
43 1.11
44 0.76
45 -1.35
46 0.76
47 1.11
48 -0.28
49 0.66
50 0.76
51 0.87
52 1.10
53 0.93
54 0.47
55 1.06
56 0.64
57 -0.30
58 0.60
59 0.66
60 1.11
61 -0.20
62 0.29
63 0.62
64 0.30
65 0.32
66 0.51
67 1.10
68 0.47
69 -0.25
70 0.08
71 0.08
72 0.62
73 0.62
74 0.27
75 0.87
76 -0.09
77 1.30
78 0.66
79 -0.58
80 1.30
81 0.76
82 0.44
83 -0.11
84 1.11
85 0.29
86 0.62
87 0.71
88 0.30
89 0.44
90 0.44
91 0.66
92 0.63
93 0.44
94 -0.46
95 0.28
#Reported_Model_Average 0.448
#Overall_Average_Reported 0.448
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
2 0.08
3 0.34
4 0.39
5 -0.22
6 0.29
7 0.56
8 0.74
9 0.76
10 -0.20
11 0.55
12 1.11
13 0.76
14 0.62
15 0.39
16 1.29
17 0.23
18 0.81
19 0.44
20 0.71
21 0.04
22 0.08
23 0.93
24 0.08
25 0.64
26 0.28
27 0.17
28 0.20
29 0.49
30 0.81
31 0.23
32 0.51
33 0.77
34 1.10
35 0.81
36 0.23
37 0.16
38 -1.37
39 -0.28
40 1.28
41 -0.46
42 0.29
43 1.11
44 0.76
45 -1.35
46 0.76
47 1.11
48 -0.28
49 0.66
50 0.76
51 0.87
52 1.10
53 0.93
54 0.47
55 1.06
56 0.64
57 -0.30
58 0.60
59 0.66
60 1.11
61 -0.20
62 0.29
63 0.62
64 0.30
65 0.32
66 0.51
67 1.10
68 0.47
69 -0.25
70 0.08
71 0.08
72 0.62
73 0.62
74 0.27
75 0.87
76 -0.09
77 1.30
78 0.66
79 -0.58
80 1.30
81 0.76
82 0.44
83 -0.11
84 1.11
85 0.29
86 0.62
87 0.71
88 0.30
89 0.44
90 0.44
91 0.66
92 0.63
93 0.44
94 -0.46
95 0.28
#Reported_Model_Average 0.448
#Overall_Average_Reported 0.448
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
2.000 0
3.000 0
4.000 0
5.000 0
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 0
21.000 0
22.000 0
23.000 0
24.000 1
25.000 1
26.000 0
27.000 0
28.000 0
29.000 0
30.000 1
31.000 1
32.000 0
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 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 0
62.000 0
63.000 0
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 1
74.000 0
75.000 0
76.000 0
77.000 0
78.000 0
79.000 0
80.000 0
81.000 0
82.000 0
83.000 0
84.000 1
85.000 0
86.000 0
87.000 0
88.000 1
89.000 0
90.000 0
91.000 1
92.000 0
93.000 0
94.000 0
95.000 1
#Reported_Model_Average 0.106
#Overall_Average_Reported 0.106
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 1451:A 95 GLU 2HG :A 91 LYS O : -0.612: 49
: 1451:A 73 GLN 1HG :A 70 THR O : -0.559: 36
: 1451:A 31 ASP OD1 :A 30 ILE 3HG2 : -0.462: 60
: 1451:A 84 ILE O :A 88 VAL 3HG2 : -0.420: 25
: 1451:A 25 PRO CD :A 24 THR HB : -0.400: 22
#sum2 ::3.45 clashscore : 2.48 clashscore B<40
#summary::1451 atoms:1211 atoms B<40:162668 potential dots:10170.0 A^2:5 bumps:3 bumps B<40:603.8 score
Output from PDB validation software
Summary from PDB validation
May. 10, 16:48:01 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 1.0 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
--------------------------------------------------------------------------------
-6.1 LEU A 55 N - CA - C 105.1 111.2
7.7 PHE A 75 N - CA - C 118.9 111.2
-8.6 VAL A 76 N - CA - C 102.6 111.2
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
MET( A -99 )
THR( A -98 )
SER( A -97 )
THR( A -96 )
PHE( A -95 )
ASP( A -94 )
ARG( A -93 )
VAL( A -92 )
ALA( A -91 )
THR( A -90 )
ILE( A -89 )
ILE( A -88 )
ALA( A -87 )
GLU( A -86 )
THR( A -85 )
CYS( A -84 )
ASP( A -83 )
ILE( A -82 )
PRO( A -81 )
ARG( A -80 )
GLU( A -79 )
THR( A -78 )
ILE( A -77 )
THR( A -76 )
PRO( A -75 )
GLU( A -74 )
SER( A -73 )
HIS( A -72 )
ALA( A -71 )
ILE( A -70 )
ASP( A -69 )
ASP( A -68 )
LEU( A -67 )
GLY( A -66 )
ILE( A -65 )
ASP( A -64 )
SER( A -63 )
LEU( A -62 )
ASP( A -61 )
PHE( A -60 )
LEU( A -59 )
ASP( A -58 )
ILE( A -57 )
ALA( A -56 )
PHE( A -55 )
ALA( A -54 )
ILE( A -53 )
ASP( A -52 )
LYS( A -51 )
ALA( A -50 )
PHE( A -49 )
GLY( A -48 )
ILE( A -47 )
LYS( A -46 )
LEU( A -45 )
PRO( A -44 )
LEU( A -43 )
GLU( A -42 )
LYS( A -41 )
TRP( A -40 )
THR( A -39 )
GLN( A -38 )
GLU( A -37 )
VAL( A -36 )
ASN( A -35 )
ASP( A -34 )
GLY( A -33 )
LYS( A -32 )
ALA( A -31 )
THR( A -30 )
THR( A -29 )
GLU( A -28 )
GLN( A -27 )
TYR( A -26 )
PHE( A -25 )
VAL( A -24 )
LEU( A -23 )
LYS( A -22 )
ASN( A -21 )
LEU( A -20 )
ALA( A -19 )
ALA( A -18 )
ARG( A -17 )
ILE( A -16 )
ASP( A -15 )
GLU( A -14 )
LEU( A -13 )
VAL( A -12 )
ALA( A -11 )
ALA( A -10 )
LYS( A -9 )
GLY( A -8 )
ALA( A -7 )
LEU( A -6 )
GLU( A -5 )
HIS( A -4 )
HIS( A -3 )
HIS( A -2 )
HIS( A -1 )
HIS( A 0 )
HIS( A 1 )
PDB Chain_ID: A
1 15
SEQRES: MET THR SER THR PHE ASP ARG VAL ALA THR ILE ILE ALA GLU THR
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 30
SEQRES: CYS ASP ILE PRO ARG GLU THR ILE THR PRO GLU SER HIS ALA ILE
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
31 45
SEQRES: ASP ASP LEU GLY ILE ASP SER LEU ASP PHE LEU ASP ILE ALA PHE
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
46 60
SEQRES: ALA ILE ASP LYS ALA PHE GLY ILE LYS LEU PRO LEU GLU LYS TRP
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
61 75
SEQRES: THR GLN GLU VAL ASN ASP GLY LYS ALA THR THR GLU GLN TYR PHE
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
76 90
SEQRES: VAL LEU LYS ASN LEU ALA ALA ARG ILE ASP GLU LEU VAL ALA ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
91 105
SEQRES: LYS GLY ALA LEU GLU HIS HIS HIS HIS HIS HIS THR SER THR PHE
COORDS: ... ... ... ... ... ... ... ... ... ... ... THR SER THR PHE
2 5
106 120
SEQRES: ASP ARG VAL ALA THR ILE ILE ALA GLU THR CYS ASP ILE PRO ARG
COORDS: ASP ARG VAL ALA THR ILE ILE ALA GLU THR CYS ASP ILE PRO ARG
6 20
121 135
SEQRES: GLU THR ILE THR PRO GLU SER HIS ALA ILE ASP ASP LEU GLY ILE
COORDS: GLU THR ILE THR PRO GLU SER HIS ALA ILE ASP ASP LEU GLY ILE
21 35
136 150
SEQRES: ASP SER LEU ASP PHE LEU ASP ILE ALA PHE ALA ILE ASP LYS ALA
COORDS: ASP SER LEU ASP PHE LEU ASP ILE ALA PHE ALA ILE ASP LYS ALA
36 50
151 165
SEQRES: PHE GLY ILE LYS LEU PRO LEU GLU LYS TRP THR GLN GLU VAL ASN
COORDS: PHE GLY ILE LYS LEU PRO LEU GLU LYS TRP THR GLN GLU VAL ASN
51 65
166 180
SEQRES: ASP GLY LYS ALA THR THR GLU GLN TYR PHE VAL LEU LYS ASN LEU
COORDS: ASP GLY LYS ALA THR THR GLU GLN TYR PHE VAL LEU LYS ASN LEU
66 80
181 195
SEQRES: ALA ALA ARG ILE ASP GLU LEU VAL ALA ALA LYS GLY ALA LEU GLU
COORDS: ALA ALA ARG ILE ASP GLU LEU VAL ALA ALA LYS GLY ALA LEU GLU
81 95