Detailed results of XCR50_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 >>>----------+
| |
| XCR50_XRay_em_bcr3_noHs_000.rin 0.0 74 residues |
| |
| Ramachandran plot: 95.4% core 4.6% allow 0.0% gener 0.0% disall |
| |
| All Ramachandrans: 0 labelled residues (out of 70) |
| Chi1-chi2 plots: 0 labelled residues (out of 43) |
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
3 -0.98
4 0.17
5 -0.83
6 0.16
7 -1.16
8 -0.32
9 -0.09
10 -2.86
11 -0.75
12 1.43
13 1.13
14 1.47
15 1.13
16 0.74
17 0.99
18 0.77
19 0.68
20 0.99
21 1.13
22 0.36
23 0.90
24 -0.46
25 -1.30
26 -0.26
27 -2.67
28 -0.40
29 -0.06
30 0.00
31 -0.14
32 -0.43
33 -0.37
34 -1.07
35 -2.58
36 -1.57
37 -0.78
38 0.09
39 0.76
40 0.65
41 0.87
42 0.87
43 -0.21
44 -0.95
45 -0.63
46 -1.55
47 -1.43
48 -2.07
49 0.37
50 0.38
51 0.08
52 -0.16
53 -0.93
57 -0.68
58 -0.43
59 -0.24
60 -0.75
61 -0.42
62 -1.09
63 -1.05
64 -0.73
65 0.09
66 0.47
67 0.84
68 0.29
69 0.96
70 0.65
71 0.95
72 0.82
73 0.30
74 -0.57
75 -0.40
#Reported_Model_Average -0.170
#Overall_Average_Reported -0.170
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 0.00
3 -0.05
4 -0.35
5 -0.22
6 0.50
7 -0.70
8 -0.45
9 -0.21
10 -1.53
11 -0.31
12 1.12
13 0.68
14 1.38
15 1.02
16 0.99
17 0.99
18 0.72
19 0.36
20 0.99
21 0.44
22 0.36
23 0.72
24 -0.46
25 -0.59
26 -0.26
27 -2.67
28 -0.40
29 -0.69
30 0.29
31 0.37
32 0.15
33 0.22
34 -0.54
35 -1.47
36 -0.65
37 -0.84
38 0.09
39 0.76
40 0.77
41 -0.16
42 0.62
43 -0.21
44 -0.06
45 -0.63
46 -1.07
47 -0.66
48 -1.31
49 0.37
50 0.56
51 -0.41
52 0.27
53 -0.43
54 0.00
56 0.00
57 0.25
58 0.21
59 0.04
60 -0.27
61 0.08
62 -1.09
63 -0.77
64 -0.77
65 0.09
66 0.47
67 0.78
68 -0.29
69 -0.39
70 0.65
71 0.50
72 0.86
73 0.60
74 -0.57
75 -0.40
76 0.00
#Reported_Model_Average -0.035
#Overall_Average_Reported -0.035
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 0.49
3 1.07
4 0.79
5 1.07
6 1.30
7 -2.03
8 0.71
9 0.23
10 0.23
11 -0.35
12 0.17
13 -0.46
14 0.95
15 0.29
16 -0.32
17 0.76
18 -0.62
19 0.62
20 0.76
21 1.30
22 0.44
23 0.62
24 0.49
25 -0.41
26 0.49
27 1.10
28 0.14
29 0.37
30 -0.83
31 0.49
32 0.08
33 0.37
34 0.81
35 0.51
36 0.23
37 0.51
38 0.44
39 0.44
40 -0.30
41 0.62
42 0.16
43 0.44
44 0.86
45 1.10
46 -1.14
47 0.71
48 0.66
49 0.59
50 0.71
51 1.07
52 0.84
53 0.34
54 0.25
56 1.10
57 0.71
58 -0.42
59 0.36
60 -0.03
61 1.12
62 0.25
63 1.40
64 0.23
65 -0.02
66 0.05
67 0.56
68 1.30
69 1.10
70 0.44
71 1.01
72 0.71
73 0.44
74 0.14
75 -0.25
76 0.25
#Reported_Model_Average 0.414
#Overall_Average_Reported 0.414
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 0.49
3 1.07
4 0.79
5 1.07
6 1.30
7 -2.03
8 0.71
9 0.23
10 0.23
11 -0.35
12 0.17
13 -0.46
14 0.95
15 0.29
16 -0.32
17 0.76
18 -0.62
19 0.62
20 0.76
21 1.30
22 0.44
23 0.62
24 0.49
25 -0.41
26 0.49
27 1.10
28 0.14
29 0.37
30 -0.83
31 0.49
32 0.08
33 0.37
34 0.81
35 0.51
36 0.23
37 0.51
38 0.44
39 0.44
40 -0.30
41 0.62
42 0.16
43 0.44
44 0.86
45 1.10
46 -1.14
47 0.71
48 0.66
49 0.59
50 0.71
51 1.07
52 0.84
53 0.34
54 0.25
56 1.10
57 0.71
58 -0.42
59 0.36
60 -0.03
61 1.12
62 0.25
63 1.40
64 0.23
65 -0.02
66 0.05
67 0.56
68 1.30
69 1.10
70 0.44
71 1.01
72 0.71
73 0.44
74 0.14
75 -0.25
76 0.25
#Reported_Model_Average 0.414
#Overall_Average_Reported 0.414
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 2
8.000 0
9.000 0
10.000 0
11.000 0
12.000 1
13.000 1
14.000 1
15.000 0
16.000 2
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 0
30.000 0
31.000 0
32.000 0
33.000 1
34.000 1
35.000 0
36.000 0
37.000 1
38.000 0
39.000 0
40.000 2
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 1
50.000 0
51.000 1
52.000 0
53.000 3
54.000 3
55.000 0
56.000 0
57.000 1
58.000 1
59.000 0
60.000 0
61.000 3
62.000 2
63.000 0
64.000 1
65.000 0
66.000 1
67.000 0
68.000 0
69.000 2
70.000 0
71.000 0
72.000 0
73.000 0
74.000 0
75.000 1
76.000 0
#Reported_Model_Average 0.427
#Overall_Average_Reported 0.427
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 1130:A 57 ARG NH2 :A 75 ALA 2HB : -0.741: 26
: 1130:A 61 TRP CD2 :A 62 PRO HA : -0.711: 9
: 1130:A 61 TRP CG :A 62 PRO HA : -0.601: 9
: 1130:A 61 TRP 1HB :A 49 PRO 1HG : -0.558: 7
: 1130:A 14 CYS SG :A 7 GLN 1HB : -0.691: 14
: 1130:A 7 GLN O :A 33 PHE HA : -0.409: 13
: 1130:A 69 ARG O :A 69 ARG 2HD : -0.582: 15
: 1130:A 53 ASP 1HB :A 54 PRO CD : -0.531: 11
: 1130:A 53 ASP 1HB :A 54 PRO 1HD : -0.465: 11
: 1130:A 53 ASP CB :A 54 PRO CD : -0.402: 11
: 1130:A 64 ASP OD1 :A 66 PRO 1HG : -0.498: 12
: 1130:A 40 LEU 2HB :A 34 ILE 2HG2 : -0.453: 13
: 1130:A 37 ASP 2HB :A 40 LEU 1HB : -0.428: 31
: 1130:A 12 HIS O :A 16 GLN 2HG : -0.452: 12
: 1130:A 16 GLN 2HE2 :A 13 LEU HA : -0.434: 11
: 1130:A 51 LEU O :A 58 GLU HA : -0.408: 7
#sum2 ::14.16 clashscore : 14.17 clashscore B<40
#summary::1130 atoms:1129 atoms B<40:128141 potential dots:8009.0 A^2:16 bumps:16 bumps B<40:394.1 score
Output from PDB validation software
Summary from PDB validation
May. 11, 04:04:46 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 1.3 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
--------------------------------------------------------------------------------
-9.9 ALA A 26 N - CA - C 101.3 111.2
-7.8 VAL A 32 N - CA - C 103.4 111.2
7.9 GLY A 45 N - CA - C 120.4 112.5
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 -85 )
ALA( A -84 )
LEU( A -83 )
THR( A -82 )
LEU( A -81 )
TYR( A -80 )
GLN( A -79 )
ARG( A -78 )
ASP( A -77 )
ASP( A -76 )
CYS( A -75 )
HIS( A -74 )
LEU( A -73 )
CYS( A -72 )
ASP( A -71 )
GLN( A -70 )
ALA( A -69 )
VAL( A -68 )
GLU( A -67 )
ALA( A -66 )
LEU( A -65 )
ALA( A -64 )
GLN( A -63 )
ALA( A -62 )
ARG( A -61 )
ALA( A -60 )
GLY( A -59 )
ALA( A -58 )
PHE( A -57 )
PHE( A -56 )
SER( A -55 )
VAL( A -54 )
PHE( A -53 )
ILE( A -52 )
ASP( A -51 )
ASP( A -50 )
ASP( A -49 )
ALA( A -48 )
ALA( A -47 )
LEU( A -46 )
GLU( A -45 )
SER( A -44 )
ALA( A -43 )
TYR( A -42 )
GLY( A -41 )
LEU( A -40 )
ARG( A -39 )
VAL( A -38 )
PRO( A -37 )
VAL( A -36 )
LEU( A -35 )
ARG( A -34 )
ASP( A -33 )
PRO( A -32 )
MSE( A -31 )
GLY( A -30 )
ARG( A -29 )
GLU( A -28 )
LEU( A -27 )
ASP( A -26 )
TRP( A -25 )
PRO( A -24 )
PHE( A -23 )
ASP( A -22 )
ALA( A -21 )
PRO( A -20 )
ARG( A -19 )
LEU( A -18 )
ARG( A -17 )
ALA( A -16 )
TRP( A -15 )
LEU( A -14 )
ASP( A -13 )
ALA( A -12 )
ALA( A -11 )
PRO( A -10 )
HIS( A -9 )
ALA( 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 )
HIS( A 1 )
PDB Chain_ID: A
1 15
SEQRES: MSE ALA LEU THR LEU TYR GLN ARG ASP ASP CYS HIS LEU CYS ASP
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 30
SEQRES: GLN ALA VAL GLU ALA LEU ALA GLN ALA ARG ALA GLY ALA PHE PHE
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
31 45
SEQRES: SER VAL PHE ILE ASP ASP ASP ALA ALA LEU GLU SER ALA TYR GLY
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
46 60
SEQRES: LEU ARG VAL PRO VAL LEU ARG ASP PRO MSE GLY ARG GLU LEU ASP
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
61 75
SEQRES: TRP PRO PHE ASP ALA PRO ARG LEU ARG ALA TRP LEU ASP ALA ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
76 90
SEQRES: PRO HIS ALA LEU GLU HIS HIS HIS HIS HIS HIS HIS ALA LEU THR
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ALA LEU THR
2 4
91 105
SEQRES: LEU TYR GLN ARG ASP ASP CYS HIS LEU CYS ASP GLN ALA VAL GLU
COORDS: LEU TYR GLN ARG ASP ASP CYS HIS LEU CYS ASP GLN ALA VAL GLU
5 19
106 120
SEQRES: ALA LEU ALA GLN ALA ARG ALA GLY ALA PHE PHE SER VAL PHE ILE
COORDS: ALA LEU ALA GLN ALA ARG ALA GLY ALA PHE PHE SER VAL PHE ILE
20 34
121 135
SEQRES: ASP ASP ASP ALA ALA LEU GLU SER ALA TYR GLY LEU ARG VAL PRO
COORDS: ASP ASP ASP ALA ALA LEU GLU SER ALA TYR GLY LEU ARG VAL PRO
35 49
136 150
SEQRES: VAL LEU ARG ASP PRO MSE GLY ARG GLU LEU ASP TRP PRO PHE ASP
COORDS: VAL LEU ARG ASP PRO MSE GLY ARG GLU LEU ASP TRP PRO PHE ASP
50 64
151 162
SEQRES: ALA PRO ARG LEU ARG ALA TRP LEU ASP ALA ALA PRO
COORDS: ALA PRO ARG LEU ARG ALA TRP LEU ASP ALA ALA PRO
65 76