Detailed results of HR3646E_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 >>>----------+
| |
| HR3646E_XRay_em_bcr3_noHs_000.rin 0.0 94 residues |
| |
| Ramachandran plot: 95.8% core 4.2% allow 0.0% gener 0.0% disall |
| |
| All Ramachandrans: 0 labelled residues (out of 85) |
+| Chi1-chi2 plots: 1 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
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
7 0.07
8 -0.75
9 1.05
10 -0.58
11 -1.68
12 -0.16
13 -0.04
14 0.38
15 -1.21
16 -0.17
17 0.16
18 -0.16
19 1.05
20 1.08
21 0.87
22 0.85
23 0.99
24 1.08
25 1.43
26 1.32
27 1.23
28 1.23
29 1.22
30 1.15
31 0.88
32 -0.72
33 -2.10
34 0.15
35 -0.23
36 -1.16
37 1.03
38 0.08
39 -0.71
40 -0.34
41 1.08
42 1.13
43 1.04
44 0.66
45 0.85
46 1.39
47 1.22
48 0.40
49 -0.59
50 -0.56
51 0.30
52 0.91
53 -0.43
54 0.40
55 1.01
56 0.07
57 0.98
58 0.85
59 0.99
60 1.23
61 1.01
62 0.95
63 0.54
64 1.13
65 -0.16
69 0.45
70 0.29
71 1.03
75 1.23
76 0.98
77 1.08
78 1.20
79 0.91
80 0.80
84 1.13
85 1.01
86 1.08
87 0.82
88 1.22
89 0.50
90 -0.21
91 0.63
92 -0.25
93 -0.17
94 -0.43
95 -0.24
96 0.43
97 -0.55
98 -0.92
99 0.03
100 0.62
#Reported_Model_Average 0.428
#Overall_Average_Reported 0.428
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
6 0.00
7 0.07
8 0.08
9 1.05
10 -0.58
11 -0.86
12 0.23
13 0.32
14 0.33
15 -1.13
16 -0.17
17 0.52
18 0.07
19 0.93
20 0.79
21 0.95
22 0.30
23 0.99
24 1.13
25 0.63
26 1.23
27 0.62
28 0.67
29 0.61
30 1.17
31 0.08
32 0.08
33 -1.24
34 0.15
35 0.32
36 -0.60
37 1.03
38 0.45
39 -0.43
40 0.15
41 1.08
42 0.10
43 0.83
44 0.66
45 1.01
46 -0.03
47 0.88
48 -0.24
49 -2.45
50 0.01
51 0.48
52 0.91
53 0.10
54 0.40
55 -0.85
56 0.07
57 0.79
58 0.88
59 0.99
60 0.99
61 0.96
62 0.19
63 0.54
64 0.75
65 -0.16
66 0.08
68 0.16
69 0.85
70 -0.10
71 1.03
72 -0.14
74 0.07
75 0.85
76 0.86
77 1.17
78 0.84
79 0.10
80 0.84
81 0.00
83 0.04
84 0.87
85 0.96
86 0.80
87 0.86
88 0.28
89 0.43
90 0.38
91 0.63
92 -0.12
93 0.02
94 0.24
95 -0.24
96 0.20
97 -0.55
98 -0.58
99 0.03
100 0.62
101 -1.08
103 0.10
#Reported_Model_Average 0.312
#Overall_Average_Reported 0.312
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
6 0.00
7 0.25
8 -1.63
9 1.10
10 1.10
11 0.34
12 -1.14
13 0.23
14 0.55
15 1.12
16 -0.25
17 -0.54
18 0.08
19 -1.25
20 0.60
21 0.09
22 1.10
23 0.44
24 0.66
25 0.61
26 0.29
27 0.29
28 0.62
29 0.87
30 0.17
31 0.16
32 0.77
33 0.47
34 0.64
35 -1.63
36 0.34
37 1.10
38 0.71
39 1.50
40 0.79
41 0.63
42 0.44
43 0.62
44 0.76
45 0.56
46 0.32
47 -0.22
48 1.28
49 -0.84
50 0.25
51 0.59
52 1.10
53 1.06
54 0.44
55 0.29
56 0.05
57 0.30
58 0.71
59 0.44
60 0.62
61 1.11
62 0.86
63 0.44
64 0.71
65 0.76
66 0.51
68 0.41
69 0.41
70 0.51
71 1.10
72 0.84
74 0.51
75 0.62
76 -0.62
77 0.09
78 1.28
79 0.47
80 1.11
81 0.76
83 0.56
84 1.30
85 1.11
86 0.66
87 0.71
88 0.56
89 -0.46
90 0.25
91 1.10
92 -0.43
93 -0.03
94 1.06
95 0.64
96 0.34
97 0.14
98 1.06
99 0.64
100 0.25
101 -0.74
103 0.47
#Reported_Model_Average 0.436
#Overall_Average_Reported 0.436
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
6 0.00
7 0.25
8 -1.63
9 1.10
10 1.10
11 0.34
12 -1.14
13 0.23
14 0.55
15 1.12
16 -0.25
17 -0.54
18 0.08
19 -1.25
20 0.60
21 0.09
22 1.10
23 0.44
24 0.66
25 0.61
26 0.29
27 0.29
28 0.62
29 0.87
30 0.17
31 0.16
32 0.77
33 0.47
34 0.64
35 -1.63
36 0.34
37 1.10
38 0.71
39 1.50
40 0.79
41 0.63
42 0.44
43 0.62
44 0.76
45 0.56
46 0.32
47 -0.22
48 1.28
49 -0.84
50 0.25
51 0.59
52 1.10
53 1.06
54 0.44
55 0.29
56 0.05
57 0.30
58 0.71
59 0.44
60 0.62
61 1.11
62 0.86
63 0.44
64 0.71
65 0.76
66 0.51
68 0.41
69 0.41
70 0.51
71 1.10
72 0.84
74 0.51
75 0.62
76 -0.62
77 0.09
78 1.28
79 0.47
80 1.11
81 0.76
83 0.56
84 1.30
85 1.11
86 0.66
87 0.71
88 0.56
89 -0.46
90 0.25
91 1.10
92 -0.43
93 -0.03
94 1.06
95 0.64
96 0.34
97 0.14
98 1.06
99 0.64
100 0.25
101 -0.74
103 0.47
#Reported_Model_Average 0.436
#Overall_Average_Reported 0.436
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
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 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 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 1
49.000 2
50.000 0
51.000 0
52.000 0
53.000 0
54.000 0
55.000 1
56.000 1
57.000 2
58.000 1
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 0
71.000 0
72.000 0
73.000 0
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 0
85.000 0
86.000 0
87.000 0
88.000 2
89.000 0
90.000 0
91.000 0
92.000 0
93.000 0
94.000 0
95.000 0
96.000 0
97.000 0
98.000 0
99.000 0
100.000 1
101.000 0
102.000 0
103.000 1
#Reported_Model_Average 0.122
#Overall_Average_Reported 0.122
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 1462:A 100 PRO HA :A 103 LYS 2HE : -0.658: 36
: 1462:A 57 VAL 1HG1 :A 88 LYS 1HG : -0.577: 21
: 1462:A 88 LYS 1HG :A 57 VAL CG1 : -0.426: 21
: 1462:A 56 PRO CD :A 55 GLN N : -0.430: 20
: 1462:A 58 LEU 2HD2 :A 48 PHE 2HB : -0.429: 10
: 1462:A 49 PHE HD1 :A 49 PHE HA : -0.408: 17
#sum2 ::4.10 clashscore : 4.12 clashscore B<40
#summary::1462 atoms:1458 atoms B<40:164564 potential dots:10290.0 A^2:6 bumps:6 bumps B<40:542.6 score
Output from PDB validation software
Summary from PDB validation
May. 10, 07:01:12 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 0.8 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-115 )
GLY( A-114 )
HIS( A-113 )
HIS( A-112 )
HIS( A-111 )
HIS( A-110 )
HIS( A-109 )
HIS( A-108 )
SER( A-107 )
HIS( A-106 )
VAL( A-105 )
ALA( A-104 )
GLN( A-103 )
PHE( A-102 )
PRO( A-101 )
THR( A-100 )
PRO( A -99 )
PHE( A -98 )
GLY( A -97 )
GLY( A -96 )
SER( A -95 )
LEU( A -94 )
ASP( A -93 )
THR( A -92 )
TRP( A -91 )
ALA( A -90 )
ILE( A -89 )
THR( A -88 )
VAL( A -87 )
GLU( A -86 )
GLU( A -85 )
ARG( A -84 )
ALA( A -83 )
LYS( A -82 )
HIS( A -81 )
ASP( A -80 )
GLN( A -79 )
GLN( A -78 )
PHE( A -77 )
HIS( A -76 )
SER( A -75 )
LEU( A -74 )
LYS( A -73 )
PRO( A -72 )
ILE( A -71 )
SER( A -70 )
GLY( A -69 )
PHE( A -68 )
ILE( A -67 )
THR( A -66 )
GLY( A -65 )
ASP( A -64 )
GLN( A -63 )
ALA( A -62 )
ARG( A -61 )
ASN( A -60 )
PHE( A -59 )
PHE( A -58 )
PHE( A -57 )
GLN( A -56 )
SER( A -55 )
GLY( A -54 )
LEU( A -53 )
PRO( A -52 )
GLN( A -51 )
PRO( A -50 )
VAL( A -49 )
LEU( A -48 )
ALA( A -47 )
GLN( A -46 )
ILE( A -45 )
TRP( A -44 )
ALA( A -43 )
LEU( A -42 )
ALA( A -41 )
ASP( A -40 )
MSE( A -39 )
ASN( A -38 )
ASN( A -37 )
ASP( A -36 )
GLY( A -35 )
ARG( A -34 )
MSE( A -33 )
ASP( A -32 )
GLN( A -31 )
VAL( A -30 )
GLU( A -29 )
PHE( A -28 )
SER( A -27 )
ILE( A -26 )
ALA( A -25 )
MSE( A -24 )
LYS( A -23 )
LEU( A -22 )
ILE( A -21 )
LYS( A -20 )
LEU( A -19 )
LYS( A -18 )
LEU( A -17 )
GLN( A -16 )
GLY( A -15 )
TYR( A -14 )
GLN( A -13 )
LEU( A -12 )
PRO( A -11 )
SER( A -10 )
ALA( A -9 )
LEU( A -8 )
PRO( A -7 )
PRO( A -6 )
VAL( A -5 )
MSE( A -4 )
LYS( A -3 )
GLN( A -2 )
GLN( A -1 )
PRO( A 0 )
VAL( A 1 )
ALA( A 2 )
ILE( A 3 )
SER( A 4 )
SER( A 5 )
PDB Chain_ID: A
1 15
SEQRES: MSE GLY HIS HIS HIS HIS HIS HIS SER HIS VAL ALA GLN PHE PRO
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
16 30
SEQRES: THR PRO PHE GLY GLY SER LEU ASP THR TRP ALA ILE THR VAL GLU
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
31 45
SEQRES: GLU ARG ALA LYS HIS ASP GLN GLN PHE HIS SER LEU LYS PRO ILE
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
46 60
SEQRES: SER GLY PHE ILE THR GLY ASP GLN ALA ARG ASN PHE PHE PHE GLN
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
61 75
SEQRES: SER GLY LEU PRO GLN PRO VAL LEU ALA GLN ILE TRP ALA LEU ALA
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
76 90
SEQRES: ASP MSE ASN ASN ASP GLY ARG MSE ASP GLN VAL GLU PHE SER ILE
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
91 105
SEQRES: ALA MSE LYS LEU ILE LYS LEU LYS LEU GLN GLY TYR GLN LEU PRO
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
106 120
SEQRES: SER ALA LEU PRO PRO VAL MSE LYS GLN GLN PRO VAL ALA ILE SER
COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
121 135
SEQRES: SER THR PRO PHE GLY GLY SER LEU ASP THR TRP ALA ILE THR VAL
COORDS: ... THR PRO PHE GLY GLY SER LEU ASP THR TRP ALA ILE THR VAL
6 19
136 150
SEQRES: GLU GLU ARG ALA LYS HIS ASP GLN GLN PHE HIS SER LEU LYS PRO
COORDS: GLU GLU ARG ALA LYS HIS ASP GLN GLN PHE HIS SER LEU LYS PRO
20 34
151 165
SEQRES: ILE SER GLY PHE ILE THR GLY ASP GLN ALA ARG ASN PHE PHE PHE
COORDS: ILE SER GLY PHE ILE THR GLY ASP GLN ALA ARG ASN PHE PHE PHE
35 49
166 180
SEQRES: GLN SER GLY LEU PRO GLN PRO VAL LEU ALA GLN ILE TRP ALA LEU
COORDS: GLN SER GLY LEU PRO GLN PRO VAL LEU ALA GLN ILE TRP ALA LEU
50 64
181 195
SEQRES: ALA ASP MSE ASN ASN ASP GLY ARG MSE ASP GLN VAL GLU PHE SER
COORDS: ALA ASP MSE ASN ASN ASP GLY ARG MSE ASP GLN VAL GLU PHE SER
65 79
196 210
SEQRES: ILE ALA MSE LYS LEU ILE LYS LEU LYS LEU GLN GLY TYR GLN LEU
COORDS: ILE ALA MSE LYS LEU ILE LYS LEU LYS LEU GLN GLY TYR GLN LEU
80 94
211 219
SEQRES: PRO SER ALA LEU PRO PRO VAL MSE LYS
COORDS: PRO SER ALA LEU PRO PRO VAL MSE LYS
95 103
==> The following residues have missing atoms:
RES MOD#C SEQ ATOMS
THR( A 6) OG1 CG2
HR3646E_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 403) in Token 'SITE' can not be found in coordinates
HR3646E_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 465) in Token 'SITE' can not be found in coordinates
HR3646E_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 485) in Token 'SITE' can not be found in coordinates
HR3646E_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 503) in Token 'SITE' can not be found in coordinates