************************************************************************
********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program **********
************************************************************************
Date : 2006-02-04
This report was created by WHAT IF version 20030529-0952
INTRODUCTION
------------
This document contains a report of findings by the WHAT IF program
during the analysis of one or more proteins. It contains a separate section
for each of the proteins that have been analysed. Each reported fact has
an assigned severity, one of:
* error: severe errors encountered during the analyses. Items marked
as errors are considered severe problems requiring immediate
attention.
* warning: Either less severe problems or uncommon structural
features. These still need special attention.
* note: Statistical values, plots, or other verbose results of
tests and analyses that have been performed.
If alternate conformations are present, only the first is
evaluated.
Hydrogen atoms are only included if explicitly requested, and even then
they are not used by all checks.
Legend
------
Some notations need a little explanation:
RESIDUE: Residues in tables are normally given in 3-5 parts:
- A number. This is the internal sequence number of the residue used
by WHAT IF.
- The residue name. Normally this is a three letter amino acid name.
- The sequence number, between brackets. This is the residue number
as it was given in the input file. It can be followed by the insertion
code.
- The chain identifier. A single character. If no chain identifier
was given in the input file, this will be invisible.
- A model number (only for NMR structures).
Z-VALUE: To indicate the normality of a score, the score may be
expressed as a Z-value or Z-score. This is just the number of
standard deviations that the score deviates from the expected
value. A property of Z-values is that the root-mean-square of a
group of Z-values (the RMS Z-value) is expected to be 1.0. Z-values
above 4.0 and below -4.0 are very uncommon. If a Z-score is used in
WHAT IF, the accompanying text will explain how the expected value
and standard deviation were obtained.
========================================================================
==== Compound code /u/lytle/at5g39720/9valid/77/refined_input/refine====.pdb
========================================================================
# 1 # Error: Missing unit cell information
No SCALE matrix is given in the PDB file.
# 2 # Error: Missing symmetry information
Problem: No CRYST1 card is given in the PDB file.
# 3 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
# 4 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
# 5 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
# 6 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
# 7 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
# 8 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.
# 9 # Warning: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2
not between -90.0 and 90.0
23 TYR ( 23 )
60 TYR ( 60 )
95 TYR ( 95 )
116 TYR ( 116 )
# 10 # Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their
chi-2 not between -90.0 and 90.0.
26 PHE ( 26 )
50 PHE ( 50 )
143 PHE ( 143 )
# 11 # Warning: Aspartic acid convention problem
The aspartic acid residues listed in the table below have their
chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of
OD2.
13 ASP ( 13 )
30 ASP ( 30 )
37 ASP ( 37 )
82 ASP ( 82 )
88 ASP ( 88 )
125 ASP ( 125 )
164 ASP ( 164 )
172 ASP ( 172 )
# 12 # Warning: Glutamic acid convention problem
The glutamic acid residues listed in the table below have their
chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead
of OE2.
41 GLU ( 41 )
67 GLU ( 67 )
91 GLU ( 91 )
94 GLU ( 94 )
109 GLU ( 109 )
129 GLU ( 129 )
133 GLU ( 133 )
134 GLU ( 134 )
145 GLU ( 145 )
171 GLU ( 171 )
# 13 # Warning: Heavy atom naming problem
The atoms listed in the table below have nonstandard names in the input
file. (Be aware that we sometomes consider an asterix and an apostrophe
identical, and thus do not warn for the use of asterixes. Swapped
OP1 and OP2 on nucleic acid phosphors also are reported elsewhere).
173 GLN ( 173 ) O <--> OT1
# 14 # Warning: Chirality deviations detected
The atoms listed in the table below have an improper dihedral value
that is deviating from expected values.
Improper dihedrals are a measure of the chirality/planarity of the
structure at a specific atom. Values around -35 or +35 are expected
for chiral atoms, and values around 0 for planar atoms. Planar side
chains are left out of the calculations, these are better handled
by the planarity checks.
Three numbers are given for each atom in the table. The first is
the Z-score for the improper dihedral. The second number is the
measured improper dihedral. The third number is the expected value
for this atom type. A final column contains an extra warning if the
chirality for an atom is opposite to the expected value.
3 HIS ( 3 ) C -4.1 -2.0 -0.1
4 HIS ( 4 ) CA -4.4 31.6 34.3
7 HIS ( 7 ) CA -6.8 30.0 34.3
7 HIS ( 7 ) C -4.6 -2.3 -0.1
8 LEU ( 8 ) CA 4.0 35.9 34.5
8 LEU ( 8 ) CG -4.9 -34.5 -33.9
9 GLU ( 9 ) CA -4.7 32.1 34.3
10 CYS ( 10 ) CA 4.5 36.4 34.4
14 SER ( 14 ) C -6.9 -2.3 0.1
15 LEU ( 15 ) CA -9.2 31.2 34.5
15 LEU ( 15 ) C -7.4 -2.7 0.0
15 LEU ( 15 ) CG 7.5 -32.9 -33.9
17 LEU ( 17 ) CA -4.1 33.0 34.5
17 LEU ( 17 ) CG 23.7 -30.8 -33.9
19 ASN ( 19 ) CA -5.8 30.4 34.0
22 VAL ( 22 ) CA -5.5 31.0 33.8
22 VAL ( 22 ) CB 5.2 -32.4 -33.7
26 PHE ( 26 ) C 4.7 1.9 -0.1
27 GLN ( 27 ) C 4.2 1.5 0.0
31 VAL ( 31 ) CA -4.7 31.5 33.8
31 VAL ( 31 ) CB 6.4 -32.1 -33.7
32 ILE ( 32 ) C 5.0 2.0 -0.2
35 MET ( 35 ) C 5.7 1.9 -0.1
36 LEU ( 36 ) CA -14.6 29.3 34.5
36 LEU ( 36 ) C 6.1 2.1 0.0
36 LEU ( 36 ) CG -14.0 -35.7 -33.9
39 THR ( 39 ) C -5.8 -2.4 -0.1
39 THR ( 39 ) CB 6.5 36.2 34.6
40 PRO ( 40 ) C -4.1 -1.5 0.0
42 ILE ( 42 ) CA 4.3 36.0 33.8
42 ILE ( 42 ) CB 5.0 34.5 33.2
47 LEU ( 47 ) C -5.0 -1.8 0.0
47 LEU ( 47 ) CG 4.8 -33.3 -33.9
51 GLN ( 51 ) C -4.4 -1.6 0.0
55 LEU ( 55 ) CA -14.3 29.4 34.5
55 LEU ( 55 ) CG 29.6 -30.1 -33.9
57 GLY ( 57 ) C 5.2 1.7 0.1
58 ARG ( 58 ) CA -6.7 31.0 34.2
58 ARG ( 58 ) C 6.7 2.6 0.0
59 LEU ( 59 ) CA -4.7 32.8 34.5
64 VAL ( 64 ) CB 5.3 -32.4 -33.7
65 PRO ( 65 ) C -5.6 -2.1 0.0
66 SER ( 66 ) C -4.3 -1.4 0.1
71 VAL ( 71 ) CA 4.3 35.9 33.8
71 VAL ( 71 ) CB 4.5 -32.6 -33.7
74 LYS ( 74 ) CA -5.5 32.0 34.3
76 LEU ( 76 ) CA 6.7 36.8 34.5
77 MET ( 77 ) CA -4.1 32.3 34.2
79 VAL ( 79 ) CB 8.8 -31.5 -33.7
80 THR ( 80 ) CB 5.6 36.0 34.6
83 GLU ( 83 ) CA 4.6 36.4 34.3
84 LEU ( 84 ) CG 13.8 -32.1 -33.9
92 GLY ( 92 ) C -5.3 -1.4 0.1
98 VAL ( 98 ) CA -4.0 31.8 33.8
99 THR ( 99 ) C -4.1 -1.7 -0.1
99 THR ( 99 ) CB -5.5 33.2 34.6
103 VAL ( 103 ) CB 4.2 -32.6 -33.7
104 ARG ( 104 ) C 4.9 2.0 0.0
106 ASP ( 106 ) CA 4.2 36.8 34.1
108 SER ( 108 ) CA -5.5 32.0 34.4
110 LYS ( 110 ) CA -5.9 31.8 34.3
113 VAL ( 113 ) CB 4.8 -32.5 -33.7
117 MET ( 117 ) CA -4.5 32.1 34.2
119 ILE ( 119 ) CA -4.2 31.7 33.8
119 ILE ( 119 ) CB 5.9 34.7 33.2
126 MET ( 126 ) CA -4.4 32.2 34.2
126 MET ( 126 ) C -7.2 -2.6 -0.1
128 GLY ( 128 ) C 5.1 1.7 0.1
129 GLU ( 129 ) CA 4.7 36.5 34.3
131 ASN ( 131 ) CA -4.0 31.5 34.0
131 ASN ( 131 ) C -7.6 -3.1 0.0
132 PHE ( 132 ) CA 5.0 37.2 34.2
138 LEU ( 138 ) CG 14.1 -32.1 -33.9
140 LYS ( 140 ) CA 4.2 36.1 34.3
141 LYS ( 141 ) CA 4.1 36.0 34.3
144 ILE ( 144 ) CA -5.5 31.0 33.8
145 GLU ( 145 ) CA -4.7 32.1 34.3
147 PHE ( 147 ) CA -8.7 29.0 34.2
148 LYS ( 148 ) C 5.1 1.7 0.0
150 ILE ( 150 ) C 4.3 1.7 -0.2
152 GLU ( 152 ) CA -5.2 31.8 34.3
158 GLN ( 158 ) CA -9.7 30.0 34.2
160 GLN ( 160 ) CA -4.4 32.3 34.2
160 GLN ( 160 ) C -5.9 -2.2 0.0
165 ILE ( 165 ) CB -5.1 31.9 33.2
166 SER ( 166 ) CA -4.0 32.6 34.4
166 SER ( 166 ) C -4.6 -1.5 0.1
168 VAL ( 168 ) CA -4.1 31.8 33.8
169 LEU ( 169 ) C -4.7 -1.7 0.0
170 ARG ( 170 ) C -6.6 -2.7 0.0
172 ASP ( 172 ) CA -4.1 31.4 34.1
# 15 # Warning: High improper dihedral angle deviations
The RMS Z-score for the improper dihedrals in the structure is high.
For well refined structures this number is expected to be around 1.0.
The fact that it is higher than 1.5 in this structure could be an
indication of overrefinement.
Improper dihedral RMS Z-score : 5.176
# 16 # Note: Chain names are OK
All chain names assigned to polymer molecules are unique, and all
residue numbers are strictly increasing within each chain.
# 17 # Note: Weights checked OK
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range.
# 18 # Note: No missing atoms detected
All expected atoms are present.
# 19 # Note: OXT check OK
All required C-terminal oxygen atoms are present.
# 20 # Note: No extra C-terminal groups found
No C-terminal groups are present for non C-terminal residues
# 21 # Note: All bond lengths OK
All bond lengths are in agreement with standard bond lengths using
a tolerance of 4 sigma (both standard values and sigma for amino
acid residues have been taken from Engh and Huber [REF], for
DNA/RNA from Parkinson et al [REF])
# 22 # Note: Normal bond length variability
Bond lengths were found to deviate normally from the standard bond
lengths (values for Protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]).
RMS Z-score for bond lengths: 0.794
RMS-deviation in bond distances: 0.016
# 23 # Note: No bond length directionality
Comparison of bond distances with Engh and Huber [REF] standard
values for protein residues and Parkinson et al [REF] values for
DNA/RNA does not show significant systematic deviations.
# 24 # Warning: Unusual bond angles
The bond angles listed in the table below were found to deviate
more than 4 sigma from standard bond angles (both standard values
and sigma for protein residues have been taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). In the table below
for each strange angle the bond angle and the number of standard
deviations it differs from the standard values is given. Please
note that disulphide bridges are neglected. Atoms starting with "-"
belong to the previous residue in the sequence.
33 ASN ( 33 ) CA CB CG 117.439 4.8
# 25 # Note: Normal bond angle variability
Bond angles were found to deviate normally from the mean standard
bond angles (normal values for protein residues were taken from
Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The
RMS Z-score given below is expected to be around 1.0 for a normally
restrained data set, and this is indeed observed for very high
resolution X-ray structures. More common values are around 1.55.
RMS Z-score for bond angles: 0.768
RMS-deviation in bond angles: 1.364
# 26 # Note: Side chain planarity OK
All of the side chains of residues that have a planar group are
planar within expected RMS deviations.
# 27 # Note: Atoms connected to aromatic rings OK
All of the atoms that are connected to planar aromatic rings in side
chains of amino-acid residues are in the plane within expected RMS
deviations.
# 28 # Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO residues are within normal ranges.
# 29 # Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase
that is not expected to occur in protein structures. Puckering
parameters were calculated by the method of Cremer and Pople
[REF]. Normal PRO rings approximately show a so-called envelope
conformation with the C-gamma atom above the plane of the ring
(phi=+72 degrees), or a half-chair conformation with C-gamma below
and C-beta above the plane of the ring (phi=-90 degrees). If phi
deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a
manual check of the data.
48 PRO ( 48 ) -52.3 half-chair C-beta/C-alpha (-54 degrees)
# 30 # Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
torsion angles.
These scores give an impression of how ``normal'' the torsion
angles in protein residues are. All torsion angles except omega are
used for calculating a `normality' score. Average values and
standard deviations were obtained from the residues in the WHAT IF
database. These are used to calculate Z-scores. A residue with a
Z-score of below -2.0 is poor, and a score of less than -3.0 is
worrying. For such residues more than one torsion angle is in a
highly unlikely position.
15 LEU ( 15 ) -2.3306
102 ILE ( 102 ) -2.1020
115 THR ( 115 ) -2.0884
# 31 # Warning: Backbone torsion angle evaluation shows unusual conformations
The residues listed in the table below have abnormal backbone torsion
angles.
Residues with ``forbidden'' phi-psi combinations are listed, as
well as residues with unusual omega angles (deviating by more than
3 sigma from the normal value). Please note that it is normal if
about 5 percent of the residues is listed here as having unusual
phi-psi combinations.
6 HIS ( 6 ) Poor phi/psi
7 HIS ( 7 ) Poor phi/psi
9 GLU ( 9 ) Poor phi/psi
11 SER ( 11 ) Poor phi/psi
15 LEU ( 15 ) Poor phi/psi
37 ASP ( 37 ) Poor phi/psi
48 PRO ( 48 ) Poor PRO-phi
108 SER ( 108 ) Poor phi/psi
121 LYS ( 121 ) Poor phi/psi
155 LYS ( 155 ) Poor phi/psi
170 ARG ( 170 ) Poor phi/psi
172 ASP ( 172 ) Poor phi/psi
# 32 # Note: Ramachandran Z-score OK
The score expressing how well the backbone conformations of all residues
are corresponding to the known allowed areas in the Ramachandran plot is
within expected ranges for well-refined structures.
Ramachandran Z-score : -2.560
# 33 # Note: Omega angle restraint OK
The omega angles for trans-peptide bonds in a structure is
expected to give a gaussian distribution with the average around
+178 degrees, and a standard deviation around 5.5. In the current
structure the standard deviation agrees with this expectation.
Standard deviation of omega values : 4.009
# 34 # Note: chi-1/chi-2 angle correlation Z-score OK
The score expressing how well the chi-1/chi-2 angles of all residues
are corresponding to the populated areas in the database is
within expected ranges for well-refined structures.
chi-1/chi-2 correlation Z-score : -1.276
# 35 # Note: Ramachandran plot
In this Ramachandran plot X-signs represent glycines, squares represent
prolines and small plus-signs represent the other residues. If too many
plus-signs fall outside the contoured areas then the molecule is poorly
refined (or worse).
In a colour picture, the residues that are part of a helix are
shown in blue, strand residues in red. "Allowed" regions for
helical residues are drawn in blue, for strand residues in red, and
for all other residues in green.
In the TeX file, a plot has been inserted here
Chain without chain identifier
# 36 # Note: Inside/Outside residue distribution normal
The distribution of residue types over the inside and the outside of the
protein is normal.
inside/outside RMS Z-score : 1.088
# 37 # Note: Inside/Outside RMS Z-score plot
The Inside/Outside distribution normality RMS Z-score over a 15
residue window is plotted as function of the residue number. High
areas in the plot (above 1.5) indicate unusual inside/outside
patterns.
In the TeX file, a plot has been inserted here
Chain without chain identifier
# 38 # Note: Secondary structure
This is the secondary structure according to DSSP. Only helix (H), strand
(S), turn (T) and coil (blank) are shown. [REF]
Secondary structure assignment
10 20 30 40 50 60
| | | | | |
1 - 60 GHHHHHHLECSSDSLQLHNVFVYGSFQDPDVINVMLDRTPEIVSATLPGFQRFRLKGRLY
1 - 60 TT T TTTT SSSSS TTT HHHHHHHTTT SSSSSSSST SSS TTT
70 80 90 100 110 120
| | | | | |
61 - 120 PCIVPSEKGEVHGKVLMGVTSDELENLDAVEGNEYERVTVGIVREDNSEKMAVKTYMWIN
61 - 120 SSS TT SSSSSSSSSS HHHHHHHHHHHTTTSSSSSSSSSSTTTT SSSSSSSSSTT
130 140 150 160 170
| | | | |
121 - 173 KADPDMFGEWNFEEWKRLHKKKFIETFKKIMECKKKPQGQGNDDISHVLREDQ
121 - 173 TT TT HHHHHHHHHHHHHHHHHHHHHHHH
# 39 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually
short distance.
The contact distances of all atom pairs have been checked. Two
atoms are said to `bump' if they are closer than the sum of their
Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs
a tolerance of 0.55 Angstrom is used. The first number in the
table tells you how much shorter that specific contact is than the
acceptable limit. The second distance is the distance between the
centers of the two atoms.
The last text-item on each line represents the status of the atom
pair. The text `INTRA' means that the bump is between atoms that
are explicitly listed in the PDB file. `INTER' means it is an
inter-symmetry bump. If the final column contains the text 'HB',
the bump criterium was relaxed because there could be a hydrogen
bond. Similarly relaxed criteria are used for 1--3 and 1--4
interactions (listed as 'B2' and 'B3', respectively). If the last
column is 'BF', the sum of the B-factors of the atoms is higher
than 80, which makes the appearance of the bump somewhat less
severe because the atoms probably aren't there anyway.
Bumps between atoms for which the sum of their occupancies is lower
than one are not reported. In any case, each bump is listed in only
one direction.
10 CYS ( 10 ) SG -- 13 ASP ( 13 ) O 0.127 2.873 INTRA BF
56 LYS ( 56 ) N -- 57 GLY ( 57 ) N 0.126 2.474 INTRA B3
104 ARG ( 104 ) CD -- 111 MET ( 111 ) SD 0.083 3.317 INTRA BF
105 GLU ( 105 ) N -- 106 ASP ( 106 ) N 0.071 2.529 INTRA B3
53 PHE ( 53 ) CD2 -- 126 MET ( 126 ) SD 0.058 3.342 INTRA
128 GLY ( 128 ) N -- 129 GLU ( 129 ) N 0.046 2.554 INTRA B3
73 GLY ( 73 ) C -- 74 LYS ( 74 ) CD 0.027 3.173 INTRA BF
59 LEU ( 59 ) CG -- 60 TYR ( 60 ) N 0.024 3.076 INTRA BF
33 ASN ( 33 ) ND2 -- 39 THR ( 39 ) OG1 0.016 2.684 INTRA BF
125 ASP ( 125 ) N -- 126 MET ( 126 ) N 0.015 2.585 INTRA BF
127 PHE ( 127 ) N -- 128 GLY ( 128 ) N 0.010 2.590 INTRA B3
104 ARG ( 104 ) NH1 -- 111 MET ( 111 ) SD 0.009 3.141 INTRA BF
# 40 # Warning: Abnormal packing environment for some residues
The residues listed in the table below have an unusual packing
environment.
The packing environment of the residues is compared with the
average packing environment for all residues of the same type in
good PDB files. A low packing score can indicate one of several
things: Poor packing, misthreading of the sequence through the
density, crystal contacts, contacts with a co-factor, or the
residue is part of the active site. It is not uncommon to see a few
of these, but in any case this requires further inspection of the
residue.
60 TYR ( 60 ) -7.26
58 ARG ( 58 ) -6.75
38 ARG ( 38 ) -6.06
8 LEU ( 8 ) -6.03
7 HIS ( 7 ) -5.80
67 GLU ( 67 ) -5.76
4 HIS ( 4 ) -5.66
5 HIS ( 5 ) -5.62
6 HIS ( 6 ) -5.57
3 HIS ( 3 ) -5.53
171 GLU ( 171 ) -5.47
160 GLN ( 160 ) -5.45
68 LYS ( 68 ) -5.31
9 GLU ( 9 ) -5.29
170 ARG ( 170 ) -5.23
169 LEU ( 169 ) -5.22
158 GLN ( 158 ) -5.15
# 41 # Warning: Abnormal packing environment for sequential residues
A stretch of at least three sequential residues with a questionable packing
environment was found. This could indicate that these residues are part
of a strange loop, but might also be an indication of misthreading.
The table below lists the first and last residue in each stretch found,
as well as the average residue score of the series.
2 HIS ( 2 ) --- 9 GLU ( 9 ) -5.49
156 LYS ( 156 ) --- 160 GLN ( 160 ) -4.56
163 ASP ( 163 ) --- 165 ILE ( 165 ) -4.18
168 VAL ( 168 ) --- 172 ASP ( 172 ) -4.88
# 42 # Note: Structural average packing environment OK
The structural average quality control value is within normal ranges.
Average for range 1 - 173 : -1.334
# 43 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain without chain identifier
# 44 # Note: Second generation packing environment OK
None of the individual amino acid residues has a bad packing environment.
# 45 # Note: No series of residues with abnormal new packing environment
There are no stretches of four or more residues each having a quality
control Z-score worse than -1.75.
# 46 # Note: Structural average packing Z-score OK
The structural average for the second generation quality control
value is within normal ranges.
All contacts : Average = -0.409 Z-score = -2.12
BB-BB contacts : Average = -0.194 Z-score = -1.23
BB-SC contacts : Average = -0.342 Z-score = -2.03
SC-BB contacts : Average = -0.437 Z-score = -2.66
SC-SC contacts : Average = -0.368 Z-score = -1.74
# 47 # Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain without chain identifier
# 48 # Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone
oxygen position.
For each of the residues in the structure, a search was performed
to find 5-residue stretches in the WHAT IF database with
superposable C-alpha coordinates, and some constraints on the
neighboring backbone oxygens.
In the following table the RMS distance between the backbone oxygen
positions of these matching structures in the database and the
position of the backbone oxygen atom in the current residue is
given. If this number is larger than 1.5 a significant number of
structures in the database show an alternative position for the
backbone oxygen. If the number is larger than 2.0 most matching
backbone fragments in the database have the peptide plane
flipped. A manual check needs to be performed to assess whether the
experimental data can support that alternative as well. The number
in the last column is the number of database hits (maximum 80) used
in the calculation. It is "normal" that some glycine residues show
up in this list, but they are still worth checking!
18 HIS ( 18 ) 3.24 23
19 ASN ( 19 ) 2.88 42
53 PHE ( 53 ) 2.80 41
63 ILE ( 63 ) 2.72 67
70 GLU ( 70 ) 2.70 39
153 CYS ( 153 ) 2.52 79
17 LEU ( 17 ) 2.49 63
42 ILE ( 42 ) 2.41 58
146 THR ( 146 ) 2.31 24
52 ARG ( 52 ) 2.30 62
141 LYS ( 141 ) 2.27 69
143 PHE ( 143 ) 2.25 71
21 PHE ( 21 ) 2.24 59
91 GLU ( 91 ) 2.14 34
22 VAL ( 22 ) 2.13 52
51 GLN ( 51 ) 2.12 28
90 VAL ( 90 ) 2.06 35
32 ILE ( 32 ) 2.05 25
133 GLU ( 133 ) 2.04 80
74 LYS ( 74 ) 1.95 18
148 LYS ( 148 ) 1.93 71
147 PHE ( 147 ) 1.81 37
116 TYR ( 116 ) 1.79 32
30 ASP ( 30 ) 1.71 80
39 THR ( 39 ) 1.70 68
115 THR ( 115 ) 1.70 42
111 MET ( 111 ) 1.60 10
144 ILE ( 144 ) 1.55 22
110 LYS ( 110 ) 1.52 49
# 49 # Warning: Unusual rotamers
The residues listed in the table below have a rotamer that is not
seen very often in the database of solved protein structures. This
option determines for every residue the position specific chi-1
rotamer distribution. Thereafter it verified whether the actual
residue in the molecule has the most preferred rotamer or not. If
the actual rotamer is the preferred one, the score is 1.0. If the
actual rotamer is unique, the score is 0.0. If there are two
preferred rotamers, with a population distribution of 3:2 and your
rotamer sits in the lesser populated rotamer, the score will be
0.667. No value will be given if insufficient hits are found in the
database.
It is not necessarily an error if a few residues have rotamer
values below 0.3, but careful inspection of all residues with these
low values could be worth it.
132 PHE ( 132 ) 0.36
# 50 # Warning: Unusual backbone conformations
For the residues listed in the table below, the backbone formed by
itself and two neighboring residues on either side is in a
conformation that is not seen very often in the database of solved
protein structures. The number given in the table is the number of
similar backbone conformations in the database with the same amino
acid in the center.
For this check, backbone conformations are compared with database
structures using C-alpha superpositions with some restraints on the
backbone oxygen positions.
A residue mentioned in the table can be part of a strange loop, or
there might be something wrong with it or its directly surrounding
residues. There are a few of these in every protein, but in any
case it is worth looking at!
4 HIS ( 4 ) 0
5 HIS ( 5 ) 0
6 HIS ( 6 ) 0
7 HIS ( 7 ) 0
8 LEU ( 8 ) 0
9 GLU ( 9 ) 0
14 SER ( 14 ) 0
15 LEU ( 15 ) 0
25 SER ( 25 ) 0
36 LEU ( 36 ) 0
37 ASP ( 37 ) 0
55 LEU ( 55 ) 0
56 LYS ( 56 ) 0
77 MET ( 77 ) 0
120 ASN ( 120 ) 0
126 MET ( 126 ) 0
127 PHE ( 127 ) 0
154 LYS ( 154 ) 0
155 LYS ( 155 ) 0
164 ASP ( 164 ) 0
170 ARG ( 170 ) 0
171 GLU ( 171 ) 0
11 SER ( 11 ) 1
13 ASP ( 13 ) 1
24 GLY ( 24 ) 1
27 GLN ( 27 ) 1
58 ARG ( 58 ) 1
94 GLU ( 94 ) 1
121 LYS ( 121 ) 1
169 LEU ( 169 ) 1
23 TYR ( 23 ) 2
35 MET ( 35 ) 2
57 GLY ( 57 ) 2
106 ASP ( 106 ) 2
# 51 # Error: Backbone conformation Z-score very low
A comparison of the backbone conformation with database proteins
shows that the backbone fold in this structure is very unusual.
Backbone conformation Z-score : -12.167
# 52 # Warning: Average B-factor problem
The average B-factor for all buried protein atoms normally lies between
10--20. Values around 3--5 are expected for X-ray studies performed
at liquid nitrogen temperature.
Because of the extreme value for the average B-factor, no further analysis
of the B-factors is performed.
Average B-factor for buried atoms : 38.340
# 53 # Note: B-factor plot
The average atomic B-factor per residue is plotted as function of
the residue number.
In the TeX file, a plot has been inserted here
Chain without chain identifier
# 54 # Error: HIS, ASN, GLN side chain flips
Listed here are Histidine, Asparagine or Glutamine residues for
which the orientation determined from hydrogen bonding analysis are
different from the assignment given in the input. Either they could
form energetically more favorable hydrogen bonds if the terminal
group was rotated by 180 degrees, or there is no assignment in the
input file (atom type 'A') but an assignment could be made. If a
residue is marked ``flexible'' the flipped conformation is only
slightly better than the non-flipped conformation.
4 HIS ( 4 )
16 GLN ( 16 )
19 ASN ( 19 )
86 ASN ( 86 )
# 55 # Note: Histidine type assignments
For all complete HIS residues in the structure a tentative
assignment to HIS-D (protonated on ND1), HIS-E (protonated on NE2),
or HIS-H (protonated on both ND1 and NE2, positively charged) is
made based on the hydrogen bond network. A second assignment is
made based on which of the Engh and Huber [REF] histidine
geometries fits best to the structure.
In the table below all normal histidine residues are listed. The
assignment based on the geometry of the residue is listed first,
together with the RMS Z-score for the fit to the Engh and Huber
parameters. For all residues where the H-bond assignment is
different, the assignment is listed in the last columns, together
with its RMS Z-score to the Engh and Huber parameters.
As always, the RMS Z-scores should be close to 1.0 if the residues
were restrained to the Engh and Huber parameters during refinement.
Please note that because the differences between the geometries of
the different types are small it is possible that the geometric
assignment given here does not correspond to the type used in
refinement. This is especially true if the RMS Z-scores are much
higher than 1.0.
If the two assignments differ, or the ``geometry'' RMS Z-score is high,
it is advisable to verify the hydrogen bond assignment, check the
HIS type used during the refinement and possibly adjust it.
2 HIS ( 2 ) HIS-H 0.71 HIS-E 0.82
3 HIS ( 3 ) HIS-H 0.68 HIS-E 0.88
4 HIS ( 4 ) HIS-H 0.75 HIS-D 0.87
5 HIS ( 5 ) HIS-H 0.69 HIS-E 0.82
6 HIS ( 6 ) HIS-H 1.02 HIS-E 1.10
7 HIS ( 7 ) HIS-H 0.66 HIS-E 0.83
18 HIS ( 18 ) HIS-H 0.66 HIS-E 0.75
72 HIS ( 72 ) HIS-H 0.51 HIS-D 0.65
139 HIS ( 139 ) HIS-H 0.69 HIS-E 0.88
167 HIS ( 167 ) HIS-H 0.62 HIS-E 0.78
# 56 # Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a
hydrogen atom that is not involved in a hydrogen bond in the
optimized hydrogen bond network.
Hydrogen bond donors that are buried inside the protein normally
use all of their hydrogens to form hydrogen bonds within the
protein. If there are any non hydrogen bonded buried hydrogen bond
donors in the structure they will be listed here. In very good
structures the number of listed atoms will tend to zero.
19 ASN ( 19 ) N
23 TYR ( 23 ) N
24 GLY ( 24 ) N
26 PHE ( 26 ) N
30 ASP ( 30 ) N
38 ARG ( 38 ) N
52 ARG ( 52 ) N
54 ARG ( 54 ) N
55 LEU ( 55 ) N
59 LEU ( 59 ) N
60 TYR ( 60 ) N
63 ILE ( 63 ) N
70 GLU ( 70 ) N
83 GLU ( 83 ) N
86 ASN ( 86 ) ND2
116 TYR ( 116 ) OH
121 LYS ( 121 ) N
122 ALA ( 122 ) N
125 ASP ( 125 ) N
128 GLY ( 128 ) N
129 GLU ( 129 ) N
# 57 # Note: Buried hydrogen bond acceptors OK
All buried polar side-chain hydrogen bond acceptors are involved in a
hydrogen bond in the optimized hydrogen bond network.
# 58 # Note: Summary report for users of a structure
This is an overall summary of the quality of the structure as
compared with current reliable structures. This summary is most
useful for biologists seeking a good structure to use for modelling
calculations.
The second part of the table mostly gives an impression of how well
the model conforms to common refinement constraint values. The
first part of the table shows a number of constraint-independent
quality indicators.
Structure Z-scores, positive is better than average:
1st generation packing quality : -2.086
2nd generation packing quality : -2.120
Ramachandran plot appearance : -2.560
chi-1/chi-2 rotamer normality : -1.276
Backbone conformation : -12.167 (bad)
RMS Z-scores, should be close to 1.0:
Bond lengths : 0.794
Bond angles : 0.768
Omega angle restraints : 0.729
Side chain planarity : 0.566 (tight)
Improper dihedral distribution : 5.176 (loose)
Inside/Outside distribution : 1.088
REFERENCES
==========
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Errors in protein structures
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R.Engh and R.Huber,
Accurate bond and angle parameters for X-ray protein structure
refinement,
Acta Crystallogr. A47, 392--400 (1991).
Bond lengths and angles, DNA/RNA
G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
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Acta Crystallogr. D52, 57--64 (1996).
DSSP
W.Kabsch and C.Sander,
Dictionary of protein secondary structure: pattern
recognition of hydrogen bond and geometrical features
Biopolymers 22, 2577--2637 (1983).
Hydrogen bond networks
R.W.W.Hooft, C.Sander and G.Vriend,
Positioning hydrogen atoms by optimizing hydrogen bond networks in
protein structures
PROTEINS, 26, 363--376 (1996).
Matthews' Coefficient
B.W.Matthews
Solvent content of Protein Crystals
J. Mol. Biol. 33, 491--497 (1968).
Protein side chain planarity
R.W.W. Hooft, C. Sander and G. Vriend,
Verification of protein structures: side-chain planarity
J. Appl. Cryst. 29, 714--716 (1996).
Puckering parameters
D.Cremer and J.A.Pople,
A general definition of ring puckering coordinates
J. Am. Chem. Soc. 97, 1354--1358 (1975).
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G.Vriend and C.Sander,
Quality control of protein models: directional atomic
contact analysis,
J. Appl. Cryst. 26, 47--60 (1993).
Ramachandran plot
G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
Stereochemistry of Polypeptide Chain Conformations
J. Mol. Biol. 7, 95--99 (1963).
Symmetry Checks
R.W.W.Hooft, C.Sander and G.Vriend,
Reconstruction of symmetry related molecules from protein
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J. Appl. Cryst. 27, 1006--1009 (1994).