************************************************************************
********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program **********
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Date : 2021-09-05
This report was created by WHAT IF version WHAT IF 15.1
This document is a WHAT_CHECK 15.0 report for a PDB-file. Each reported
fact has an assigned severity, one of:
error : 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 in all checks. The software functions less well for non-canonical amino
acids and exotic ligands than for the 20 canonical residues and canonical
nucleic acids.
Some remarks regarding the output:
Residues/atoms in tables are normally given in a few parts:
A number. This is the internal sequence number of the residue used by WHAT IF.
The first residues in the file get number 1, 2, etc.
The residue type. Normally this is a three letter amino acid type.
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 a minus sign or a blank.
A model number. If no model number exists, like in most X-ray files, this will
be a blank or occasionally a minus sign.
In case an atom is part of the output, the atom will be listed using the PDB
nomenclature for type and identifier.
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.
The names of nucleic acids are DGUA, DTHY, OCYT, OADE, etc. The first character
is a D or O for DNA or RNA respectively. This circumvents ambiguities in the
many old PDB files in which DNA and RNA were both called A, C, G, and T.
=========================================
==== Compound code 5ukechain2analhbonds.pdb
=========================================
# 1 # Note: Introduction
WHAT CHECK needs to read a PDB file before it can check it. It does a
series of checks upon reading the file. The results of these checks are
reported in this section (section 2.1). The rest of the report will be more
systematic in that section 2.2 reports on administrative problems. Section
2.3 gives descriptive output that is not directly validating things but
more telling you how WHAT CHECK interpreted the input file. Section 2.4
looks at B-factors, occupancies, and the presence/absence of (spurious)
atoms. Section 2.5 deals with nomenclature problems. Section 2.6 deals with
geometric problems like bond lengths and bond angles. Section 2.7 deals with
torsion angle issues. Section 2.8 looks at atomic clashes. Section 2.9 deals
with packing, accessibility, etc, issues. Section 2.10 deals with hydrogen
bonds, ion packing, and other things that can be summarized under the common
name charge-charge interactions. Section 2.11 gives a summary of whole report
and tells you (if applicable) which symmetry matrices were used. Section 2.12
tells the crystallographer which are the things most in need of manual
correction. And the last section, section 2.13, lists all residues sorted
by their need for visual inspection in light of the electron density.
# 2 # Warning: No header information
No, or very inadequate, header information was observed upon reading the
PDB file header records. This information should be available in the form
of a series of TITLE, KEYWRDS, and JRNL lines. Missing this information
does not hamper the validation in any way, but it is nevertheless not nice
that this information is missing.
# 3 # Error: Missing unit cell information
No SCALE matrix is given in the PDB file.
# 4 # Error: Missing symmetry information
Problem: No CRYST1 card is given in the PDB file.
SYMMETRY will be unavailable for this molecule.
# 5 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
# 6 # Note: No residues detected inside ligands
Either this structure does not contain ligands with amino acid groups inside
it, or their naming is proper (enough).
# 7 # Note: No attached groups interfere with hydrogen bond calculations
It seems there are no sugars, lipids, etc., bound (or very close) to atoms
that otherwise could form hydrogen bonds.
# 8 # Note: No probable side chain atoms with zero occupancy detected.
Either there are no side chain atoms with zero occupancy, or the side chain
atoms with zero occupancy were not present in the input PDB file (in which
case they are listed as missing atoms), or their positions are sufficiently
improbable to warrant a zero occupancy.
# 9 # Note: No probable backbone atoms with zero occupancy detected.
Either there are no backbone atoms with zero occupancy, or the backbone
atoms with zero occupancy were left out of the input PDB file (in
which case they are listed as missing atoms), or their positions are
sufficiently improbable to warrant a zero occupancy.
# 10 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
# 11 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
# 12 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.umcn.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
1 1 ( 16) 90 ( 105) A Protein SET.5ukechain2ana...
MODELs skipped upon reading PDB file: 0
The total number of amino acids found is 90.
No nucleic acids observed in input file
No sugars recognized in input file
No water observed in input file
Residue numbers increase monotonously OK
# 13 # Note: Ramachandran plot
In this Ramachandran plot x-signs represent glycines, squares represent
prolines, and +-signs represent the other residues. If too many
+-signs fall outside the contoured areas then the molecule is poorly
refined (or worse). Proline can only occur in the narrow region around
phi=-60 that also falls within the other contour islands.
In a colour picture, the residues that are part of a helix are shown in blue,
strand residues in red. Preferred regions for helical residues are drawn in
blue, for strand residues in red, and for all other residues in green. A full
explanation of the Ramachandran plot together with a series of examples can
be found at the WHAT CHECK website [REF].
In the TeX file, a plot has been inserted here
Chain identifier: A
# 14 # Note: Secondary structure
This is the secondary structure according to DSSP. Only helix (H), overwound
or 3/10-helix (3), strand (S), turn (T) and coil (blank) are shown [REF].
All DSSP related information can be found at swift.cmbi.umcn.nl/gv/dssp/
This is not really a structure validation option, but a very scattered
secondary structure (i.e. many strands of only a few residues length, many
Ts inside helices, etc) tends to indicate a poor structure. A full
explanation of the DSSP secondary structure determination program together
with a series of examples can be found at the WHAT CHECK website [REF].
Secondary structure assignment
10 20 30 40 50 60
| | | | | |
1 - 60 LLFDLPPALLGELCAVLDSCDGALGWRGLAERLSSSWLDVDHIEKEVDQGKSGTRELLWS
( 16)-( 75) TTTHHHHHHHHHH HHHHHHHH TTHHHHHHHHHHHT HHHHHHHT
70 80 90
| | |
61 - 90 WAQKNKTIGDLLQVLQEMGHRRAIHLITNY
( 76)-( 105) HHHHHHHHHHHT HHHHHHHTT
# 15 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
# 16 # Note: No artificial side chains detected
No artificial side-chain positions characterized by chi-1=0.0 or chi-1=180.0
have been detected.
# 17 # Note: No missing atoms detected in residues
All expected atoms are present in residues. This validation option has not
looked at 'things' that can or should be attached to the elementary building
blocks (amino acids, nucleotides). Even the C-terminal oxygens are treated
separately.
# 18 # Note: All B-factors fall in the range 0.0 - 100.0
All B-factors are larger than zero, and none are observed above 100.0.
# 19 # Note: C-terminus capping
The residues listed in the table below are either C-terminal or pseudo
C-terminal (i.e. last residue before a missing residue).
In X-ray the coordinates must be located in density. Mobility or disorder
sometimes cause this density to be so poor that the positions of the atoms
cannot be determined. Crystallographers tend to leave out the atoms in such
cases. In many cases the N- or C-terminal residues are too disordered to see.
In case of the N-terminus, you can often see from the residue numbers if
there are missing residues; at the C-terminus this is impossible. Therefore,
often the position of the backbone nitrogen of the first residue missing
at the C-terminal end is calculated and added to indicate that there
are missing residues. As a single N causes validation trouble, we remove
these single-N-residues before doing the validation. If this happened,
the label -N is added to the pseudo C-terminus. Other labels can be +X
in case something weird is bound to the backbone C, or +OXT if something
`extra` is found. -OXT indicates that an expected OXT is missing, or not
100% OK while -O means the same for the `normal` C-terminal oxygen. 'Swap'
means that the O' and O'' (O and OXT in PDB files) have been swapped in
terms of nomenclature. 'Bad' means that something bad happened that WHAT IF
does not understand. In such cases you might some information and numbers in
square brackets; one of those might be what WHAT IF had expected to find,
but then it also might not). In case of chain breaks the number of missing
residues is listen in round brackets. OK means what it suggests...
Be aware that we cannot easily see the difference between these errors and
errors in the chain and residue numbering schemes. So do not blindly trust
the table below. If you get weird errors at, or near, the left-over
incomplete C-terminal residue, please check by hand if a missing OXT or
a removed single N is the cause. Also, many peptidic ligands get the same
chain identifier as the larger protein they are bound to. In such cases there
are more than one C-termini and OXTs with the same ID. WHAT IF gives some
random warnings about these cases. So, don't take everything at face value,
but think for yourself.
90 TYR ( 105-) A - -OXT
# 20 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
Number of residues with occupancy below 1.0 0
# 21 # Warning: What type of B-factor?
WHAT CHECK does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. TLS seems not mentioned in the header of the PDB
file. But anyway, if WHAT CHECK complains about your B-factors, and you think
that they are OK, then check for TLS related B-factor problems first.
In case this is not your own PDB file, but one downloaded from the PDB, then
check the BDB (https://swift.cmbi.umcn.nl/gv/facilities/) first.
Temperature not mentioned in PDB file. This most likely means
that the temperature record is absent.
Room temperature assumed
# 22 # Warning: Low M-factor
The B-factor flatness, the M-factor, is very low. This is very worrisome.
I suggest you consult the WHAT CHECK website and/or a seasoned
crystallographer.
The M-factor = 0.000
# 23 # Warning: More than 5 percent of buried atoms has low B-factor
For normal protein structures, no more than about 1 percent of the B factors
of buried atoms is below 5.0. The fact that this value is much higher in the
current structure could be a signal that the B-factors were restraints or
constraints to too-low values, misuse of B-factor field in the PDB file, or
a TLS/scaling problem. If the average B factor is low too, it is probably a
low temperature structure determination. In liquid nitrogen this
percentage is allowed to be higher, of course.
Percentage of buried atoms with B less than 5 : 100.00
# 24 # Warning: B-factor plot useless
All average B-factors are equal. Plot suppressed.
Chain identifier: A
# 25 # Note: Introduction to the nomenclature section.
Nomenclature problems seem, at first, rather unimportant. After all who
cares if we call the delta atoms in leucine delta2 and delta1 rather than
the other way around. Chemically speaking that is correct. But structures
have not been solved and deposited just for chemists to look at them. Most
times a structure is used, it is by software in a bioinformatics lab. And
if they compare structures in which the one used C delta1 and delta2 and the
other uses C delta2 and delta1, then that comparison will fail. Also, we
recalculate all structures every so many years to make sure that everybody
always can get access to the best coordinates that can be obtained from
the (your?) experimental data. These recalculations will be troublesome if
there are nomenclature problems.
Several nomenclature problems actually are worse than that. At the
WHAT CHECK website [REF] you can get an overview of the importance of all
nomenclature problems that we list.
# 26 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
# 27 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
# 28 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
# 29 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
# 30 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.
# 31 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
# 32 # Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
3 PHE ( 18-) A -
# 33 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
# 34 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
# 35 # Note: Phosphate group names OK in DNA/RNA
No errors were detected in nucleic acid phosphate group naming conventions
(or this structure contains no nucleic acids).
# 36 # Note: Heavy atom naming OK
No errors were detected in the atom names for non-hydrogen atoms. Please
be aware that the PDB wants us to deliberately make some nomenclature errors;
especially in non-canonical amino acids.
# 37 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
# 38 # 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 acids
have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson
et al [REF]).
# 39 # Warning: Low bond length variability
Bond lengths were found to deviate less than normal from the mean Engh and
Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS
Z-score given below is expected to be near 1.0 for a normally restrained
data set. The fact that it is lower than 0.667 in this structure might
indicate that too-strong restraints have been used in the refinement. This
can only be a problem for high resolution X-ray structures.
RMS Z-score for bond lengths: 0.302
RMS-deviation in bond distances: 0.006
# 40 # 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.
# 41 # Note: All bond angles OK
All bond angles are in agreement with standard bond angles using a tolerance
of 4 sigma (both standard values and sigma for protein residues have been
taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al. [REF]).
Please note that disulphide bridges are neglected.
# 42 # Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the 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 near 1.0 for a normally restrained data set. The fact that
it is lower than 0.667 in this structure might indicate that too-strong
restraints have been used in the refinement. This can only be a problem for
high resolution X-ray structures.
RMS Z-score for bond angles: 0.414
RMS-deviation in bond angles: 0.742
# 43 # Note: Residue hand check OK
No atoms are observed that have the wrong handedness. Be aware, though, that
WHAT CHECK might have corrected the handedness of some atoms already. The
handedness has not been corrected for any case where the problem is worse
than just an administrative discomfort.
# 44 # Note: Chirality OK
All protein atoms have proper chirality, or there is no intact protein
present in the PDB file.
The average deviation= 0.452
# 45 # Note: Improper dihedral angle distribution OK
The RMS Z-score for all improper dihedrals in the structure is within normal
ranges.
Improper dihedral RMS Z-score : 0.384
# 46 # Note: Tau angles OK
All of the tau angles (N-C-alpha-C) of amino acids fall within expected
RMS deviations.
# 47 # Note: Normal tau angle deviations
The RMS Z-score for the tau angles (N-C-alpha-C) in the structure falls
within the normal range that we guess to be 0.5 - 1.5. Be aware, we
determined the tau normal distributions from 500 high-resolution X-ray
structures, rather than from CSD data, so we cannot be 100 percent certain
about these numbers.
Tau angle RMS Z-score : 0.584
# 48 # Note: Side chain planarity OK
All of the side chains of residues that have an intact planar group are
planar within expected RMS deviations.
# 49 # 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.
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
# 50 # Warning: Ramachandran Z-score low
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is a bit low.
Ramachandran Z-score : -3.754
# 51 # Note: Ramachandran check
The list contains per-residue Z-scores describing how well each residue
fits into the allowed areas of the Ramachandran plot will not be printed
because WHAT CHECK found no reason to cry.
# 52 # 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 CHECK 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.
66 LYS ( 81-) A - -2.4
6 PRO ( 21-) A - -2.3
51 LYS ( 66-) A - -2.2
# 53 # Warning: Backbone evaluation reveals 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.
5 LEU ( 20-) A - Omega to (next) Pro poor
6 PRO ( 21-) A - Poor phi/psi, omega to (next)
9 LEU ( 24-) A - Poor phi/psi
51 LYS ( 66-) A - Poor phi/psi
52 SER ( 67-) A - Poor phi/psi
61 TRP ( 76-) A - Poor phi/psi
62 ALA ( 77-) A - Poor phi/psi
# 54 # Error: Chi-1/chi-2 rotamer problems
List of residues with a poor chi-1/chi-2 combination. Be aware that for this
validation option the individual scores are far less important than the
overall score that is given below the table.
10 LEU ( 25-) A - -1.43
71 LEU ( 86-) A - -1.43
75 LEU ( 90-) A - -1.43
86 LEU ( 101-) A - -1.43
1 LEU ( 16-) A - -1.34
9 LEU ( 24-) A - -1.33
4 ASP ( 19-) A - -1.27
26 TRP ( 41-) A - -1.16
46 GLU ( 61-) A - -1.19
12 GLU ( 27-) A - -1.05
27 ARG ( 42-) A - -1.00
42 HIS ( 57-) A - -1.04
64 LYS ( 79-) A - -1.01
66 LYS ( 81-) A - -1.02
68 ILE ( 83-) A - -1.04
And so on for a total of 34 lines.
# 55 # Note: chi-1/chi-2 angle correlation Z-score OK
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
within expected ranges for well-refined structures.
chi-1/chi-2 correlation Z-score : -0.385
# 56 # 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.
26 TRP ( 41-) A - 0.34
37 TRP ( 52-) A - 0.36
# 57 # Warning: Unusual backbone conformations
For the residues listed in the table below, the backbone formed by itself and
two neighbouring 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 centre.
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,
especially if a regular DSSP secondary structure (H or S for helix or strand,
respectively) is indicated!
49 GLN ( 64-) A - H 0
51 LYS ( 66-) A - 0
61 TRP ( 76-) A - 0
62 ALA ( 77-) A - 0
63 GLN ( 78-) A - 0
64 LYS ( 79-) A - 0
9 LEU ( 24-) A - 2
23 ALA ( 38-) A - 2
# 58 # 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 : -4.696
# 59 # Warning: Omega angles too tightly restrained
The omega angles for trans-peptide bonds in a structure are expected to give
a gaussian distribution with the average around +178 degrees and a standard
deviation around 5.5 degrees. These expected values were obtained from very
accurately determined structures. Many protein structures are too tightly
restrained. This seems to be the case with the current structure too, as the
observed standard deviation is below 4.0 degrees.
Omega average and std. deviation= 180.000 1.170
# 60 # Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO residues are within normal ranges.
# 61 # 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. Be aware that this is a warning with a low confidence
level. See: Who checks the checkers? Four validation tools applied to eight
atomic resolution structures [REF].
6 PRO ( 21-) A - -146.5 envelop C-delta (-144 degrees)
# 62 # Note: Backbone oxygen evaluation OK
All residues for which similar local backbone conformations could be found
in the WHAT CHECK database have a backbone oxygen position that has been
observed at least a few times in that database.
# 63 # Note: Peptide bond conformations
There was no need to complain about the peptide bond of a single amino acid.
# 64 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
interactomic distance; each bump is listed in only one direction.
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 centres of the two atoms. Although we believe that two
water atoms at 2.4 A distance are too close, we only report water pairs that
are closer than this rather short distance.
INTRA and INTER indicate whether the clashes are between atoms in the same
asymmetric unit, or atoms in symmetry related asymmetric units, respectively.
The last text-item on each line represents the status of the atom pair. If
the final column contains the text 'HB', the bump criterion 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 are not there anyway. BL, on the other hand, indicates
that the bumping atoms both have a low B-factor, and that makes the bumps
more worrisome.
Bumps between atoms for which the sum of their occupancies is lower than one
are not reported. If the MODEL number does not exist (as is the case in most
X-ray files), a minus sign is printed instead.
20 CYS ( 35-) A - SG <--> 25 GLY ( 40-) A - N 0.35 2.95 INTRA BL
20 CYS ( 35-) A - SG <--> 24 LEU ( 39-) A - N 0.18 3.12 INTRA BL
7 PRO ( 22-) A - O <--> 12 GLU ( 27-) A - N 0.13 2.57 INTRA BL
32 ARG ( 47-) A - NH1 <--> 78 MET ( 93-) A - SD 0.12 3.18 INTRA BL
6 PRO ( 21-) A - O <--> 8 ALA ( 23-) A - N 0.09 2.61 INTRA BL
27 ARG ( 42-) A - O <--> 31 GLU ( 46-) A - N 0.05 2.65 INTRA BL
83 ALA ( 98-) A - O <--> 87 ILE ( 102-) A - N 0.04 2.66 INTRA BL
52 SER ( 67-) A - O <--> 56 GLU ( 71-) A - CB 0.03 2.77 INTRA BL
6 PRO ( 21-) A - C <--> 8 ALA ( 23-) A - N 0.01 2.89 INTRA BL
# 65 # Note: Some notes regarding these bumps
The bumps have been binned in 5 categories ranging from 'please look at'
till 'must fix'. Additionally, the integrated sum of all bumps, the squared
sum of all bumps, and these latter two values normalized by the number of
contacts are listed too for comparison purposes between, for example, small
and large proteins.
Total bump value: 0.999
Total bump value per residue: 0.100
Total number of bumps: 9
Total squared bump value: 0.198
Total number of bumps in the mildest bin: 8
Total number of bumps in the second bin: 1
Total number of bumps in the middle bin: 0
Total number of bumps in the fourth bin: 0
Total number of bumps in the worst bin: 0
# 66 # Note: Inside/outside distribution check
The following list contains per-residue Z-scores describing how well the
residue's observed accessibility fits the expected one. A positive Z-score
indicates "more exposure than usual", whereas a negative Z-score means
"more buried than usual". The absolute value of the Z-score must be used to
judge the quality. Today WHAT CHECK saw no reason to complain.
# 67 # Warning: Inside/Outside residue distribution unusual
The distribution of residue types over the inside and the outside of the
protein is unusual. Normal values for the RMS Z-score below are between
0.84 and 1.16. The fact that it is higher in this structure could be caused
by transmembrane helices, by the fact that it is part of a multimeric active
unit, or by mistraced segments in the density.
inside/outside RMS Z-score : 1.198
# 68 # 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 identifier: A
# 69 # 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.
49 GLN ( 64-) A - -5.62
26 TRP ( 41-) A - -5.62
# 70 # Note: No series of residues with bad packing environment
There are no stretches of three or more residues each having a packing score
worse than -4.0.
# 71 # Warning: Structural average packing environment a bit worrisome
The structural average packing score is a bit low.
The protein is probably threaded correctly, but either poorly refined, or it
is just a protein with an unusual (but correct) structure. The average
packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].
Average for range 1 - 90 : -1.610
# 72 # 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 identifier: A
# 73 # Note: Second generation packing environment OK
None of the individual amino acid residues has a bad packing environment.
# 74 # Note: No series of residues with abnormal new packing environment
There are no stretches of four or more residues each having a packing
Z-score worse than -1.75.
# 75 # 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 identifier: A
# 76 # Warning: No crystallisation information
No, or very inadequate, crystallisation information was observed upon
reading the PDB file header records. This information should be available
in the form of a series of REMARK 280 lines. Without this information a
few things, such as checking ions in the structure, cannot be performed
optimally.
# 77 # Note: His, Asn, Gln side chains OK
All of the side chain conformations of Histidine, Asparagine and Glutamine
residues were found to be optimal for hydrogen bonding.
# 78 # 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, and if
enough (high resolution) data is available.
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.
42 HIS ( 57-) A - HIS-D 0.21 HIS-E 1.02
80 HIS ( 95-) A - HIS-D 0.23 HIS-E 1.03
85 HIS ( 100-) A - HIS-D 0.20 HIS-E 1.01
# 79 # 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.
Waters are not listed by this option.
3 PHE ( 18-) A - N
5 LEU ( 20-) A - N
8 ALA ( 23-) A - N
10 LEU ( 25-) A - N
18 ASP ( 33-) A - N
22 GLY ( 37-) A - N
24 LEU ( 39-) A - N
25 GLY ( 40-) A - N
26 TRP ( 41-) A - N
27 ARG ( 42-) A - N
29 LEU ( 44-) A - N
30 ALA ( 45-) A - N
38 LEU ( 53-) A - N
39 ASP ( 54-) A - N
40 VAL ( 55-) A - N
48 ASP ( 63-) A - N
51 LYS ( 66-) A - NZ
52 SER ( 67-) A - N
53 GLY ( 68-) A - N
54 THR ( 69-) A - N
55 ARG ( 70-) A - N
61 TRP ( 76-) A - N
63 GLN ( 78-) A - N
64 LYS ( 79-) A - N
64 LYS ( 79-) A - NZ
68 ILE ( 83-) A - N
80 HIS ( 95-) A - NE2
83 ALA ( 98-) A - N
# 80 # Warning: Buried unsatisfied hydrogen bond acceptors
The buried side-chain hydrogen bond acceptors listed in the table below are
not involved in a hydrogen bond in the optimized hydrogen bond network.
Side-chain hydrogen bond acceptors buried inside the protein normally form
hydrogen bonds within the protein. If there are any not hydrogen bonded in
the optimized hydrogen bond network they will be listed here.
Waters are not listed by this option.
12 GLU ( 27-) A - OE1
12 GLU ( 27-) A - OE2
56 GLU ( 71-) A - OE1
80 HIS ( 95-) A - ND1
# 81 # Note: Some notes regarding these donors and acceptors
The donors and acceptors have been counted, also as function of their
accessibility. The buried donors and acceptors have been binned in five
categories ranging from not forming any hydrogen bond till forming a poor
till perfect hydrogen bond. Obviously, the buried donors and acceptors
with no or just a poor hydrogen bond should be a topic of concern. As every
protein contains more acceptors than donors, unsatisfied donors are more in
need of attention than unsatisfied acceptors.
Total number of donors: 130
- of which buried: 70
Total number of acceptors: 138
- of which buried: 40
Total number of donor+acceptors: 10
(e.g. the Ser Ogamma that can donate and accept)
- of which buried: 2
Buried donors: 70
- without H-bond: 26
- essentially without H-bond: 0
- with only a very poor H-bond: 0
- with a poor H-bond: 1
- with a H-bond: 43
Buried acceptors: 40
- without H-bond: 12
- essentially without H-bond: 0
- with only a very poor H-bond: 0
- with a poor H-bond: 1
- with a H-bond: 27
# 82 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK has read your PDB file, and stored it internally in what is called
'the soup'. The content of this soup is listed here. An extensive explanation
of all frequently used WHAT CHECK output formats can be found at
swift.cmbi.umcn.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
1 1 ( 16) 90 ( 105) A Protein SET.5ukechain2ana...
# 83 # Note: Summary report
This is an overall summary of the quality of the structure as compared with
current reliable structures. Numbers in brackets are the average and standard
deviation observed for a large number of files determined with a similar
resolution.
The second table mostly gives an impression of how well the model conforms
to common refinement restraint values. These numbers are less than 1.0 if the
spread in data is too little, and larger than 1.0 when the spread is too
large. The former does not need to be a problem, the latter always is bad.
Structure Z-scores, positive is better than average:
Resolution read from PDB file : -1.000
1st generation packing quality : -2.775
2nd generation packing quality : -4.048 (bad)
Ramachandran plot appearance : -3.754 (poor)
chi-1/chi-2 rotamer normality : -0.385
Backbone conformation : -4.696 (bad)
RMS Z-scores, should be close to 1.0:
Bond lengths : 0.302 (tight)
Bond angles : 0.414 (tight)
Omega angle restraints : 0.213 (tight)
Side chain planarity : 0.402 (tight)
Improper dihedral distribution : 0.384
Inside/Outside distribution : 1.198 (unusual)
WHAT IF
G.Vriend,
WHAT IF: a molecular modelling and drug design program,
J. Mol. Graph. 8, 52--56 (1990).
WHAT_CHECK (verification routines from WHAT IF)
R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
Errors in protein structures
Nature 381, 272 (1996).
(see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra
information)
PDB facilities
Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G.
A series of PDB-related databanks for everyday needs.
Nucleic Acids Research D364-368 Database issue (2015).
Bond lengths and angles, protein residues
R.Engh and R.Huber,
Accurate bond and angle parameters for X-ray protein structure
refinement,
Acta Crystallogr. A47, 392--400 (1991) and
R.Engh and R.Huber,
International Tables for Crystallography (2001)
Bond lengths and angles, DNA/RNA
G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
New parameters for the refinement of nucleic acid-containing structures
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).
Peptide flips
Touw WG, Joosten RP, Vriend G.
Detection of trans-cis flips and peptide-plane flips in protein
structures.
Acta Crystallogr D Biological Crystallograhy 71, 1604-1614 (2015).
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).
Quality Control
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).
R.W.W. Hooft, C.Sander and G.Vriend,
Objectively judging the quality of a protein structure from a
Ramachandran plot
CABIOS (1997), 13, 425--430.
Symmetry Checks
R.W.W.Hooft, C.Sander and G.Vriend,
Reconstruction of symmetry related molecules from protein
data bank (PDB) files
J. Appl. Cryst. 27, 1006--1009 (1994).
Tau angle
W.G.Touw and G.Vriend
On the complexity of Engh and Huber refinement restraints: the angle
tau as example.
Acta Crystallogr D 66, 1341--1350 (2010).
Ion Checks
I.D.Brown and K.K.Wu,
Empirical Parameters for Calculating Cation-Oxygen Bond Valences
Acta Cryst. B32, 1957--1959 (1975).
M.Nayal and E.Di Cera,
Valence Screening of Water in Protein Crystals Reveals Potential Na+
Binding Sites
J.Mol.Biol. 256 228--234 (1996).
P.Mueller, S.Koepke and G.M.Sheldrick,
Is the bond-valence method able to identify metal atoms in protein
structures?
Acta Cryst. D 59 32--37 (2003).
Checking checks
K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
Who checks the checkers
J.Mol.Biol. (1998) 276,417-436.