WHAT IF Check report
This file was created 2009-05-11 from WHAT_CHECK output by a conversion
script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also
exists a legend to the
output.

Verification log for pdb2ywr.ent

Sect 0) Symmetry related problems

Note: Matthews coefficient OK

The Matthews coefficient [REF] is defined
as the density of the protein structure in cubic Angstroms per Dalton. Normal
values are between 1.5 (tightly packed, little room for solvent) and 4.0
(loosely packed, much space for solvent). Some very loosely packed structures
can get values a bit higher than that.

Molecular weight of all polymer chains: 24010.859
Volume of the Unit Cell
V= 380792.125
Cell multiplicity: 8
Matthews coefficient for observed
atoms Vm= 1.982

Note: All atoms are sufficiently far away from symmetry axes
None of
the atoms in the structure is closer than 0.77 Angstrom to a proper symmetry
axis.

Sect 1) Administrative problems that can generate validation
failures

Note: No strange inter-chain connections detected
No covalent bonds
have been detected between molecules with non-identical chain identifiers.

Note: No duplicate atom names in ligands
All atom names in ligands
seem adequately unique.

Note: No mixed usage of alternate atom problems detected
Either this
structure does not contain alternate atoms, or they have not been mixed up, or
the errors have remained unnoticed.

Note: In all cases the primary alternate atom was used
WHAT IF saw
no need to make any alternate atom corrections (which means they are all
correct, or there aren't any).

Note: No overlapping non-alternates detected
Either this structure
does not contain overlapping non-alternate atoms, or they are all correct, or
the errors have remained unnoticed.

Note: No residues detected inside ligands
Either this structure does
not contain ligands with amino acid groups in it, or their naming is proper
(enough).

Note: Ligand topologies OK
The topology could be determined for all
ligands (or there are no ligands for which a topology is needed, in which case
there is absolutely no problem, of course). That is good because it means that
all ligands can be included in the hydrogen bond optimization and related
options.

Note: No attached groups interfere with hydrogen bond
calculations
It seems there are no sugars, lipids, etc., bound (very
close) to atoms that otherwise could form hydrogen bonds.

Note: No atoms with high occupancy detected at special
positions
Either there were no atoms at special positions, or all atoms
at special positions have adequately reduced occupancies.

Note: All residues have a complete backbone.
No residues have
missing backbone atoms.

Note: No probable atoms with zero occupancy detected.
Either there
are no atoms with zero occupancy, or they are not present in the file, or their
positions are sufficiently improbable to warrant a zero occupancy.

Sect 2) Non-validating, descriptive output paragraph

Note: Content of the PDB file as interpreted by WHAT IF
Content of
the PDB file as interpreted by WHAT IF. WHAT IF 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 IF output
formats can be found at http://swift.cmbi.ru.nl/. Look under output
formats.

1 1 ( 1) 216 ( 216) A Protein pdb2ywr.ent
2 217 ( 216) 217 ( 216) A F O2 <- 216 pdb2ywr.ent
3 218 ( 703) 218 ( 703) A MG pdb2ywr.ent
4 219 ( 704) 219 ( 704) A CO pdb2ywr.ent
5 220 ( 727) 220 ( 727) A CO pdb2ywr.ent
6 221 ( 766) 221 ( 766) A CO pdb2ywr.ent
7 222 ( 767) 222 ( 767) A CO pdb2ywr.ent
8 223 ( HOH ) 223 ( HOH ) A water ( 266) pdb2ywr.ent

Note: Ramachandran plot
In this Ramachandran plot x-signs represent
glycines, squares represent prolines, and plus-signs represent the other
residues. If too many plus-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. "Allowed" regions for helical residues are drawn in
blue, for strand residues in red, and for all other residues in green.

Chain identifier: A

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 the DSSP page. 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.
10 20 30 40 50 60
| | | | | |
1 - 60 MLKIGVLVSGRGSNLQAIIDAIESGKVNASIELVISDNPKAYAIERCKKHNVECKVIQRK
( 1)-( 60) SSSSSSS T HHHHHHHHHHHTTTT SSSSSSSST TT HHHHHHHHHT SSS 33
70 80 90 100 110 120
| | | | | |
61 - 120 EFPSKKEFEERMALELKKKGVELVVLAGFMRILSHNFLKYFPNKVINIHPSLIPAFQGLH
( 61)-( 120)3TTTHHHHHHHHHHHHHHTT SSSSTT T HHHHTTTTT SSSSSTT TTTT TTT
130 140 150 160 170 180
| | | | | |
121 - 180 AQKQAVEFGVKFSGCTVHIVDESVDAGPVIVQAVVPVLPEDDENTLADRILKWEHKILPQ
( 121)-( 180)HHHHHHHHT TSSSSSSSS TTTT T SSSSSSSS TT HHHHHHHHHHHHHHHHHH
190 200 210
| | |
181 - 216 TVQWFAQDRIIIDGRKVIVKDATYGTLPVNPALEIF
( 181)-( 216)HHHHHHTT SSSSTTSSSSTT T TTSST T

Sect 3) Coordinate problems, unexpected atoms, B-factor and occupancy
checks

Note: No rounded coordinates detected
No significant rounding of
atom coordinates has been detected.

Note: No artificial side chains detected
No artificial side-chain
positions characterized by chi-1=0.00 or chi-1=180.00 have been detected.

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 elemantary building blocks (amino acids,
nucleotides). Even the C-terminal oxygens are treated separately.

Note: No C-terminal nitrogen detected
It is becoming habit to
indicate that a residue is not the true C-terminus by including only the
backbone N of the next residue. This has not been observed in this PDB file.

Note: Test capping of (pseudo) C-termini
No extra capping groups
were found on pseudo C-termini. This can imply that no pseudo C-termini are
present.

Note: Proper C-terminal capping groups found
All (presumably) real
C-termini either contain a proper capping group (OXT, or something else), or
they are followed by a single Nitrogen, indicating that the rest of the chain is
invisible.

Note: No OXT found in the middle of chains
No C-terminal OXT groups
were found in the middle of protein chains.

Note: Weights checked OK
All atomic occupancy factors ('weights')
fall in the 0.0--1.0 range.

Note: Normal distribution of occupancy values

The distribution of the occupancy values in this file seems 'normal'.

Be aware that this evaluation is merely the result of comparing this file
with about 500 well-refined high-resolution files in the PDB. If this file has
much higher or much lower resolution than the PDB files used in WHAT IF's
trainig set, non-normal values might very well be perfectly fine, or normal
values might actually be not so normal. So, this check is actually more an
indicator and certainly not a check in which I have great confidence.

Note: All occupancies seem to add up to 1.0.
In principle, the
occupancy of all alternates of one atom should add up till 1.0. A valid
exception is the missing atom (i.e. an atom not seen in the electron density)
that is allowed to have a 0.0 occupancy. Obviously, there is nothing wrong with
occupancies that don't add up to 1.0, because the mathematics of refinement
allow for that. However, if it happens often, it seems worth evaluating this in
light of the refinement protocol used.

Note: Average B-factor OK
The average B-factor of buried atoms is
within expected values for a room-temperature X-ray study.

Average B-factor for buried atoms : 16.818

Note: Number of buried atoms with low B-factor is OK
For protein
structures determined at room temperature, no more than about 1 percent of the B
factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 0.00

Note: B-factor distribution normal
The distribution of B-factors
within residues is within expected ranges. A value over 1.5 here would mean that
the B-factors show signs of over-refinement.

RMS Z-score : 0.521 over 1498 bonds
Average difference in B over a bond :
1.27
RMS difference in B over a bond : 1.72

Note: B-factor plot
The average atomic B-factor per residue is
plotted as function of the residue number.

Chain identifier: A

Sect 4) Nomenclature related problems

Note: Valine nomenclature OK
No errors were detected in valine
nomenclature.

Note: Threonine nomenclature OK
No errors were detected in threonine
nomenclature.

Note: Isoleucine nomenclature OK
No errors were detected in
isoleucine nomenclature.

Note: Leucine nomenclature OK
No errors were detected in leucine
nomenclature.

Note: Arginine nomenclature OK
No errors were detected in arginine
nomenclature.

Note: Tyrosine torsion conventions OK
No errors were detected in
tyrosine torsion angle conventions.

Warning: Phenylalanine convention problem
The phenylalanine residues
listed in the table below have their chi-2 not between -90.0 and 90.0.

97 PHE ( 97-) A -
128 PHE ( 128-) A -
216 PHE ( 216-) A -

Note: Aspartic acid torsion conventions OK
No errors were detected
in aspartic acid torsion angle conventions.

Note: Glutamic acid torsion conventions OK
No errors were detected
in glutamic acid torsion angle conventions.

Note: Phosphate group names OK
No errors were detected in phosphate
group naming conventions.

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.

Note: Chain names are OK
All chain names assigned to polymer
molecules are unique, and all residue numbers are strictly increasing within
each chain.

Sect 5) Geometric checks

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])

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 around 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 constraints have been used in the
refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.292
RMS-deviation in bond distances:
0.007

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.

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.

72 MSE ( 72-) A - -O -C N 64.32 -36.7
73 ALA ( 73-) A - -O -C N 116.01 -4.4
90 MSE ( 90-) A - -O -C N 89.54 -20.9
142 GLU ( 142-) A - -C N CA 114.26 -4.1
145 ASP ( 145-) A - N CA CB 101.95 -5.0
145 ASP ( 145-) A - C CA CB 100.57 -5.0
146 ALA ( 146-) A - -O -C N 140.73 11.1
146 ALA ( 146-) A - -CA -C N 97.82 -9.2
146 ALA ( 146-) A - -C N CA 110.47 -6.2
147 GLY ( 147-) A - -O -C N 111.49 -7.2
147 GLY ( 147-) A - -CA -C N 127.61 5.7
147 GLY ( 147-) A - -C N CA 131.93 6.7
169 ARG ( 169-) A - CA CB CG 96.93 -8.6

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: 0.750
RMS-deviation in bond angles: 1.550

Note: Residue Hand Error(s)
You are asking for a hand-check. WHAT IF
has over the course of this session perhaps corrected the handedness of atoms in
several residues. These residues are listed here. You better check these by
hand.

Warning: Chirality deviations detected
The atoms listed in the table
below have an improper dihedral value that is deviating from expected values. As
the improper dihedral values are all getting very close to ideal values in
recent X-ray structures, and as we actually don't know how big the spread around
these values should be, this check only warns for 6 sigma deviations.

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.

71 ARG ( 71-) A - C -39.4 -59.42 0.11
89 PHE ( 89-) A - C -26.2 -42.66 0.24
145 ASP ( 145-) A - CA 6.3 46.37 33.74

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 2.0
worries us a bit. However, we determined the improper normal distribution from
500 high-resolution X-ray structures, rather than from CSD data, so we cannot be
100% certain about these numbers.

Improper dihedral RMS Z-score : 2.117

Note: Side chain planarity OK
All of the side chains of residues
that have a planar group are planar within expected RMS deviations.

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.

Sect 6) Torsion-related checks

Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO
residues are within normal ranges.

Note: PRO puckering phases OK
Puckering phases for all PRO residues
are normal

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.

116 PHE ( 116-) A - -2.8
208 PRO ( 208-) A - -2.6
4 ILE ( 4-) A - -2.3
151 VAL ( 151-) A - -2.1
144 VAL ( 144-) A - -2.1
113 ILE ( 113-) A - -2.0

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.

9 SER ( 9-) A - Poor phi/psi
51 ASN ( 51-) A - Poor phi/psi
103 ASN ( 103-) A - Poor phi/psi
110 PRO ( 110-) A - Poor phi/psi
113 ILE ( 113-) A - PRO omega poor
133 SER ( 133-) A - Poor phi/psi
141 ASP ( 141-) A - Poor phi/psi
188 ASP ( 188-) A - Poor phi/psi
207 LEU ( 207-) A - PRO omega poor
208 PRO ( 208-) A - Poor PRO-phi
210 ASN ( 210-) A - PRO omega poor

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 : 0.273

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 constrained. This seems to
be the case with the current structure too, as the observed standard deviation
is below 4.0 degrees.

Standard deviation of omega values : 0.283

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 : 0.239

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!

71 ARG ( 71-) A - 1.66 80

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.

152 GLN ( 152-) A - 0.39

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!

11 ARG ( 11-) A - 0
72 MSE ( 72-) A - 0
90 MSE ( 90-) A - 0
103 ASN ( 103-) A - 0
113 ILE ( 113-) A - 0
115 ALA ( 115-) A - 0
117 GLN ( 117-) A - 0
142 GLU ( 142-) A - 0
144 VAL ( 144-) A - 0
207 LEU ( 207-) A - 0
87 ALA ( 87-) A - 1
119 LEU ( 119-) A - 1
210 ASN ( 210-) A - 1
9 SER ( 9-) A - 2
189 ARG ( 189-) A - 2
212 ALA ( 212-) A - 2

Note: Backbone conformation Z-score OK
The backbone conformation
analysis gives a score that is normal for well refined protein structures.

Backbone conformation Z-score : -0.512

Sect 7) Bump checks

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. 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.

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. If the
MODEL number doesn't exist (like in most X-ray files), an underscore is printed
instead.

120 HIS ( 120-) A - CE1 <--> 223 HOH (1034 ) A - O 0.46 2.34 INTRA
1 MSE ( 1-) A - N <--> 223 HOH ( 998 ) A - O 0.45 2.25 INTRA
71 ARG ( 71-) A - O <--> 72 MSE ( 72-) A - N 0.42 1.38 INTRA B2
71 ARG ( 71-) A - O <--> 72 MSE ( 72-) A - CA 0.37 2.03 INTRA B3
95 HIS ( 95-) A - CD2 <--> 223 HOH ( 982 ) A - O 0.35 2.45 INTRA
150 ILE ( 150-) A - CD1 <--> 197 VAL ( 197-) A - CG1 0.30 2.90 INTRA
18 ILE ( 18-) A - O <--> 22 ILE ( 22-) A - CD1 0.28 2.52 INTRA
54 CYS ( 54-) A - CB <--> 222 CO ( 767-) A - CO 0.25 2.95 INTRA BF
50 HIS ( 50-) A - ND1 <--> 223 HOH ( 879 ) A - O 0.21 2.49 INTRA
166 LEU ( 166-) A - CD1 <--> 170 ILE ( 170-) A - CD1 0.17 3.03 INTRA
41 ALA ( 41-) A - CB <--> 44 ILE ( 44-) A - CD1 0.15 3.05 INTRA
131 LYS ( 131-) A - NZ <--> 223 HOH ( 929 ) A - O 0.15 2.55 INTRA
55 LYS ( 55-) A - NZ <--> 223 HOH ( 923 ) A - O 0.14 2.56 INTRA
180 GLN ( 180-) A - NE2 <--> 214 GLU ( 214-) A - N 0.14 2.71 INTRA
192 ILE ( 192-) A - CD1 <--> 197 VAL ( 197-) A - CG2 0.13 3.07 INTRA
107 ASN ( 107-) A - ND2 <--> 138 HIS ( 138-) A - CE1 0.12 2.98 INTRA
59 ARG ( 59-) A - NH1 <--> 62 PHE ( 62-) A - O 0.11 2.59 INTRA
95 HIS ( 95-) A - CE1 <--> 223 HOH (1033 ) A - O 0.11 2.69 INTRA BF
172 LYS ( 172-) A - NZ <--> 223 HOH ( 930 ) A - O 0.08 2.62 INTRA
147 GLY ( 147-) A - N <--> 223 HOH ( 839 ) A - O 0.08 2.62 INTRA
144 VAL ( 144-) A - C <--> 145 ASP ( 145-) A - CG 0.07 3.03 INTRA
23 GLU ( 23-) A - CD <--> 223 HOH ( 879 ) A - O 0.07 2.73 INTRA
183 GLN ( 183-) A - NE2 <--> 223 HOH ( 865 ) A - O 0.06 2.64 INTRA
158 LEU ( 158-) A - N <--> 161 ASP ( 161-) A - OD2 0.06 2.64 INTRA
223 HOH ( 833 ) A - O <--> 223 HOH ( 930 ) A - O 0.06 2.14 INTRA
23 GLU ( 23-) A - OE2 <--> 223 HOH ( 879 ) A - O 0.05 2.35 INTRA
142 GLU ( 142-) A - OE2 <--> 223 HOH ( 829 ) A - O 0.04 2.36 INTRA
142 GLU ( 142-) A - OE2 <--> 223 HOH ( 972 ) A - O 0.04 2.36 INTRA BF
37 ASP ( 37-) A - N <--> 38 ASN ( 38-) A - N 0.04 2.56 INTRA B3
107 ASN ( 107-) A - CG <--> 108 ILE ( 108-) A - N 0.04 2.96 INTRA
138 HIS ( 138-) A - CD2 <--> 223 HOH ( 839 ) A - O 0.03 2.77 INTRA
123 LYS ( 123-) A - NZ <--> 223 HOH ( 838 ) A - O 0.03 2.67 INTRA
53 GLU ( 53-) A - CB <--> 223 HOH (1010 ) A - O 0.03 2.77 INTRA
164 ASN ( 164-) A - ND2 <--> 223 HOH ( 854 ) A - O 0.02 2.68 INTRA
58 GLN ( 58-) A - N <--> 61 GLU ( 61-) A - OE1 0.01 2.69 INTRA
69 GLU ( 69-) A - OE2 <--> 94 SER ( 94-) A - N 0.01 2.69 INTRA
205 GLY ( 205-) A - N <--> 210 ASN ( 210-) A - ND2 0.01 2.84 INTRA
118 GLY ( 118-) A - N <--> 145 ASP ( 145-) A - OD2 0.01 2.69 INTRA
145 ASP ( 145-) A - CA <--> 146 ALA ( 146-) A - N 0.00 2.20 INTRA B2
4 ILE ( 4-) A - CD1 <--> 6 VAL ( 6-) A - CG2 0.00 3.20 INTRA
189 ARG ( 189-) A - NH1 <--> 214 GLU ( 214-) A - OE1 0.00 2.70 INTRA

Sect 8) Packing, accessibility and threading

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 : 0.977

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.

Chain identifier: A

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.

11 ARG ( 11-) A - -6.24
195 ARG ( 195-) A - -5.86
50 HIS ( 50-) A - -5.73
119 LEU ( 119-) A - -5.73
207 LEU ( 207-) A - -5.43
117 GLN ( 117-) A - -5.06

Note: No series of residues with bad packing environment
There are
no stretches of three or more residues each having a quality control score worse
than -4.0.

Note: Structural average packing environment OK
The structural
average quality control value is within normal ranges.

Average for range 1 - 216 : -0.460

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.

Chain identifier: A

Note: Second generation packing environment OK
None of the
individual amino acid residues has a bad packing environment.

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.

Note: Structural average packing Z-score OK
The structural average
for the second generation quality control value is within normal ranges.

All contacts : Average = -0.144 Z-score = -0.86
BB-BB contacts : Average
= -0.141 Z-score = -0.91
BB-SC contacts : Average = 0.061 Z-score = 0.40

SC-BB contacts : Average = -0.167 Z-score = -0.94
SC-SC contacts :
Average = -0.097 Z-score = -0.51

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.

Chain identifier: A

Sect 9) Water and hydrogenbond related checks

Note: Water contacts OK
All water clusters make at least one contact
with a non-water atom.

Warning: Water molecules need moving
The water molecules listed in
the table below were found to be significantly closer to a symmetry related
non-water molecule than to the ones given in the coordinate file. For optimal
viewing convenience revised coordinates for these water molecules should be
given.

The number in brackets is the identifier of the water molecule in the input
file. Suggested coordinates are also given in the table. Please note that
alternative conformations for protein residues are not taken into account for
this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the
moved waters can be found in PDB format in the file: MOVED-H2O.pdb.

223 HOH ( 881 ) A - O 7.57 22.57 17.05
223 HOH ( 884 ) A - O 22.50 21.82 40.99
223 HOH ( 887 ) A - O 10.01 24.04 17.07
223 HOH ( 949 ) A - O 32.35 -5.06 22.94
223 HOH ( 962 ) A - O 34.31 3.10 41.72
223 HOH ( 977 ) A - O 22.47 -3.46 31.12
223 HOH ( 984 ) A - O 19.34 9.85 39.73
223 HOH ( 985 ) A - O 12.67 22.72 11.17
223 HOH (1003 ) A - O -1.79 1.43 22.04
223 HOH (1006 ) A - O -3.61 8.78 16.00
223 HOH (1012 ) A - O 3.87 23.77 29.40
223 HOH (1020 ) A - O 8.85 23.51 9.03
223 HOH (1026 ) A - O 1.21 17.09 1.23
223 HOH (1028 ) A - O 19.41 -0.84 0.34

Error: Water molecules without hydrogen bonds
The water molecules
listed in the table below do not form any hydrogen bonds, neither with the
protein or DNA/RNA, nor with other water molecules. This is a strong indication
of a refinement problem. The last number on each line is the identifier of the
water molecule in the input file.

223 HOH (1032 ) A - O
223 HOH (1033 ) A - O

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. Be aware, though,
that if the topology could not be determined for one or more ligands, then this
option will make errors.

14 ASN ( 14-) A -
138 HIS ( 138-) A -
180 GLN ( 180-) A -
210 ASN ( 210-) A -

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.

50 HIS ( 50-) A - HIS-H 0.06 HIS-D 0.57
95 HIS ( 95-) A - HIS-H 0.05 HIS-D 0.55
109 HIS ( 109-) A - HIS-H 0.10 HIS-E 0.59
120 HIS ( 120-) A - HIS-H 0.06 HIS-D 0.56
138 HIS ( 138-) A - HIS-H 0.04 HIS-D 0.56
175 HIS ( 175-) A - HIS-H 0.07 HIS-E 0.60

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.

14 ASN ( 14-) A - ND2
46 ARG ( 46-) A - NH2
75 GLU ( 75-) A - N
89 PHE ( 89-) A - N
91 ARG ( 91-) A - N
108 ILE ( 108-) A - N
184 TRP ( 184-) A - NE1
216 PHE ( 216-) A - N

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.

Final summary

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 : 0.101
2nd generation packing quality : -0.855
Ramachandran plot appearance : 0.273
chi-1/chi-2 rotamer normality : 0.239
Backbone conformation : -0.512

RMS Z-scores, should be close to 1.0:

Bond lengths : 0.292 (tight)
Bond angles : 0.750
Omega angle restraints : 0.051 (tight)
Side chain planarity : 0.487 (tight)
Improper dihedral distribution : 2.117 (loose)
B-factor distribution : 0.521
Inside/Outside distribution : 0.977

Note: Summary report for depositors of a structure
This is an
overall summary of the quality of the X-ray structure as compared with
structures solved at similar resolutions. This summary can be useful for a
crystallographer to see if the structure makes the best possible use of the
data. Warning. This table works well for structures solved in the resolution
range of the structures in the WHAT IF database, which is presently (early 2008)
mainly 1.1 - 1.4 Angstrom. The further the resolution of your file deviates from
this range the more meaningless this table becomes.

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, which have been
calibrated against structures of similar resolution.

Resolution found in PDB file : 1.77

Structure Z-scores, positive is better than average:

1st generation packing quality : 0.4
2nd generation packing quality : -0.9
Ramachandran plot appearance : 0.3
chi-1/chi-2 rotamer normality : 0.4
Backbone conformation : -0.8

RMS Z-scores, should be close to 1.0:

Bond lengths : 0.292 (tight)
Bond angles : 0.750
Omega angle restraints : 0.051 (tight)
Side chain planarity : 0.487 (tight)
Improper dihedral distribution : 2.117 (loose)
B-factor distribution : 0.521
Inside/Outside distribution : 0.977
==============

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).

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).

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).

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).

Symmetry Checks
R.W.W.Hooft, C.Sander and G.Vriend,
Reconstruction of symmetry related molecules from protein
data bank (PDB) files