************************************************************************
********** REPORT OF PROTEIN ANALYSIS  by the WHAT IF program **********
************************************************************************

Date : 2020-09-17
This report was created by WHAT IF version WHATCHECK15.0

This document is a WHAT_CHECK 14.0 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 /zata/tempdir/4xtp/wctemp_besttls/4xtp_besttls.pd====
=========================================
 
# 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 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER    SUGAR BINDING PROTEIN                   23-JAN-15   4XTP
 COMPLEXED WITH TN ANTIGEN
 
# 3 # Warning: Problem detected upon counting molecules and matrices
The parameter Z as given on the CRYST card represents the molecular
multiplicity in the crystallographic cell. Normally, Z equals the number of
matrices of the space group multiplied by the number of NCS relations. The
value of Z is multiplied by the integrated molecular weight of the molecules
in the file to determine the Matthews coefficient. This relation is being
validated in this option. Be aware that the validation can get confused if
both multiple copies of the molecule are present in the ATOM records and
MTRIX records are present in the header of the PDB file.
 
 Space group as read from CRYST card: I 2 2 2
 Number of matrices in space group: 8
 Highest polymer chain multiplicity in structure: 1
 Highest polymer chain multiplicity according to SEQRES: 1
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 BIOMT matrices have been found but not enough to explain the difference
 
# 4 # Error: Matthews Coefficient (Vm) very high
 
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.
 
Numbers this high are almost always caused by giving the wrong value for Z
on the CRYST1 card (or not giving this number at all).
 
 Molecular weight of all polymer chains: 25761.832
 Volume of the Unit Cell V= 621868.562
 Space group multiplicity: 8
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 24.139
 BIOMT matrices observed in the PDB file: 4
 But accounting for these BIOMT matrices does not make Vm reasonable yet
 Matthews coefficient read from REMARK 280 Vm= 3.040
 Vm by authors and this calculated Vm do not agree very well
 Could it be that Z must be: 8
 This number is the multiplication of the spacegroup and NCS symmetry count
 Matthews coefficient for observed atoms and corrected Z: Vm= 3.017
 
# 5 # Note: Z missing on CRYST1 card
The messages above seem likely caused by the fact that Z is missing from the
CRYST1 card.
 
# 6 # 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.
 
# 7 # Note: Chain identifiers OK
WHAT CHECK has not detected any serious chain identifier problems. But be
aware that WHAT CHECK doesn't care about the chain identifiers of waters.
 
# 8 # Warning: Ligands for which a topology was generated automatically
The topology for the ligands in the table below were determined
automatically. WHAT CHECK uses a local copy of the CCP4 monomer library to
generate topology information for ligands. Be aware that automatic topology
generation is a complicated task. So, if you get messages that you fail to
understand or that you believe are wrong, and one of these ligands is
involved, then check the ligand topology entry first. This topology is either
present in the monomer library, or as a libcheck-generated file in the local
directory.
 
  238 CIT  ( 303-) A  -
  246 A2G  ( 312-) A  -
 
# 9 # Warning: Covalently bound ligands
The ligands in this table are covalently bound to something else. It is
already difficult to automatically generate topologies for ligands,
but when they are covalently bound to something it becomes even more
complicated to do everything right. So, if you get weird error messages
that seem related to this covalent bond, then please feel free to
ignore those, or even better, make a topology entry by hand.
 
The comment `Other ligand` indicates that the covalent bond is to another
ligand. In that case you might want to convert the two ligands into one
bigger ligand.
 
  246 A2G  ( 312-) A  -
 
# 10 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 11 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 12 # Note: In all cases the primary alternate atom was used
WHAT CHECK saw no need to make any alternate atom corrections (which means
they either are all correct, or there are none).
 
# 13 # 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).
 
# 14 # 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.
 
# 15 # 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.
 
# 16 # 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.
 
# 17 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 18 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 19 # 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.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (    1)   235 (  311) A Protein             /zata/tempdir/4xt...
     2   236 (  301)   236 (  301) A CA                  /zata/tempdir/4xt...
     3   237 (  302)   237 (  302) A MN                  /zata/tempdir/4xt...
     4   238 (  303)   238 (  303) A CIT                 /zata/tempdir/4xt...
     5   239 (  304)   239 (  304) A SO4                 /zata/tempdir/4xt...
     6   240 (  305)   240 (  305) A SO4                 /zata/tempdir/4xt...
     7   241 (  306)   241 (  306) A SO4                 /zata/tempdir/4xt...
     8   242 (  307)   242 (  307) A SO4                 /zata/tempdir/4xt...
     9   243 (  308)   243 (  308) A SO4                 /zata/tempdir/4xt...
    10   244 (  309)   244 (  309) A SO4                 /zata/tempdir/4xt...
    11   245 (  310)   245 (  310) A SO4                 /zata/tempdir/4xt...
    12   246 (  312)   246 (  312) A A2G  <-             /zata/tempdir/4xt...
    13   247 (  311)   247 (  311) A S O2 <-   235       /zata/tempdir/4xt...
    14   248 ( HOH )   248 ( HOH ) A water   (  135)     /zata/tempdir/4xt...
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 235.
No nucleic acids observed in input file
No sugars recognized in input file
Number of water molecules: 135
Residue numbers increase monotonously OK
 
# 20 # Note: Chain identifiers seem OK
All ions seem to have a logical chain identifier, or there are no ions
present in the input file.
 
# 21 # 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. 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
 
# 22 # 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.ru.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 SEVVSFSFTKFNPNPKDIILQGDALVTSKGKLQLTKVKDGKPVDHSLGRALYAAPIHIWD
(   1)-(  60)  SSSSSS         SSSSST SS TT  SS   SSTTSS    SSSSSS   SS
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 DSTDRVASFATSFSFVVEAPDESKTADGIAFFLAPPDTQPQKDGGFLGLFNDSNKSIQTV
(  61)-( 120)TTT    SSSSSSSSS     TT   SSSSSSSS TT      HHHTTT          S
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 AVEFDTFSNTWDPSARHIGINVNSIESMKYVKWGWENGKVANVYISYEASTKTLTASLTY
( 121)-( 180)SSSSS    TT     SSSSSS      SSSS    TT  SSSSSSSSHHHTSSSSSSSS
                    190       200       210       220       230
                      |         |         |         |         |
  181 -  235 PSNATSYIVSANVDLKSALPEWVRVGFSATSGLSRDHVETHDVLDWSFTSTLQAS
( 181)-( 311)TTTTSSSSSSSS  HHHH   SSSSSSSSSS   TT     SSSSSSSSSS
 
 
 
 
# 23 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 24 # 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.
 
# 25 # Warning: Unexpected atoms encountered
While reading the PDB file, at least one atom was encountered that
was not expected in the residue. This might be caused by a naming
convention problem. It can also mean that a residue was found protonated
that normally is not (e.g. aspartic acid). The unexpected atoms have been
discarded; in case protons were deleted that actually might be needed, they
will later be put back by the hydrogen bond validation software.
This normally is not a warning you should worry too much about.
 
# 26 # 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.
 
# 27 # 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.
 
# 28 # 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 a spurious
OXT atom is found. -OXT indicates that an expected OXT is missing. '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 get three residue 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.
 
  234 ALA  ( 234-) A  -        OK (76)
  235 SER  ( 311-) A  -        +OXT [ 235 ; 250 ; 311]
 
# 29 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 30 # 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 CHECK's training 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.
 
# 31 # Note: All occupancies seem to add up to 0.0 - 1.0.
In principle, the occupancy of all alternates of one atom should add up till
0.0 - 1.0. 0.0 is used for the missing atom (i.e. an atom not seen in the
electron density). Obviously, there is nothing terribly wrong when a few
occupancies add up to a bit more than 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.
 
# 32 # 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. The header of the PDB file states that TLS groups
were used. So, if WHAT CHECK complains about your  B-factors, while you think
that they are OK, then check for TLS related B-factor problems first.
 
Number of TLS groups mentione in PDB file header: 0
 
Crystal temperature (K) :100.000
 
# 33 # 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. In liquid
nitrogen this percentage is allowed to be higher, of course.
 
Percentage of buried atoms with B less than 5 :   0.00
 
# 34 # 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 :  0.518 over    1630 bonds
Average difference in B over a bond :    1.10
RMS difference in B over a bond :    1.63
 
# 35 # 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 identifier: A
 
# 36 # 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.
 
# 37 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 38 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 39 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 40 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 41 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.
 
# 42 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
 
# 43 # Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
 
    8 PHE  (   8-) A  -
   73 PHE  (  73-) A  -
  127 PHE  ( 127-) A  -
 
# 44 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 45 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 46 # 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).
 
# 47 # Warning: SO4/PO4 problem
There is something wrong with the SO4 and/or PO4 groups listed in the table.
The message 'geometry' is listed if an SO4 or PO4 group is deformed in any
way. 'Hand' is listed if two atoms have been swapped so that it is the
nomenclature technical mirror image of a standard SO4/PO4. 'Incomplete' is
listed if atoms are missing. This often happens if the group is located
at a symmetry axis (a so-called special position); if that is the case
'Special position' is listed to indicate that the missing atoms might be
genuinely missing. 'Bound' is listed if the SO4 is observed bound to
something; this, of course, is not an error of any kind, but SO4 groups
bound to something often are a cause of hard to detect problems...
 
  241 SO4  ( 306-) A  - Hand
  243 SO4  ( 308-) A  - Hand
 
# 48 # 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.
 
# 49 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 50 # Warning: Unusual bond lengths
The bond lengths listed in the table below were found to deviate more than 4
sigma from standard bond lengths (both standard values and sigmas for amino
acid residues have been taken from Engh and Huber [REF], for DNA they were
taken from Parkinson et al [REF]). In the table below for each unusual bond
the bond length and the number of standard deviations it differs from the
normal value is given.
 
Atom names starting with "-" belong to the previous residue in the chain. If
the second atom name is "-SG*", the disulphide bridge has a deviating length.
 
   20 LEU  (  20-) A  -    C    O     1.15   -4.2
 
# 51 # 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: 0.707
 RMS-deviation in bond distances: 0.015
 
# 52 # 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.
 
# 53 # 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.
 
   45 HIS  (  45-) A  -    CG   ND1  CE1 109.70    4.1
   57 HIS  (  57-) A  -    CG   ND1  CE1 110.12    4.5
   65 ARG  (  65-) A  -    CG   CD   NE  118.17    4.5
 
# 54 # 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 near 1.0 for a normally restrained data set, and this is indeed
observed for very high resolution X-ray structures.
 
 RMS Z-score for bond angles: 0.835
 RMS-deviation in bond angles: 1.703
 
# 55 # 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.
 
# 56 # Note: Chirality OK
All protein atoms have proper chirality, or there is no intact protein
present in the PDB file.
The average deviation= 1.196
 
# 57 # 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 : 0.992
 
# 58 # Note: Tau angles OK
All of the tau angles (N-C-alpha-C) of amino acids fall within expected
RMS deviations.
 
# 59 # 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 : 1.124
 
# 60 # Note: Side chain planarity OK
All of the side chains of residues that have an intact planar group are
planar within expected RMS deviations.
 
# 61 # 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.
 
# 62 # Note: Ramachandran Z-score OK
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is within
expected ranges for well-refined structures.
 
 Ramachandran Z-score : -0.235
 
# 63 # 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.
 
# 64 # 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.
 
   25 LEU  (  25-) A  -   -2.6
  119 THR  ( 119-) A  -   -2.4
   58 ILE  (  58-) A  -   -2.3
   71 THR  (  71-) A  -   -2.2
   98 THR  (  98-) A  -   -2.1
 
# 65 # 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.
 
    9 THR  (   9-) A  - omega poor
   12 ASN  (  12-) A  - Omega to (next) Pro poor
   14 ASN  (  14-) A  - Omega to (next) Pro poor
   22 GLY  (  22-) A  - Poor phi/psi
   30 GLY  (  30-) A  - Poor phi/psi
   40 GLY  (  40-) A  - Poor phi/psi
   41 LYS  (  41-) A  - Omega to (next) Pro poor
   54 ALA  (  54-) A  - Omega to (next) Pro poor
   64 ASP  (  64-) A  - Poor phi/psi
   67 ALA  (  67-) A  - omega poor
   79 ALA  (  79-) A  - Omega to (next) Pro poor
   86 ALA  (  86-) A  - Poor phi/psi, omega poor
   88 GLY  (  88-) A  - Poor phi/psi
   90 ALA  (  90-) A  - omega poor
   94 ALA  (  94-) A  - Omega to (next) Pro poor
And so on for a total of    32 lines.
 
# 66 # 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.
 
   25 LEU  (  25-) A  -    -1.31
   47 LEU  (  47-) A  -    -1.34
   93 LEU  (  93-) A  -    -1.32
   51 LEU  (  51-) A  -    -1.29
   58 ILE  (  58-) A  -    -1.20
   64 ASP  (  64-) A  -    -1.23
   87 ASP  (  87-) A  -    -1.23
  117 ILE  ( 117-) A  -    -1.25
   17 ASP  (  17-) A  -    -1.12
   49 ARG  (  49-) A  -    -1.11
   61 ASP  (  61-) A  -    -1.15
  145 ILE  ( 145-) A  -    -1.13
  178 LEU  ( 178-) A  -    -1.13
  225 ASP  ( 225-) A  -    -1.11
   10 LYS  (  10-) A  -    -1.03
And so on for a total of    82 lines.
 
# 67 # Warning: chi-1/chi-2 angle correlation Z-score low
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
a bit low.
 
 chi-1/chi-2 correlation Z-score : -3.077
 
# 68 # 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.
 
   72 SER  (  72-) A  -   0.35
  182 SER  ( 182-) A  -   0.38
    7 SER  (   7-) A  -   0.39
  189 VAL  ( 189-) A  -   0.39
  210 THR  ( 210-) A  -   0.39
 
# 69 # 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!
 
   86 ALA  (  86-) A  -       0
   87 ASP  (  87-) A  - S     1
   10 LYS  (  10-) A  -       2
 
# 70 # 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 : 0.545
 
# 71 # 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.
 
Omega average and std. deviation= 178.900 6.946
 
# 72 # Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO residues are within normal ranges.
 
# 73 # Note: PRO puckering phases OK
Puckering phases for all PRO residues are normal
 
# 74 # 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 CHECK database with superposable C-alpha
coordinates, and some restraints on the neighbouring 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!
 
  154 GLY  ( 154-) A  -  1.65   31
 
# 75 # Warning: Possible peptide flips
For the residues listed in the table below, the backbone formed by the
residue mentioned and the one N-terminal of it show systematic deviations
from normality that are consistent with a peptide flip. This can either
be a 180 degree flip of the entire peptide plane or a trans to cis flip.
(Cis to trans flips cannot be detected yet). The type can be TT+, TC-,
or TC+:
TT+ indicates a 180 degree flip of the entire peptide plane.
TC- indicates a trans to cis conversion that requires a flip of the N atom.
TC+ indicates a trans to cis conversion that requires a flip of the O atom.
Note that the method will only work correctly for PDB files with full
isotropic B-factors.
 
  114 ASN  ( 114-) A  - TT+   Likely
 
# 76 # 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.
 
  219 GLU  ( 219-) A  -    OE2 <-->   221 HIS  ( 221-) A  -    NE2    0.21    2.49  INTRA BL
    1 SER  (   1-) A  -    N   <-->    57 HIS  (  57-) A  -    ND1    0.13    2.87  INTRA
  113 SER  ( 113-) A  -    O   <-->   114 ASN  ( 114-) A  -    CB     0.13    2.47  INTRA BF
   65 ARG  (  65-) A  -    NE  <-->   233 GLN  ( 233-) A  -    OE1    0.12    2.58  INTRA BF
   56 ILE  (  56-) A  -    N   <-->   203 VAL  ( 203-) A  -    O      0.07    2.63  INTRA BL
  160 VAL  ( 160-) A  -    N   <-->   245 SO4  ( 310-) A  -    O1     0.05    2.65  INTRA
   65 ARG  (  65-) A  -    NH1 <-->   234 ALA  ( 234-) A  -    O      0.05    2.65  INTRA BF
   58 ILE  (  58-) A  -    O   <-->    67 ALA  (  67-) A  -    N      0.05    2.65  INTRA BL
  101 GLN  ( 101-) A  -    NE2 <-->   243 SO4  ( 308-) A  -    O2     0.04    2.66  INTRA BF
   87 ASP  (  87-) A  -    CG  <-->   104 GLY  ( 104-) A  -    C      0.03    3.17  INTRA BL
  162 ASN  ( 162-) A  -    N   <-->   179 THR  ( 179-) A  -    O      0.02    2.68  INTRA BL
  217 HIS  ( 217-) A  -    NE2 <-->   239 SO4  ( 304-) A  -    O4     0.02    2.68  INTRA
    8 PHE  (   8-) A  -    N   <-->   226 TRP  ( 226-) A  -    O      0.02    2.68  INTRA
  219 GLU  ( 219-) A  -    CG  <-->   221 HIS  ( 221-) A  -    CE1    0.01    3.19  INTRA BL
   81 ASP  (  81-) A  -    OD1 <-->    83 SER  (  83-) A  -    N      0.01    2.69  INTRA
 
# 77 # 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: 0.942
Total bump value per residue: 0.064
Total number of bumps: 15
Total squared bump value: 0.108
Total number of bumps in the mildest bin: 15
Total number of bumps in the second bin: 0
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
 
# 78 # 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.
 
# 79 # 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 : 0.961
 
# 80 # 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
 
# 81 # 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.
 
  233 GLN  ( 233-) A  -  -6.73
  213 LEU  ( 213-) A  -  -5.03
 
# 82 # 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.
 
# 83 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 -  235 :  -0.063
 
# 84 # 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
 
# 85 # Note: Second generation packing environment OK
None of the individual amino acid residues has a bad packing environment.
 
# 86 # 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.
 
# 87 # 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
 
# 88 # Note: Crystallisation conditions from REMARK 280
Crystallisation conditions as found in the PDB file header.
 
CRYSTAL
SOLVENT CONTENT, VS   (%): 59.48
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04
CRYSTALLIZATION CONDITIONS: CUBIC-LIKE CRYSTALS, PH 3.5, VAPOR
DIFFUSION, SITTING DROP, TEMPERATURE 293K
 
# 89 # Note: Water contacts OK
All water clusters make at least one contact with a non-water atom.
 
# 90 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 91 # Note: Water hydrogen bonds OK
All water molecules can form hydrogen bonds.
 
# 92 # 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 favourable 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.
 
   45 HIS  (  45-) A  -
  114 ASN  ( 114-) A  -
  192 ASN  ( 192-) A  -
 
# 93 # 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.
 
   45 HIS  (  45-) A  -   HIS-D   0.57
   57 HIS  (  57-) A  -   HIS-H   0.46 HIS-E   0.64
  137 HIS  ( 137-) A  -   HIS-H   0.44 HIS-D   0.48
  217 HIS  ( 217-) A  -   HIS-H   0.45 HIS-E   0.64
  221 HIS  ( 221-) A  -   HIS-H   0.49 HIS-E   0.60
 
# 94 # 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.
 
   18 ILE  (  18-) A  -    N
   36 LYS  (  36-) A  -    N
   46 SER  (  46-) A  -    OG
   49 ARG  (  49-) A  -    NH2
   54 ALA  (  54-) A  -    N
   63 THR  (  63-) A  -    N
   86 ALA  (  86-) A  -    N
  144 SER  ( 144-) A  -    N
  147 SER  ( 147-) A  -    OG
  154 GLY  ( 154-) A  -    N
  213 LEU  ( 213-) A  -    N
  214 SER  ( 214-) A  -    N
  219 GLU  ( 219-) A  -    N
  225 ASP  ( 225-) A  -    N
  234 ALA  ( 234-) A  -    N
 
# 95 # 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.
 
   87 ASP  (  87-) A  -    OD2
  141 ASN  ( 141-) A  -    OD1
  219 GLU  ( 219-) A  -    OE1
 
# 96 # 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: 335
- of which buried: 180
Total number of acceptors: 365
- of which buried: 151
Total number of donor+acceptors: 53
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 14
Buried donors: 180
- without H-bond: 14
- essentially without H-bond: 0
- with only a very poor H-bond: 0
- with a poor H-bond: 1
- with a H-bond: 165
Buried acceptors: 151
- without H-bond: 22
- essentially without H-bond: 0
- with only a very poor H-bond: 0
- with a poor H-bond: 3
- with a H-bond: 126
 
# 97 # 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.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (    1)   234 (  234) A Protein             /zata/tempdir/4xt...
     2   235 (  311)   235 (  311) A Prote<=             /zata/tempdir/4xt...
     3   236 (  301)   236 (  301) A CA                  /zata/tempdir/4xt...
     4   237 (  302)   237 (  302) A MN                  /zata/tempdir/4xt...
     5   238 (  303)   238 (  303) A CIT                 /zata/tempdir/4xt...
     6   239 (  304)   239 (  304) A SO4                 /zata/tempdir/4xt...
     7   240 (  305)   240 (  305) A SO4                 /zata/tempdir/4xt...
     8   241 (  306)   241 (  306) A SO4                 /zata/tempdir/4xt...
     9   242 (  307)   242 (  307) A SO4                 /zata/tempdir/4xt...
    10   243 (  308)   243 (  308) A SO4                 /zata/tempdir/4xt...
    11   244 (  309)   244 (  309) A SO4                 /zata/tempdir/4xt...
    12   245 (  310)   245 (  310) A SO4                 /zata/tempdir/4xt...
    13   246 (  312)   246 (  312) A A2G  <-             /zata/tempdir/4xt...
    14   247 (  311)   247 (  311) A S O2 <-   235       /zata/tempdir/4xt...
    15   248 ( HOH )   248 ( HOH ) A water   (  135)     /zata/tempdir/4xt...
 
# 98 # 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  :   1.970
  1st generation packing quality :   1.092 (          (  -0.3,  2.5))
  2nd generation packing quality :  -0.118 (          (  -1.1,  1.4))
  Ramachandran plot appearance   :  -0.235 (          (  -0.9,  1.2))
  chi-1/chi-2 rotamer normality  :  -3.077 (poor      (  -2.5,  1.4))
  Backbone conformation          :   0.545 (          (  -0.5,  3.3))
  Inside/Outside distribution    :   0.961
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.707
  Bond angles                    :   0.835
  Omega angle restraints         :   1.263
  Side chain planarity           :   1.132
  Improper dihedral distribution :   0.992
  B-factor distribution          :   0.518
 
# 99 # Note: Introduction to refinement recommendations
First, be aware that the recommendations for crystallographers listed below
are produced by a computer program that was written by a guy who got his
PhD in NMR...
 
We have tried to convert the messages written in this report into a small
set of things you can do with your refinement software to get a better
structure. The things you should do first are listed first. And in some
cases you should first fix that problem, then refine a bit further, and
then run WHAT CHECK again before looking at other problems. If, for example,
WHAT CHECK has found a problem with the SCALE and CRYST cards, then you must
first fix that problem, refine the structure a bit further, and run WHAT
CHECK again because errors in the SCALE and or CRYST card can lead to many
problems elsewhere in the validation process.
 
It is also important to keep in mind that WHAT CHECK is software and that it
occasionally totally misunderstands what is the cause of a problem. But, if
WHAT CHECK lists a problem there normally is a problem albeit that it not
always is the actual problem that gets listed.
 
# 100 # Note: Matthews coefficient problem
WHAT CHECK detected a Matthews coefficient problem. Most times this is an
administrative problem caused by typing the wrong cell multiplicity number
on the CRYST card (or not typing it at all). Occasionally it is caused by
typing the wrong space group on the CRYST card. You better fix this problem,
but normally this problem does not cause WHAT CHECK to give any erroneous
error messages further down in the report.
 
# 101 # Error: Bumps in your structure
Upon analysing the bumps in your structure, WHAT CHECK got a bit
worried. Sometimes this means that you have forgotten to lower the
occupancy of overlapping ligands, residues, or water molecules. But,
whatever is the origin of this problem, you have to analyse it and
fix it.
 
# 102 # Note: His, Asn, Gln side chain flips.
His, Asn, and Gln have an asymmetry in their side chain that is hard to
detect unless you have data at much better than 1.0 Angstrom resolution.
WHAT CHECK thinks that your structure contains His, Asn, or Gln residues that
will make better hydrogen bonds when flipped around their chi-2, chi-2, or
chi-3 side chain torsion angle, respectively. You better
check these Asn, His, and Gln residues, and if you use a refinement program
that includes molecular dynamics, then you must (after the
flips were made) refine a bit further before running WHAT CHECK again.
 
# 103 # Warning: Troublesome residues
The residues listed in the table below need to be inspected
 
This table is a very rough attempt to sort the residues according to how
badly they need your attention. The idea is that when you sit in  in front
of the graphics screen and study the residues with the electron density
present that you improve the structure most by dealing with the top residues
in this list first.
 
  233 GLN  ( 233-) A  -     13.57
  213 LEU  ( 213-) A  -     11.05
  235 SER  ( 311-) A  -     10.29
  219 GLU  ( 219-) A  -      5.46
   45 HIS  (  45-) A  -      5.08
   57 HIS  (  57-) A  -      3.91
   65 ARG  (  65-) A  -      3.52
  221 HIS  ( 221-) A  -      3.46
  114 ASN  ( 114-) A  -      2.14
   20 LEU  (  20-) A  -      2.09
   49 ARG  (  49-) A  -      2.00
  192 ASN  ( 192-) A  -      2.00
   87 ASP  (  87-) A  -      1.43
  203 VAL  ( 203-) A  -      1.24
   56 ILE  (  56-) A  -      1.20
   54 ALA  (  54-) A  -      1.04
   86 ALA  (  86-) A  -      1.04
  234 ALA  ( 234-) A  -      1.04
==============
 
 
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.
==============
 
 
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.
