\documentclass[a4paper]{article}
\usepackage{epsfig}
\usepackage{supertab}
\setlength{\textwidth}{16.0cm}
\setlength{\textheight}{24.0cm}
\setlength{\headheight}{0.0cm}
\setlength{\headsep}{0.0cm}
\setlength{\oddsidemargin}{0.5cm}
\setlength{\evensidemargin}{0.5cm}
\setlength{\topmargin}{0.5cm}

%%%%
% $Id: HEADER.TEX 7276 2010-05-31 16:10:04Z vriend $
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This file contains LaTeX textformatting
% commands. To print it on a PostScript(TM)
% printer, run this file through "latex" and
% the output of "latex" through "dvips". A lot
% of other possibilities exist. Ask your local
% TeXnician for advice. There is some coverage in
% the WHAT IF manual.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This is the header of a LaTeX file created by
% WHAT IF. If you are not a TeXnician, please
% do not try to understand the commands here. They
% are needed to create a consistent output, while
% the input is (1) Standard LaTeX (2) moderately
% readable. Portions of this top matter were
% copied from a file marked:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Comment.sty   version 3.0, 3 September 1992     %
% selectively in/exclude pieces of text           %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Copyright status of this file: The information in
% This file is a product of WHAT IF. You may use the
% it in publications provided that the WHAT IF
% program and its authors are appropriately
% acknowledged. This header is considered to be in
% the public domain.
%
% Implementation: Rob W.W. Hooft, 1993--1996
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\def\makeinnocent#1{\catcode`#1=12 }
\def\csarg#1#2{\expandafter#1\csname#2\endcsname}
\def\TreatAsPart#1{\begingroup
    \def\CurrentPart{#1}%
    \let\do\makeinnocent \dospecials
    \makeinnocent\^^L% and whatever other special cases
    \endlinechar`\^^M \catcode`\^^M=12 \xPart}
{\catcode`\^^M=12 \endlinechar=-1 %
 \gdef\xPart#1^^M{\def\test{#1}
      \csarg\ifx{PlainEnd\CurrentPart Test}\test
          \def\next{\endgroup\AfterPart}%
      \else \csarg\ifx{LolliEnd\CurrentPart Test}\test
          \def\next{\endgroup\AfterPart}%
      \else \csarg\ifx{LaLaEnd\CurrentPart Test}\test
            \edef\next{\endgroup\noexpand\AfterPart
                       \noexpand\end{\CurrentPart}}
      \else \ThisPart{#1}\let\next\xPart
      \fi \fi \fi \next}
}
\def\includepart
 #1{\message{Including the #1s}%
    \expandafter\def\csname#1\endcsname{}%
    \expandafter\def\csname end#1\endcsname{}}
\def\excludepart
 #1{\message{Excluding the #1s}%
    \csarg\def{#1}{\let\AfterPart\relax
           \def\ThisPart####1{}\TreatAsPart{#1}}%
    {\escapechar=-1\relax
     \csarg\xdef{PlainEnd#1Test}{\string\\end#1}%
     \csarg\xdef{LolliEnd#1Test}{\string\\#1Stop}%
     \csarg\xdef{LaLaEnd#1Test}{\string\\end\string\{#1\string\}}%
    }}
\def\showsect#1{
  \thesect\gdef\thesect{}
  \thessect\gdef\thessect{}
  \subsubsection{#1}
}
\def\sect#1{
  \gdef\thesect{\pagebreak[2]\section{#1}}
  \gdef\thessect{\subsection{General}}
}
\def\ssect#1{
  \gdef\thessect{\subsection{#1}}
}
\gdef\thesect{\pagebreak[2]\section{WHAT-IF BUG: NO TITLE!!!!!}}
\gdef\thessect{\subsection{General}}
\def\mark#1{{\bf #1:}}
\def\halfpage#1{\makebox[0.5\textwidth]{#1}}
\def\fullpage#1{\makebox[1\textwidth]{#1}}
\def\hdr#1{{\makebox[1\textwidth]{#1}}\\[-0.3\baselineskip]\nopagebreak}
\def\hdrhdr#1#2{{\halfpage{#1}\halfpage{#2}}\\[-0.3\baselineskip]\nopagebreak}
\def\psplot#1{\begin{center}
\mbox{\epsfig{file=#1,height=8.0cm}}
\end{center}}
\def\bsplot#1{\begin{center}
\mbox{\epsfig{file=#1,width=10.0cm}}
\end{center}}
\def\psstraightplot#1#2{\begin{center}
\mbox{\epsfig{file=#1,width=6cm}}
\mbox{\epsfig{file=#2,width=6cm}}
\end{center}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% The command just above this comment defines the way of displaying
% stereo-plots. In "real life" there are two possible ways of doing
% this: Normal, and Cross-eye. The default when this file is unmodified
% is to use normal stereo. If you are able to cross your eyes and that
% way see stereo plots without mechanical help, exchange the "{#1}{#2}"
% in the command just below here, such that it reads "{#2}{#1}".
% theoretically it is very easy to make so-called A-B-A plots, but an
% A4 page is just too narrow to contain three pictures in a row neatly.
%
% If you don't have the epsfig.sty file: don't panic: it should be in
% the whatif/dbdata directory. Copy it to your TEXINPUTS directory and
% you should be all set. If you don't have Rokiki's dvips program, or
% you don't want to convert to postscript, you could define the \psplot
% and psstereoplot macros to do nothing.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\def\psstereoplot#1#2{\psstraightplot{#1}{#2}}

\parskip .7em
\parindent 0pt
\raggedbottom
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This marks the end of the top matter. The customizable variables
% follow. For the three next lines, please use either "includepart" or
% "excludepart". Use at least one "includepart"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\includepart{error}
\includepart{warning}
\includepart{note}

\begin{document}
\title{Report of protein analysis}
\author{By the {\sc WHAT IF} program}

\date{2010-07-21%
\footnote{This report was created by WHAT IF version WHATCHECK 8.0}}
\maketitle
\section{Introduction}
This document contains a report of findings by the {\sc what if} program
during the analysis of a PDB-file. Each reported fact has
an assigned severity, one of:
\begin{description}
\item[{\bf error}]: severe errors encountered during the analyses. Items
   marked as errors are considered severe problems requiring immediate
   attention.
\item[{\bf warning}]: Either less severe problems or uncommon structural
   features. These still need special attention.
\item[{\bf note}]: Statistical values, plots, or other verbose results of
   tests and analyses that have been performed.
\end{description}

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 resid
and canonical nucleic acids.

\subsection{Some remarks regarding the output:}

\begin{description}
\item[Residue.] Residues/atoms in tables are normally given in a few parts:
\begin{itemize}
\item 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.
\item The residue type. Normally this is a three letter amino acid type.
\item 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.
\item 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.
\item A model number. If no model number exists, like in most X-ray files,
    this will be a blank or occasionally a minus sign.
\item In case an atom is part of the output, the atom will be listed using
    the PDB nomenclature for type and identifier.
\end{itemize}
\item[Z-Value.] To indicate the normality of a score, the score
   may be expressed as a Z-value or Z-score. This is just the number
   of standard deviations that the score deviates from the expected
   value.  A property of Z-values is that the root-mean-square of a
   group of Z-values (the RMS Z-value) is expected to be 1.0. Z-values
   above 4.0 and below $-4.0$ are very uncommon. If a Z-score is used
   in WHAT IF, the accompanying text will explain how the expected
   value and standard deviation were obtained.
\item[Nucleic acids.] 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 is done to circumvent ambiguities in the many old PDB files in which
   DNA and RNA were both called A, C, G, and T.
\end{description}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% End of the preface, start of WHAT IF generated output
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\sect{pdb1crn.ent}
\ssect{Checks that need to be done early-on in validation}
\begin{warning}
\showsect{Warning: Class of conventional cell differs from CRYST1 cell}
The crystal class of the conventional cell is different from the
crystal class of the cell given on the CRYST1 card. If the new
class is supported by the coordinates this is an indication of a
wrong space group assignment.

\parbox{1\textwidth}{
\hdr{The CRYST1 cell dimensions}

\fullpage{
$\begin{array}{lrlrlr}
A =&  40.960&B =&  18.650&C =&  22.520\\
\alpha =&  90.000&\beta =&  90.770&\gamma =&  90.000\\
\end{array}$}
}% End of ParBox


\parbox{1\textwidth}{
\hdr{Dimensions of a reduced cell}

\fullpage{
$\begin{array}{lrlrlr}
A =&  18.650&B =&  22.520&C =&  40.960\\
\alpha =&  89.230&\beta =&  90.000&\gamma =&  90.000\\
\end{array}$}
}% End of ParBox


\parbox{1\textwidth}{
\hdr{Dimensions of the conventional cell}

\fullpage{
$\begin{array}{lrlrlr}
A =&  18.650&B =&  22.520&C =&  40.960\\
\alpha =&  90.770&\beta =&  90.000&\gamma =&  90.000\\
\end{array}$}
}% End of ParBox


\parbox{1\textwidth}{
\hdr{Transformation to conventional cell}

\fullpage{
$\left[
\begin{array}{rrr}
  0.000000&  1.000000&  0.000000\\
  0.000000&  0.000000& -1.000000\\
 -1.000000&  0.000000&  0.000000\\
\end{array}
\right]$}
}% End of ParBox


\parbox{1\textwidth}{
Crystal class of the cell: MONOCLINIC
}% End of ParBox


\parbox{1\textwidth}{
Crystal class of the conventional CELL: ORTHORHOMBIC
}% End of ParBox


\parbox{1\textwidth}{
Space group name: P 1 21 1
}% End of ParBox


\parbox{1\textwidth}{
Bravais type of conventional cell is: P
}% End of ParBox

\end{warning}

\begin{error}
\showsect{Error: Negated value in scale matrix}
One or more of the values of the scale matrix are wrong.

Possible cause: Comparison with the matrix derived from the CRYST1
card reveals that values have been inverted in sign.

\parbox{1\textwidth}{
\hdrhdr{SCALE matrix}{Calculated from CRYST1}

\halfpage{$\left[
\begin{array}{rrr}
  0.024414&  0.000000& -0.000328\\
  0.000000&  0.053619&  0.000000\\
  0.000000&  0.000000&  0.044409\\
\end{array}
\right]$}%
\halfpage{$\left[
\begin{array}{rrr}
  0.024414&  0.000000&  0.000328\\
  0.000000&  0.053619&  0.000000\\
  0.000000&  0.000000&  0.044409\\
\end{array}
\right]$}
}% End of ParBox

\end{error}

\begin{warning}
\showsect{Warning: Conventional cell is pseudo-cell}
The extra symmetry that would be implied by the transition to the
previously mentioned conventional cell has not been observed. It must be
concluded that the crystal lattice has pseudo-symmetry.
\end{warning}

\begin{note}
\showsect{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.

\parbox{1\textwidth}{
 Molecular weight of all polymer chains: 4722.412

 Volume of the Unit Cell V= 17201.699

 Cell multiplicity: 2

 Matthews coefficient for observed atoms Vm= 1.821
}% End of ParBox

\end{note}

\begin{note}
\showsect{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.
An atom is considered to be located at a special position if it is
within 0.3 {\AA} from one of its own symmetry copies. See also the
next check{\ldots}
\end{note}

\begin{note}
\showsect{Note: All atoms are sufficiently far away from symmetry axes}
None of the atoms in the structure is closer than 0.77 {\AA} to
a proper symmetry axis.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\ssect{Administrative problems that can generate validation failures}
\begin{note}
\showsect{Note: No strange inter-chain connections detected}
No covalent bonds have been detected between molecules with
non-identical chain identifiers.
\end{note}

\begin{note}
\showsect{Note: No duplicate atom names in ligands}
All atom names in ligands seem adequately unique.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{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).
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{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).
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{Note: All residues have a complete backbone.}
No residues have missing backbone atoms.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{Note: No crippling errors.}
Problems can exist that make it impossible to continue the validation.
WHAT IF seems not to have encountered any of these.
\end{note}

\begin{note}
\showsect{Note: Non-canonicals}
WHAT IF has not detected any non-canonical residue that it doesn't
understand, or there are no non-canonical residues in the PDB file.
\end{note}

\ssect{Non-validating, descriptive output paragraph}
\begin{note}
\showsect{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.
A course on reading this 'Molecules' table is part of the WHAT\_CHECK
web pages [REF].


\begin{center}\begin{supertabular}{rr@{ (}r@{) }r@{ (}r@{) }rlrrr}
\multicolumn{10}{c}{'Molecules'} \\ \hline
     1&    1&    1&   46&   46&A&Protein&        &  &pdb1crn.ent\\
     2&   47&   46&   47&   46&A&N O2 $<$-&   46   &  &pdb1crn.ent\\
\end{supertabular}\end{center}
\end{note}

\begin{note}
\showsect{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.
A full explanation of the Ramachandran plot together with a series of
examples can be found at the WHAT\_CHECK website [REF].

\parbox{1\textwidth}{
\psplot{eps0001.eps}
}% End of ParBox


\parbox{1\textwidth}{
\hdr{Chain identifier: A}
}% End of ParBox

\end{note}

\begin{note}
\showsect{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
http://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].

\hdr{Secondary structure assignment}

\fullpage{\tt\begin{tabular}{r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r@{}r}
\multicolumn{10}{r@{}}{  10}&
\multicolumn{10}{r@{}}{  20}&
\multicolumn{10}{r@{}}{  30}&
\multicolumn{10}{r@{}}{  40}&
\\
T&T&C&C&P&S&I&V&A&R&S&N&F&N&V&C&R&L&P&G&T&P&E&A&I&C&A&T&Y&T&G&C&I&I&I&P&G&A&T&C&P&G&D&Y&A&N
\\
 &S&S& &T&T&H&H&H&H&H&H&H&H&H&H&H&T&T&T& & &H&H&H&H&H&H&H&H&T& &S&S& &T&T&T& & & &3&3&3& & 
\\
\end{tabular}}
\end{note}

\ssect{Coordinate problems, unexpected atoms, B-factor and occupancy checks}
\begin{note}
\showsect{Note: No rounded coordinates detected}
No significant rounding of atom coordinates has been detected.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{Note: No C-terminal nitrogen detected}
The PDB indicates 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.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{Note: No OXT found in the middle of chains}
No OXT groups were found in the middle of protein chains.
\end{note}

\begin{note}
\showsect{Note: Weights checked OK}
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range.
\end{note}

\begin{note}
\showsect{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 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.
\end{note}

\begin{note}
\showsect{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.
\end{note}

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

\parbox{1\textwidth}{
Average B-factor for buried atoms :  5.509
}% End of ParBox


\parbox{1\textwidth}{
Crystal temperature : -1.000
}% End of ParBox

\end{note}

\begin{warning}
\showsect{Warning: More than 5 percent of buried atoms has low B-factor}
For normal protein structures, no more than about 1 percent of the
B factors of buried atoms is below 5.0. The fact that this value is
much higher in the current structure could be a signal of overrefined
B-factors, restraints or constraints to too-low values, misuse of the
B-factor field in the PDB file, or a scaling problem. If the
average B factor is low too, it is probably a low temperature
structure determination.

\parbox{1\textwidth}{
Percentage of buried atoms with B less than 5 :  49.12
}% End of ParBox

\end{warning}

\begin{note}
\showsect{Note: B-factor plot}
The average atomic B-factor per residue is plotted as function of
the residue number.

\parbox{1\textwidth}{
\bsplot{sct0001.eps}
}% End of ParBox


\parbox{1\textwidth}{
\hdr{Chain identifier: A}
}% End of ParBox

\end{note}

\ssect{Nomenclature related problems}
\begin{note}
\showsect{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 $\delta$ 2 and $\delta$ 1 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 $\delta$ 1 and 2 and the
other uses C $\delta$ 2 and 1, 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
WHTA\_CHECK website [REF] you can get an overview of the importance of all
nomenclature problems that we list.
\end{note}

\begin{note}
\showsect{Note: Valine nomenclature OK}
No errors were detected in valine nomenclature.
\end{note}

\begin{note}
\showsect{Note: Threonine nomenclature OK}
No errors were detected in threonine nomenclature.
\end{note}

\begin{note}
\showsect{Note: Isoleucine nomenclature OK}
No errors were detected in isoleucine nomenclature.
\end{note}

\begin{note}
\showsect{Note: Leucine nomenclature OK}
No errors were detected in leucine nomenclature.
\end{note}

\begin{note}
\showsect{Note: Arginine nomenclature OK}
No errors were detected in arginine nomenclature.
\end{note}

\begin{note}
\showsect{Note: Tyrosine torsion conventions OK}
No errors were detected in tyrosine torsion angle conventions.
\end{note}

\begin{note}
\showsect{Note: Phenylalanine torsion conventions OK}
No errors were detected in phenylalanine torsion angle conventions.
\end{note}

\begin{note}
\showsect{Note: Aspartic acid torsion conventions OK}
No errors were detected in aspartic acid torsion angle conventions.
\end{note}

\begin{note}
\showsect{Note: Glutamic acid torsion conventions OK}
No errors were detected in glutamic acid torsion angle conventions.
\end{note}

\begin{note}
\showsect{Note: Phosphate group names OK}
No errors were detected in phosphate group naming conventions.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{Note: Chain names are OK}
All chain names assigned to polymer molecules are unique, and all
residue numbers are strictly increasing within each chain.
\end{note}

\ssect{Geometric checks}
\begin{warning}
\showsect{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.


\begin{center}\begin{supertabular}{rr@{ (}r@{) }rlllrr}
\multicolumn{5}{c}{Residue} & \multicolumn{2}{c}{Atom pair} &
Distance & Z-value \\ \hline
  37&GLY  &  37-& A& - & N  & CA &  1.52&   4.2\\
\end{supertabular}\end{center}
\end{warning}

\begin{note}
\showsect{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]).

\parbox{1\textwidth}{
 RMS Z-score for bond lengths: 1.124

 RMS-deviation in bond distances: 0.024
}% End of ParBox

\end{note}

\begin{warning}
\showsect{Warning: Possible cell scaling problem}
Comparison of bond distances with Engh and Huber [REF] standard
values for protein residues and Parkinson et al [REF] values for
DNA/RNA shows a significant systematic deviation. It could be that
the unit cell used in refinement was not accurate enough. The
deformation matrix given below gives the deviations found: the
three numbers on the diagonal represent the relative corrections
needed along the A, B and C cell axis. These values are 1.000 in a
normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)

There are a number of different possible causes for the
discrepancy.  First the cell used in refinement can be different
from the best cell calculated. Second, the value of the wavelength
used for a synchrotron data set can be miscalibrated. Finally, the
discrepancy can be caused by a dataset that has not been corrected
for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained
to obey the space group symmetry. This is done on purpose. The
distortions can give you an indication of the accuracy of the
determination.

If you intend to use the result of this check to change the cell dimension
of your crystal, please read the extensive literature on this topic first.
This check depends on the wavelength, the cell dimensions, and on the
standard bond lengths and bond angles used by your refinement software.

\parbox{1\textwidth}{
\hdr{Unit Cell deformation matrix}

\fullpage{
$\left[
\begin{array}{rrr}
  0.987188&  0.000293& -0.008811\\
  0.000293&  0.991730& -0.001286\\
 -0.008811& -0.001286&  0.992544\\
\end{array}
\right]$}

\hdr{Proposed new scale matrix}

\fullpage{
$\left[
\begin{array}{rrr}
  0.024730& -0.000007& -0.000111\\
 -0.000015&  0.054066&  0.000070\\
  0.000399&  0.000058&  0.044746\\
\end{array}
\right]$}

\hdr{With corresponding cell}

\fullpage{
$\begin{array}{lrlrlr}
A =&  40.437&B =&  18.496&C =&  22.348\\
\alpha =&  90.148&\beta =&  90.254&\gamma =&  89.965\\
\end{array}$}
}% End of ParBox


\parbox{1\textwidth}{
\hdr{The CRYST1 cell dimensions}

\fullpage{
$\begin{array}{lrlrlr}
A =&  40.960&B =&  18.650&C =&  22.520\\
\alpha =&  90.000&\beta =&  89.230&\gamma =&  90.000\\
\end{array}$}
}% End of ParBox


\parbox{1\textwidth}{
 Variance: 144.753

 (Under-)estimated Z-score: 8.867
}% End of ParBox

\end{warning}

\begin{warning}
\showsect{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.


\begin{center}\begin{supertabular}{rr@{ (}r@{) }rllllrr}
\multicolumn{5}{c}{Residue} & \multicolumn{3}{c}{Atom Triplet} &
Bond Angle & Z-value \\ \hline
   1&THR  &   1-& A& - & CA & CB & OG1&103.06&  -4.4\\
   1&THR  &   1-& A& - & CG2& CB & OG1&117.41&   4.1\\
  12&ASN  &  12-& A& - & ND2& CG & OD1&127.61&   5.0\\
  14&ASN  &  14-& A& - & ND2& CG & OD1&128.63&   6.0\\
  39&THR  &  39-& A& - & CA & CB & OG1&103.59&  -4.0\\
  45&ALA  &  45-& A& - & N  & CA & CB &103.98&  -4.3\\
\end{supertabular}\end{center}
\end{warning}

\begin{note}
\showsect{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.

\parbox{1\textwidth}{
 RMS Z-score for bond angles: 1.285

 RMS-deviation in bond angles: 2.346
}% End of ParBox

\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{Note: Chirality OK}
All protein atoms have proper chirality.
\end{note}

\begin{note}
\showsect{Note: Improper dihedral angle distribution OK}
The RMS Z-score for all improper dihedrals in the structure is within
normal ranges.

\parbox{1\textwidth}{
 Improper dihedral RMS Z-score : 1.110
}% End of ParBox

\end{note}

\begin{note}
\showsect{Note: Tau angles OK}
All of the tau angles of amino acids that actually have a tau angle
fall within expected RMS deviations.
\end{note}

\begin{note}
\showsect{Note: Normal tau angle deviations}
The RMS Z-score for the tau angles in the structure falls within the
normal rannge 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.

\parbox{1\textwidth}{
 Tau angle RMS Z-score : 1.287
}% End of ParBox

\end{note}

\begin{note}
\showsect{Note: Side chain planarity OK}
All of the side chains of residues that have a planar group are
planar within expected RMS deviations.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\ssect{Torsion-related checks}
\begin{warning}
\showsect{Warning: Unusual PRO puckering amplitudes}
The proline residues listed in the table below have a puckering
amplitude that is outside of normal ranges. Puckering parameters
were calculated by the method of Cremer and Pople [REF]. Normal PRO
rings have a puckering amplitude Q between 0.20 and 0.45
{\AA}. If Q is lower than 0.20 {\AA} for a PRO residue, this
could indicate disorder between the two different normal ring forms
(with C-$\gamma$ below and above the ring, respectively). If Q is
higher than 0.45 {\AA} something could have gone wrong during the
refinement. Be aware that this is a warning with a low confidence level.
See: Who checks the checkers? Four validation tools applied to eight
atomic resolution structures [REF]


\begin{center}\begin{supertabular}{rr@{ (}r@{) }rlrl}
\multicolumn{5}{c}{Residue} & Pucker Amplitude & Qualifier \\ \hline
  19&PRO  &  19-& A& -&  0.13&LOW\\
  36&PRO  &  36-& A& -&  0.04&LOW\\
\end{supertabular}\end{center}
\end{warning}

\begin{note}
\showsect{Note: PRO puckering phases OK}
Puckering phases for all PRO residues are normal
\end{note}

\begin{note}
\showsect{Note: Torsion angles OK}
All individual residues have normal overall torsion angle scores.
\end{note}

\begin{note}
\showsect{Note: Backbone torsion angles OK}
All individual residues have normal backbone torsion angles.
\end{note}

\begin{note}
\showsect{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.

\parbox{1\textwidth}{
 Ramachandran Z-score : -0.307
}% End of ParBox

\end{note}

\begin{warning}
\showsect{Warning: Omega angles too tightly restrained}
The $\omega$ angles for trans-peptide bonds in a structure are
expected to give a gaussian distribution with the average around
+178 degrees and a standard deviation around 5.5 degrees. These
expected values were obtained from very accurately determined
structures.  Many protein structures are too tightly restrained.
This seems to be the case with the current structure too, as the
observed standard deviation is below 4.0 degrees.

\parbox{1\textwidth}{
 Standard deviation of $\omega$ values : 3.769
}% End of ParBox

\end{warning}

\begin{note}
\showsect{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.

\parbox{1\textwidth}{
 $\chi$-1/$\chi$-2 correlation Z-score : -0.900
}% End of ParBox

\end{note}

\begin{note}
\showsect{Note: Backbone oxygen evaluation OK}
All residues for which the local backbone conformation could be
found in the WHAT IF database have a normal backbone oxygen
position.
\end{note}

\begin{note}
\showsect{Note: Rotamers checked OK}
None of the residues that have a normal backbone environment have
abnormal rotamers.
\end{note}

\begin{warning}
\showsect{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!


\begin{center}\begin{supertabular}{rr@{ (}r@{) }rlr}
\multicolumn{5}{c}{Residue} & \# hits \\ \hline
  19&PRO  &  19-& A& -&    0\\
   5&PRO  &   5-& A& -&    1\\
  30&THR  &  30-& A& -&    1\\
  44&TYR  &  44-& A& -&    1\\
   4&CYS  &   4-& A& -&    2\\
  32&CYS  &  32-& A& -&    2\\
  36&PRO  &  36-& A& -&    2\\
  38&ALA  &  38-& A& -&    2\\
\end{supertabular}\end{center}
\end{warning}

\begin{note}
\showsect{Note: Backbone conformation Z-score OK}
The backbone conformation analysis gives a score that is normal
for well refined protein structures.

\parbox{1\textwidth}{
 Backbone conformation Z-score : 0.109
}% End of ParBox

\end{note}

\ssect{Bump checks}
\begin{note}
\showsect{Note: No Van der Waals overlaps}
All interatomic distances (including symmetry transformations) have
been verified. No unusual contacts were found.  No pair of atoms
has an unusual short contact distance.
\end{note}

\ssect{Packing, accessibility and threading}
\begin{note}
\showsect{Note: Inside/Outside residue distribution normal}
The distribution of residue types over the inside and the outside of the
protein is normal.

\parbox{1\textwidth}{
inside/outside RMS Z-score : 1.012
}% End of ParBox

\end{note}

\begin{note}
\showsect{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.

\parbox{1\textwidth}{
\bsplot{sct0002.eps}
}% End of ParBox


\parbox{1\textwidth}{
\hdr{Chain identifier: A}
}% End of ParBox

\end{note}

\begin{note}
\showsect{Note: Packing environment OK}
None of the individual amino acid residues has a bad packing environment.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{Note: Structural average packing environment OK}
The structural average quality control value is within normal ranges.

\parbox{1\textwidth}{
Average for range     1 -   46 :  -0.435
}% End of ParBox

\end{note}

\begin{note}
\showsect{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.

\parbox{1\textwidth}{
\bsplot{sct0003.eps}
}% End of ParBox


\parbox{1\textwidth}{
\hdr{Chain identifier: A}
}% End of ParBox

\end{note}

\begin{note}
\showsect{Note: Second generation packing environment OK}
None of the individual amino acid residues has a bad packing environment.
\end{note}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{Note: Structural average packing Z-score OK}
The structural average for the second generation quality control
value is within normal ranges.

\parbox{1\textwidth}{
 All   contacts    : Average = -0.057 Z-score =  -0.34

 BB-BB contacts    : Average =  0.038 Z-score =   0.19

 BB-SC contacts    : Average = -0.110 Z-score =  -0.91

 SC-BB contacts    : Average = -0.036 Z-score =  -0.17

 SC-SC contacts    : Average = -0.135 Z-score =  -0.62
}% End of ParBox

\end{note}

\begin{note}
\showsect{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.

\parbox{1\textwidth}{
\bsplot{sct0004.eps}
}% End of ParBox


\parbox{1\textwidth}{
\hdr{Chain identifier: A}
}% End of ParBox

\end{note}

\ssect{Water, ion, and hydrogenbond related checks}
\begin{note}
\showsect{Note: HIS, ASN, GLN side chains OK}
All of the side chain conformations of Histidine, Asparagine and
Glutamine residues were found to be optimal for hydrogen bonding.
\end{note}

\begin{warning}
\showsect{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.


\begin{center}\begin{supertabular}{rr@{ (}r@{) }rll}
\multicolumn{5}{c}{Residue} & {Atom} \\ \hline
   6&SER  &   6-& A& -&  N\\
   8&VAL  &   8-& A& -&  N\\
  45&ALA  &  45-& A& -&  N\\
\end{supertabular}\end{center}
\end{warning}

\begin{note}
\showsect{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.
\end{note}

\begin{note}
\showsect{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.
A course on reading this 'Molecules' table is part of the WHAT\_CHECK
web pages [REF].


\begin{center}\begin{supertabular}{rr@{ (}r@{) }r@{ (}r@{) }rlrrr}
\multicolumn{10}{c}{'Molecules'} \\ \hline
     1&    1&    1&   46&   46&A&Protein&        &  &pdb1crn.ent\\
     2&   47&   46&   47&   46&A&N O2 $<$-&   46   &  &pdb1crn.ent\\
\end{supertabular}\end{center}
\end{note}

\begin{warning}
\showsect{Warning: No crystallisation information}
No, or very inadequate, crystallisation information was observed upon
reading the PDB file header records. This information should be available
in the form of a series of REMARK 280 lines. Without this information a
few things, such as checking ions in the structure, cannot be performed
optimally.
\end{warning}

\begin{note}
\showsect{Note: No ions (of a type we can validate) in structure}
Since there are no ions in the structure of a type we can validate, this
check will not be executed.
\end{note}

\ssect{Final summary}
\begin{note}
\showsect{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 restraint values. The
first part of the table shows a number of restraint-independent
quality indicators.

\parbox{1\textwidth}{

 Structure Z-scores, positive is better than average:

\begin{tabular}{lrc}
  1st generation packing quality :&   0.163\\
  2nd generation packing quality :&  -0.344\\
  Ramachandran plot appearance   :&  -0.307\\
  $\chi$-1/$\chi$-2 rotamer normality  :&  -0.900\\
  Backbone conformation          :&   0.109\\
\end{tabular}

 RMS Z-scores, should be close to 1.0:

\begin{tabular}{lrc}
  Bond lengths                   :&   1.124\\
  Bond angles                    :&   1.285\\
  Omega angle restraints         :&   0.685& (tight)\\
  Side chain planarity           :&   0.842\\
  Improper dihedral distribution :&   1.110\\
  Inside/Outside distribution    :&   1.012\\
\end{tabular}
}% End of ParBox

\end{note}

\begin{note}
\showsect{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
(summer 2008) mainly 1.1 - 1.3 {\AA}. 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 restraint values. The
first part of the table shows a number of restraint-independent
quality indicators, which have been calibrated against structures
of similar resolution.

\parbox{1\textwidth}{
 Resolution found in PDB file        :   1.50
}% End of ParBox


\parbox{1\textwidth}{

 Structure Z-scores, positive is better than average:

\begin{tabular}{lrc}
  1st generation packing quality :&   0.5\\
  2nd generation packing quality :&  -0.8\\
  Ramachandran plot appearance   :&  -0.8\\
  $\chi$-1/$\chi$-2 rotamer normality  :&  -1.4\\
  Backbone conformation          :&  -0.4\\
\end{tabular}

 RMS Z-scores, should be close to 1.0:

\begin{tabular}{lrc}
  Bond lengths                   :&   1.124\\
  Bond angles                    :&   1.285\\
  Omega angle restraints         :&   0.685& (tight)\\
  Side chain planarity           :&   0.842\\
  Improper dihedral distribution :&   1.110\\
  Inside/Outside distribution    :&   1.012\\
\end{tabular}
}% End of ParBox

\end{note}


% $Id: TRAILER.TEX 7325 2010-07-20 18:10:35Z vriend $
%
\appendix
\section{References}
\raggedright

\begin{description}

\item [WHAT IF]

G.Vriend,
{\em WHAT IF: a molecular modelling and drug design program}
J. Mol. Graph. {\bf 8} 52--56 (1990).

\item [WHAT\_CHECK (verification routines from WHAT IF)]

R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
{\em Errors in protein structures}
Nature {\bf 381}, 272 (1996).
(see http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra information)

\item [Bond lengths and angles, protein residues]

R.Engh and R.Huber,
{\em Accurate bond and angle parameters for X-ray protein structure refinement}
Acta Crystallogr. {\bf A47}, 392--400 (1991).

\item [Bond lengths and angles, DNA/RNA]

G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Br\"unger and H.Berman,
{\em New parameters for the refinement of nucleic acid-containing structures}
Acta Crystallogr. {\bf D52}, 57--64 (1996).

\item [DSSP]

W.Kabsch and C.Sander,
{\em Dictionary of protein secondary structure: pattern
     recognition of hydrogen bond and geometrical features}
Biopolymers {\bf 22}, 2577--2637 (1983).

\item [Hydrogen bond networks]

R.W.W.Hooft, C.Sander and G.Vriend,
{\em Positioning hydrogen atoms by optimizing hydrogen bond networks in
protein structures}
PROTEINS, {\bf 26}, 363--376 (1996).

\item [Matthews' Coefficient]

B.W.Matthews,
{\em Solvent Content of Protein Crystals}
J. Mol. Biol, {\bf 33}, 491--497 (1968).

\item [Protein side chain planarity]

R.W.W. Hooft, C. Sander and G. Vriend,
{\em Verification of protein structures: side-chain planarity}
J. Appl. Cryst, {\bf 29}, 714--716 (1996).

\item [Puckering parameters]

D.Cremer and J.A.Pople,
{\em A general definition of ring puckering coordinates}
J. Am. Chem. Soc. {\bf 97}, 1354--1358 (1975).

\item [Quality Control]

G.Vriend and C.Sander,
{\em Quality control of protein models: directional atomic
     contact analysis}
J. Appl. Cryst. {\bf 26}, 47--60 (1993).

\item [Ramachandran plot]

G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan.
{\em Stereochemistry of Polypeptide Chain Conformations}
J. Mol. Biol. {\bf 7} 95--99 (1963).

\item [Symmetry Checks]

R.W.W.Hooft, C.Sander and G.Vriend,
{\em Reconstruction of symmetry related molecules from protein
     data bank {(PDB)} files}
J. Appl. Cryst. {\bf 27}, 1006--1009 (1994).

\item [Ion Checks]

I.D.Brown and K.K.Wu,
{\em Empirical Parameters for Calculating Cation-Oxygen Bond Valences}
Acta Cryst. B {\bf 32}, 1957--1959 (1975).

M.Nayal and E.Di Cera,
{\em Valence Screening of Water in Protein Crystals Reveals Potential Na+
     Binding Sites}
J. Mol. Biol. {\bf 256} 228--234 (1996).

P.Mueller, S.Koepke and G.M.Sheldrick,
{\em Is the bond-valence method able to identify metal atoms in protein
     structures?}
Acta Cryst. D {\bf 59} 32--37 (2003).

\item [Checking checks]

K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
{\em Who checks the checkers}
J. Mol. Biol. {\bf 276} 417--436 (1998).

\end{description}
\end{document}
