\documentstyle[epsfig,supertab]{article} %%%% % $Id: HEADER.TEX,v 1.5 1997/06/12 12:30:42 hooft Exp $ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % 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=6.0cm}} \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{1998-09-26% \footnote{This report was created by WHAT IF version 19980925-1713}} \maketitle \section{Introduction} This document contains a report of findings by the {\sc what if} program during the analysis of one or more proteins. It contains a separate section for each of the proteins that have been analysed. Each reported fact has an assigned severity, one of: \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 by all checks. \subsection{legend} Some notations need a little explanation: \begin{description} \item[Residue] Residues in tables are normally given in 3--5 parts: \begin{itemize} \item A number. This is the internal sequence number of the residue used by WHAT IF. \item The residue name. Normally this is a three letter amino acid name. \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 invisible. \item A model number (only for NMR structures). \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. \end{description} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % End of the preface, start of WHAT IF generated output %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \sect{jingchu2.pdb} \ssect{Symmetry related problems} \begin{warning} \showsect{Warning: Class of space group could be incorrect} The space group symbol indicates a different class than the unit cell given on the CRYST1 card of the PDB file. Possible cause: The unit cell may have pseudo-symmetry, or one of the cell dimensions or the space group might be given incorrectly. \parbox{1\textwidth}{ Crystal class of the cell: CUBIC }% End of ParBox \parbox{1\textwidth}{ Crystal class of the space group: TRICLINIC }% End of ParBox \parbox{1\textwidth}{ Space group name: P 1 }% End of ParBox \end{warning} \ssect{Atom coordinate problems and/or unexpected atoms} \begin{note} \showsect{Note: No rounded coordinates detected} No significant rounding of atom coordinates has been detected. \end{note} \ssect{Symmetry related problems} \begin{error} \showsect{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. \parbox{1\textwidth}{ Molecular weight of all polymer chains: 3909.396 Volume of the Unit Cell V= 0.1000E+10 Cell multiplicity: 0 Matthews coefficient for observed atoms Vm= 255793.922 }% End of ParBox \end{error} \ssect{Nomenclature related problems} \begin{note} \showsect{Note: Valine nomenclature OK} No errors were detected in valine nomenclature. \end{note} \begin{note} \showsect{Note: Isoleucine nomenclature OK} No errors were detected in isoleucine 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: Heavy atom naming OK} No errors were detected in the atom names for non-hydrogen atoms. \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 : 0.754 }% End of ParBox \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} \begin{note} \showsect{Note: Weights checked OK} All atomic occupancy factors ('weights') fall in the 0.0--1.0 range. \end{note} \ssect{Geometric checks} \begin{note} \showsect{Note: No missing atoms detected} All expected atoms are present. \end{note} \begin{note} \showsect{Note: OXT check OK} All required C-terminal oxygen atoms are present. \end{note} \begin{note} \showsect{Note: No extra C-terminal groups found} No C-terminal groups are present for non C-terminal residues \end{note} \begin{note} \showsect{Note: All bond lengths OK} All bond lengths are in agreement with standard bond lengths using a tolerance of 4 sigma (both standard values and sigma for amino acid residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]) \end{note} \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: 0.868 RMS-deviation in bond distances: 0.019 }% End of ParBox \end{note} \begin{note} \showsect{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. \end{note} \begin{note} \showsect{Note: All bond angles OK} All bond angles are in agreement with standard bond angles using a tolerance of 4 sigma (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al. [REF]). Please note that disulphide bridges are neglected. \end{note} \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. More common values are around 1.55. \parbox{1\textwidth}{ RMS Z-score for bond angles: 1.001 RMS-deviation in bond angles: 1.970 }% 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} \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. \begin{center}\begin{supertabular}{rl@{ (}r@{}c@{) }l@{}rrl} \multicolumn{6}{c}{Residue} & Amplitude & Qualifier \\ \hline 16&PRO & 16& & && 0.47&HIGH\\ \end{supertabular}\end{center} \end{warning} \begin{warning} \showsect{Warning: Unusual PRO puckering phases} The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-$\gamma$ atom above the plane of the ring ($\phi$=+72 degrees), or a half-chair conformation with C-$\gamma$ below and C-$\beta$ above the plane of the ring ($\phi$=-90 degrees). If $\phi$ deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. \begin{center}\begin{supertabular}{rl@{ (}r@{}c@{) }l@{}rrl} \multicolumn{6}{c}{Residue} & Pucker Phase & Conformation \\ \hline 16&PRO & 16& & && -22.1&half-chair C-$\alpha$/N (-18 degrees)\\ 17&PRO & 17& & && 40.0&envelop C-$\delta$ (36 degrees)\\ \end{supertabular}\end{center} \end{warning} \begin{warning} \showsect{Warning: Torsion angle evaluation shows unusual residues} The residues listed in the table below contain bad or abnormal torsion angles. These scores give an impression of how ``normal'' the torsion angles in protein residues are. All torsion angles except $\omega$ are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position. \begin{center}\begin{supertabular}{rl@{ (}r@{}c@{) }l@{}rr} \multicolumn{6}{c}{Residue} & Z-Score \\ \hline 36&ILE & 36& & &&-2.4872\\ 25&PHE & 25& & &&-2.4324\\ 22&SER & 22& & &&-2.3914\\ 31&SER & 31& & &&-2.2629\\ 17&PRO & 17& & &&-2.0965\\ 16&PRO & 16& & &&-2.0250\\ \end{supertabular}\end{center} \end{warning} \begin{warning} \showsect{Warning: Backbone torsion angle evaluation shows unusual conformations} The residues listed in the table below have abnormal backbone torsion angles. Residues with ``forbidden'' $\phi$-$\psi$ combinations are listed, as well as residues with unusual $\omega$ angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual $\phi$-$\psi$ combinations. \begin{center}\begin{supertabular}{rl@{ (}r@{}c@{) }l@{}rl} \multicolumn{6}{c}{Residue} & Description \\ \hline 14&ALA & 14& & &&Poor $\phi$/$\psi$\\ 16&PRO & 16& & &&Poor PRO-$\phi$\\ 17&PRO & 17& & &&Poor PRO-$\phi$\\ 22&SER & 22& & &&Poor $\phi$/$\psi$\\ 31&SER & 31& & &&Poor $\phi$/$\psi$\\ \end{supertabular}\end{center} \end{warning} \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 : -2.797 }% End of ParBox \end{note} \begin{note} \showsect{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. \parbox{1\textwidth}{ Standard deviation of $\omega$ values : 4.285 }% End of ParBox \end{note} \begin{error} \showsect{Error: chi-1/chi-2 angle correlation Z-score very low} The score expressing how well the $\chi$-1/$\chi$-2 angles of all residues are corresponding to the populated areas in the database is very low. \parbox{1\textwidth}{ $\chi$-1/$\chi$-2 correlation Z-score : -4.088 }% End of ParBox \end{error} \begin{note} \showsect{Note: Ramachandran plot} In this Ramachandran plot X-signs represent glycines, squares represent prolines and small plus-signs represent the other residues. If too many plus-signs fall outside the contoured areas then the molecule is poorly refined (or worse). In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. "Allowed" regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. \parbox{1\textwidth}{ \psplot{eps0001.eps} }% End of ParBox \parbox{1\textwidth}{ \hdr{Chain without chain identifier} }% End of ParBox \end{note} \ssect{Accessibility related checks} \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 : 0.905 }% 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}{ \psplot{sct0001.eps} }% End of ParBox \parbox{1\textwidth}{ \hdr{Chain without chain identifier} }% End of ParBox \end{note} \ssect{Secondary structure} \begin{note} \showsect{Note: Secondary structure} This is the secondary structure according to DSSP. Only helix (H), strand (S), turn (T) and coil (blank) are shown. [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} \multicolumn{10}{r@{}}{ 10}& \multicolumn{10}{r@{}}{ 20}& \multicolumn{10}{r@{}}{ 30}& \\ A&G&C&I&K&N&G&G&R&C&N&A&S&A&G&P&P&Y&C&C&S&S&Y&C&F&Q&I&A&G&Q&S&Y&G&V&C&I&N&R \\ & &T& & &T&T&T& & & & & &T&T&T& & & &T&T&T& &S&S&S& &T&T&T& & &S&S&S& & & \\ \end{tabular}} \end{note} \ssect{Bump checks} \begin{error} \showsect{Error: Abnormally short interatomic distances} The pairs of atoms listed in the table below have an unusually short distance. The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 {\AA}. For hydrogen bonded pairs a tolerance of 0.55 {\AA} is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centers of the two atoms. The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterium was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1--3 and 1--4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably aren't there anyway. Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. \begin{center}\begin{supertabular}{rl@{ (}r@{}c@{) }l@{}rl@{ -- }rl@{ (}r@{}c@{) }l@{}rlrrll} \multicolumn{7}{c}{Atom 1} & \multicolumn{7}{c}{Atom 2} & Bump & Dist & \multicolumn{2}{c}{Status} \\ \hline 6&ASN & 6& & & & CB & 37&ASN & 37& & & & CB & 0.874& 2.326&INTRA&\\ 13&SER & 13& & & & O & 16&PRO & 16& & & & CD & 0.770& 2.030&INTRA&\\ 34&VAL & 34& & & & CG2 & 35&CYS & 35& & & & N & 0.513& 2.587&INTRA&\\ 14&ALA & 14& & & & C & 16&PRO & 16& & & & CD & 0.487& 2.713&INTRA&\\ 13&SER & 13& & & & C & 16&PRO & 16& & & & CD & 0.450& 2.750&INTRA&\\ 13&SER & 13& & & & O & 16&PRO & 16& & & & CG & 0.424& 2.376&INTRA&\\ 6&ASN & 6& & & & CG & 37&ASN & 37& & & & CB & 0.283& 2.917&INTRA&\\ 15&GLY & 15& & & & N & 16&PRO & 16& & & & CD & 0.283& 2.717&INTRA&\\ 10&CYS & 10& & & & SG & 34&VAL & 34& & & & O & 0.259& 2.741&INTRA&\\ 30&GLN & 30& & & & O & 31&SER & 31& & & & CB & 0.167& 2.633&INTRA&\\ 6&ASN & 6& & & & CB & 37&ASN & 37& & & & CA & 0.163& 3.037&INTRA&\\ 25&PHE & 25& & & & CG & 26&GLN & 26& & & & N & 0.089& 3.011&INTRA&\\ 18&TYR & 18& & & & O & 19&CYS & 19& & & & C & 0.060& 2.740&INTRA&\\ 10&CYS & 10& & & & SG & 34&VAL & 34& & & & C & 0.044& 3.356&INTRA&\\ 10&CYS & 10& & & & CB & 19&CYS & 19& & & & SG & 0.038& 3.362&INTRA&\\ 10&CYS & 10& & & & SG & 19&CYS & 19& & & & SG & 0.027& 3.573&INTRA&\\ 21&SER & 21& & & & N & 22&SER & 22& & & & N & 0.018& 2.582&INTRA&B3\\ 5&LYS & 5& & & & O & 6&ASN & 6& & & & C & 0.007& 2.793&INTRA&\\ \end{supertabular}\end{center} \end{error} \ssect{3D-database related checks} \begin{warning} \showsect{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. \begin{center}\begin{supertabular}{rl@{ (}r@{}c@{) }l@{}rr} \multicolumn{6}{c}{Residue} & Qualty value \\ \hline 18&TYR & 18& & && -6.57\\ 37&ASN & 37& & && -5.03\\ 5&LYS & 5& & && -5.02\\ \end{supertabular}\end{center} \end{warning} \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{error} \showsect{Error: Abnormal average packing environment} The average quality control value for the structure is very low. A molecule is certain to be incorrect if the average quality score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average quality of 200 highly refined Xray structures was -0.5$\pm$0.4 [REF]. \parbox{1\textwidth}{ Average for range 1 - 38 : -2.889 }% End of ParBox \end{error} \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}{ \psplot{sct0002.eps} }% End of ParBox \parbox{1\textwidth}{ \hdr{Chain without chain identifier} }% 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 = -0.444 Z-score = -2.79 BB-BB contacts : Average = 0.325 Z-score = 2.34 BB-SC contacts : Average = -0.866 Z-score = -4.68 SC-BB contacts : Average = 0.010 Z-score = 0.23 SC-SC contacts : Average = -0.660 Z-score = -3.32 }% 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}{ \psplot{sct0003.eps} }% End of ParBox \parbox{1\textwidth}{ \hdr{Chain without chain identifier} }% 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 neighboring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the center. For this check, backbone conformations are compared with database structures using C-$\alpha$ superpositions with some restraints on the backbone oxygen positions. A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at! \begin{center}\begin{supertabular}{rl@{ (}r@{}c@{) }l@{}rr} \multicolumn{6}{c}{Residue} & \# hits \\ \hline 16&PRO & 16& & && 0\\ 3&CYS & 3& & && 1\\ 14&ALA & 14& & && 1\\ 18&TYR & 18& & && 1\\ 30&GLN & 30& & && 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 : 6.298 }% End of ParBox \end{note} \ssect{B-factor analysis} \begin{warning} \showsect{Warning: Average B-factor out of normal range} The average B-factor for all buried protein atoms normally lies between 10--20. Values around 3--5 are expected for X-ray studies performed at liquid nitrogen temperature. \parbox{1\textwidth}{ Average B-factor for buried atoms : 3.787 }% End of ParBox \end{warning} \begin{warning} \showsect{Warning: More than 5\% 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, constaints 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 : 74.67 }% 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}{ \psplot{sct0004.eps} }% End of ParBox \parbox{1\textwidth}{ \hdr{Chain without chain identifier} }% End of ParBox \end{note} \ssect{Hydrogen bond related checks} \begin{error} \showsect{Error: HIS, ASN, GLN side chain flips} Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favorable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. If a residue is marked ``flexible'' the flipped conformation is only slightly better than the non-flipped conformation. \begin{center}\begin{supertabular}{rl@{ (}r@{}c@{) }l@{}rll} \multicolumn{6}{c}{Residue} \\ \hline 26&GLN & 26& & &\\ 37&ASN & 37& & &\\ \end{supertabular}\end{center} \end{error} \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. \begin{center}\begin{supertabular}{rl@{ (}r@{}c@{) }l@{}rl} \multicolumn{6}{c}{Residue} & Atom \\ \hline 4&ILE & 4& & & & N\\ 6&ASN & 6& & & & N\\ 11&ASN & 11& & & & N\\ 19&CYS & 19& & & & N\\ 22&SER & 22& & & & N\\ 26&GLN & 26& & & & N\\ 30&GLN & 30& & & & N\\ 32&TYR & 32& & & & 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} \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 constraint values. The first part of the table shows a number of constraint-independent quality indicators. \parbox{1\textwidth}{ Structure Z-scores, positive is better than average: \begin{tabular}{lrc} 1st generation packing quality :& -5.972& (poor)\\ 2nd generation packing quality :& -2.785\\ Ramachandran plot appearance :& -2.797\\ $\chi$-1/$\chi$-2 rotamer normality :& -4.088& (bad)\\ Backbone conformation :& 6.298\\ \end{tabular} RMS Z-scores, should be close to 1.0: \begin{tabular}{lrc} Bond lengths :& 0.868\\ Bond angles :& 1.001\\ Omega angle restraints :& 0.779\\ Side chain planarity :& 0.050& (tight)\\ Improper dihedral distribution :& 0.754\\ Inside/Outside distribution :& 0.905\\ \end{tabular} }% End of ParBox \end{note} % $Id: TRAILER.TEX,v 1.12 1997/04/08 09:56:22 hooft Exp $ % % If this file is changed, please make corresponding changes in the % CheckServer file "~/html/whatifrefs.html" % \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). \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). \end{description} \end{document}