From: swissmodel@unibas.ch Sent: Wednesday, November 12, 2003 3:44 PM To: Kathrin_Schrick@kgi.edu Subject: SwissModel WhatCheck AAAa0DOdN Batch.0 ------------------------------------------------------------- WhatCheck Report generated for your SWISS MODEL request Project: AAAa0DOdN AC code: Model: Batch.0.pdb For details about the WhatCheck output, please see: http://www.cmbi.kun.nl/gv/checkhelp/ ------------------------------------------------------------- ************************************************************************ ********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program ********** ************************************************************************ Date : 2003-11-12 This report was created by WHAT IF version 19970813-1517 INTRODUCTION ------------ This document contains a report of findings by the 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: * error: severe errors encountered during the analyses. 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 by all checks. Legend ------ Some notations need a little explanation: RESIDUE: Residues in tables are normally given in 3-5 parts: - A number. This is the internal sequence number of the residue used by WHAT IF. - The residue name. Normally this is a three letter amino acid name. - 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 invisible. - A model number (only for NMR structures). 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. ======================================================================== ==== Compound code Model.pdb ==== ======================================================================== # 1 # Error: Missing unit cell information No SCALE matrix is given in the PDB file. # 2 # Error: Missing symmetry information Problem: No CRYST1 card is given in the PDB file. # 3 # Note: No rounded coordinates detected No significant rounding of atom coordinates has been detected. # 4 # Note: Valine nomenclature OK No errors were detected in valine nomenclature. # 5 # Note: Threonine nomenclature OK No errors were detected in threonine nomenclature. # 6 # Note: Isoleucine nomenclature OK No errors were detected in isoleucine nomenclature. # 7 # Note: Leucine nomenclature OK No errors were detected in leucine nomenclature. # 8 # Note: Arginine nomenclature OK No errors were detected in arginine nomenclature. # 9 # Warning: Tyrosine convention problem The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0 123 TYR ( 135 ) # 10 # Note: Phenylalanine torsion conventions OK No errors were detected in phenylalanine torsion angle conventions. # 11 # Note: Aspartic acid torsion conventions OK No errors were detected in aspartic acid torsion angle conventions. # 12 # Note: Glutamic acid torsion conventions OK No errors were detected in glutamic acid torsion angle conventions. # 13 # Note: Heavy atom naming OK No errors were detected in the atom names for non-hydrogen atoms. # 14 # Warning: Chirality deviations detected The atoms listed in the table below have an improper dihedral value that is deviating from expected values. Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks. Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value. 11 TRP ( 23 ) C 4.2 7.6 0.1 15 ILE ( 27 ) C 4.2 7.8 -0.2 31 PRO ( 43 ) N 4.8 17.9 -1.6 42 GLY ( 54 ) C -9.6 -15.4 0.1 49 SER ( 61 ) C -5.2 -9.9 0.0 51 THR ( 63 ) CB -4.8 23.9 34.1 61 LEU ( 73 ) C 4.4 7.9 -0.1 105 THR ( 117 ) C -5.8 -11.1 -0.1 108 GLU ( 120 ) C -4.1 -7.6 0.0 118 GLY ( 130 ) C -6.0 -9.5 0.1 120 ASP ( 132 ) C -5.0 -9.0 -0.1 124 CYS ( 136 ) C -7.5 -13.5 -0.1 153 ARG ( 165 ) C 7.3 13.5 0.0 157 GLY ( 169 ) C -4.4 -7.1 0.1 161 CYS ( 173 ) CA 5.1 45.3 34.4 161 CYS ( 173 ) C 5.7 10.1 -0.1 168 GLN ( 180 ) C 8.2 14.7 -0.1 172 GLY ( 184 ) C -4.3 -6.9 0.1 184 ARG ( 196 ) C 4.4 8.1 0.0 195 ASN ( 207 ) C 4.8 8.5 -0.1 # 15 # Warning: High improper dihedral angle deviations The RMS Z-score for the improper dihedrals in the structure is high. For well refined structures this number is expected to be around 1.0. The fact that it is higher than 1.5 in this structure could be an indication of overrefinement. Improper dihedral RMS Z-score : 1.877 # 16 # Note: Chain names are OK All chain names assigned to polymer molecules are unique, and all residue numbers are strictly increasing within each chain. # 17 # Note: Weights checked OK All atomic occupancy factors ('weights') fall in the 0.0--1.0 range. # 18 # Note: No missing atoms detected All expected atoms are present. # 19 # Note: OXT check OK All required C-terminal oxygen atoms are present. # 20 # Note: No extra C-terminal groups found No C-terminal groups are present for non C-terminal residues # 21 # 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 sigma 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 "--SS", the disulphide bridge has a deviating length. 131 HIS ( 143 ) CG CD2 1.309 -4.3 150 TRP ( 162 ) CG CD2 1.349 -4.7 150 TRP ( 162 ) NE1 CE2 1.320 -4.5 150 TRP ( 162 ) CD2 CE2 1.314 -5.6 162 GLU ( 174 ) C O 1.106 -6.3 168 GLN ( 180 ) N