************************************************************************ ********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program ********** ************************************************************************ Date : 2006-02-04 This report was created by WHAT IF version 20030529-0952 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 /u/lytle/at5g39720/9valid/77/refined_input/refine====.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 # Note: Tyrosine torsion conventions OK No errors were detected in tyrosine torsion angle conventions. # 10 # Warning: Phenylalanine convention problem The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0. 21 PHE ( 21 ) 127 PHE ( 127 ) 143 PHE ( 143 ) 147 PHE ( 147 ) # 11 # Warning: Aspartic acid convention problem The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2. 13 ASP ( 13 ) 28 ASP ( 28 ) 30 ASP ( 30 ) 37 ASP ( 37 ) 82 ASP ( 82 ) 106 ASP ( 106 ) 172 ASP ( 172 ) # 12 # Warning: Glutamic acid convention problem The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2. 9 GLU ( 9 ) 41 GLU ( 41 ) 67 GLU ( 67 ) 70 GLU ( 70 ) 83 GLU ( 83 ) 85 GLU ( 85 ) 105 GLU ( 105 ) 109 GLU ( 109 ) 129 GLU ( 129 ) 134 GLU ( 134 ) 152 GLU ( 152 ) 171 GLU ( 171 ) # 13 # Warning: Heavy atom naming problem The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometomes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Swapped OP1 and OP2 on nucleic acid phosphors also are reported elsewhere). 173 GLN ( 173 ) O <--> O2 # 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. 8 LEU ( 8 ) C -6.4 -2.3 0.0 9 GLU ( 9 ) C -5.4 -2.0 0.0 11 SER ( 11 ) C -4.6 -1.5 0.1 13 ASP ( 13 ) CA -8.9 28.3 34.1 13 ASP ( 13 ) C -5.0 -2.0 0.0 14 SER ( 14 ) CA 4.5 36.3 34.4 14 SER ( 14 ) C -4.2 -1.4 0.1 15 LEU ( 15 ) CA -12.8 30.0 34.5 15 LEU ( 15 ) C -7.5 -2.7 0.0 15 LEU ( 15 ) CG 19.0 -31.4 -33.9 16 GLN ( 16 ) C -5.6 -2.1 0.0 17 LEU ( 17 ) CA -8.9 31.3 34.5 19 ASN ( 19 ) CA -5.5 30.6 34.0 24 GLY ( 24 ) C 5.1 1.6 0.1 36 LEU ( 36 ) CA -12.1 30.2 34.5 36 LEU ( 36 ) C 8.1 2.8 0.0 36 LEU ( 36 ) CG -12.1 -35.4 -33.9 38 ARG ( 38 ) CA -5.9 31.4 34.2 40 PRO ( 40 ) C -4.9 -1.8 0.0 42 ILE ( 42 ) CB 4.2 34.3 33.2 43 VAL ( 43 ) CB 6.1 -32.2 -33.7 44 SER ( 44 ) C -4.7 -1.6 0.1 47 LEU ( 47 ) C -5.3 -1.9 0.0 53 PHE ( 53 ) CA -5.0 31.2 34.2 54 ARG ( 54 ) CA 6.4 37.3 34.2 55 LEU ( 55 ) C -5.7 -2.1 0.0 55 LEU ( 55 ) CG 9.2 -32.7 -33.9 56 LYS ( 56 ) CA -13.7 28.5 34.3 56 LYS ( 56 ) C -5.2 -1.8 0.0 59 LEU ( 59 ) CA -9.6 31.1 34.5 68 LYS ( 68 ) CA -15.8 27.7 34.3 68 LYS ( 68 ) C -5.2 -1.9 0.0 74 LYS ( 74 ) CA 4.5 36.2 34.3 76 LEU ( 76 ) CA 5.6 36.4 34.5 76 LEU ( 76 ) CG 5.7 -33.2 -33.9 77 MET ( 77 ) CA -6.6 31.2 34.2 79 VAL ( 79 ) CB 6.2 -32.2 -33.7 84 LEU ( 84 ) CG 11.0 -32.5 -33.9 93 ASN ( 93 ) CA -6.4 30.0 34.0 98 VAL ( 98 ) CA -4.0 31.8 33.8 104 ARG ( 104 ) C 4.1 1.6 0.0 108 SER ( 108 ) CA -8.8 30.5 34.4 108 SER ( 108 ) C -7.7 -2.6 0.1 112 ALA ( 112 ) CA -4.6 33.3 34.3 114 LYS ( 114 ) CA -4.3 32.5 34.3 117 MET ( 117 ) CA -13.2 28.3 34.2 117 MET ( 117 ) C -4.7 -1.7 -0.1 121 LYS ( 121 ) CA -7.0 31.4 34.3 124 PRO ( 124 ) CA 4.2 39.4 37.8 130 TRP ( 130 ) CA 4.2 37.0 34.3 134 GLU ( 134 ) C 7.4 2.7 0.0 136 LYS ( 136 ) CA -17.3 27.1 34.3 137 ARG ( 137 ) CA -10.0 29.4 34.2 138 LEU ( 138 ) CG 5.9 -33.1 -33.9 147 PHE ( 147 ) CA -11.5 27.4 34.2 148 LYS ( 148 ) CA -6.4 31.6 34.3 148 LYS ( 148 ) C 5.9 2.0 0.0 154 LYS ( 154 ) C 7.6 2.6 0.0 161 GLY ( 161 ) C -4.9 -1.3 0.1 163 ASP ( 163 ) C -8.3 -3.3 0.0 164 ASP ( 164 ) C -4.5 -1.8 0.0 166 SER ( 166 ) C -4.9 -1.6 0.1 169 LEU ( 169 ) C -4.3 -1.6 0.0 # 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 : 4.912 # 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 # 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]) # 22 # 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: 0.750 RMS-deviation in bond distances: 0.015 # 23 # 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. # 24 # 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. 2 HIS ( 2 ) CG ND1 CE1 109.603 4.0 5 HIS ( 5 ) CG ND1 CE1 109.721 4.1 18 HIS ( 18 ) CG ND1 CE1 109.776 4.2 37 ASP ( 37 ) CA CB CG 116.799 4.2 167 HIS ( 167 ) CG ND1 CE1 109.695 4.1 # 25 # Note: Normal bond angle variability Bond angles were found to deviate normally from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be around 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. More common values are around 1.55. RMS Z-score for bond angles: 0.755 RMS-deviation in bond angles: 1.307 # 26 # Note: Side chain planarity OK All of the side chains of residues that have a planar group are planar within expected RMS deviations. # 27 # 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. # 28 # Note: PRO puckering amplitude OK Puckering amplitudes for all PRO residues are within normal ranges. # 29 # 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. 61 PRO ( 61 ) -147.1 envelop C-delta (-144 degrees) 124 PRO ( 124 ) -63.0 half-chair C-beta/C-alpha (-54 degrees) # 30 # 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. 61 PRO ( 61 ) -2.6557 68 LYS ( 68 ) -2.4290 124 PRO ( 124 ) -2.4076 115 THR ( 115 ) -2.3860 55 LEU ( 55 ) -2.2252 57 GLY ( 57 ) -2.1535 108 SER ( 108 ) -2.1005 24 GLY ( 24 ) -2.0877 102 ILE ( 102 ) -2.0391 # 31 # 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. 13 ASP ( 13 ) Poor phi/psi 48 PRO ( 48 ) Poor PRO-phi 61 PRO ( 61 ) Poor PRO-phi 108 SER ( 108 ) Poor phi/psi 121 LYS ( 121 ) Poor phi/psi 124 PRO ( 124 ) Poor PRO-phi # 32 # Warning: Ramachandran Z-score low The score expressing how well the backbone conformations of all residues are corresponding to the known allowed areas in the Ramachandran plot is a bit low. Ramachandran Z-score : -3.275 # 33 # Warning: Omega angles too tightly restrained The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly constrained. This seems to be the case with the current structure, as the observed standard deviation is below 4.0 degrees. Standard deviation of omega values : 3.400 # 34 # Note: chi-1/chi-2 angle correlation Z-score OK The score expressing how well the chi-1/chi-2 angles of all residues are corresponding to the populated areas in the database is within expected ranges for well-refined structures. chi-1/chi-2 correlation Z-score : -1.377 # 35 # 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. In the TeX file, a plot has been inserted here Chain without chain identifier # 36 # 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 : 1.136 # 37 # 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 without chain identifier # 38 # Note: Secondary structure This is the secondary structure according to DSSP. Only helix (H), strand (S), turn (T) and coil (blank) are shown. [REF] Secondary structure assignment 10 20 30 40 50 60 | | | | | | 1 - 60 GHHHHHHLECSSDSLQLHNVFVYGSFQDPDVINVMLDRTPEIVSATLPGFQRFRLKGRLY 1 - 60 T SSSSSTTTTT HHHHHHHTTT SSSSSSSSSSSSS TTT 70 80 90 100 110 120 | | | | | | 61 - 120 PCIVPSEKGEVHGKVLMGVTSDELENLDAVEGNEYERVTVGIVREDNSEKMAVKTYMWIN 61 - 120 SSSSSSSSSSSSSSSSSS HHHHHHHHHHHTTTSSSSSSSSSSTTTTSSSSSSSSSSTT 130 140 150 160 170 | | | | | 121 - 173 KADPDMFGEWNFEEWKRLHKKKFIETFKKIMECKKKPQGQGNDDISHVLREDQ 121 - 173 TTT HHHHHHHHHHHHHHHHHHHHHHHHTT # 39 # Error: Abnormally short interatomic distances The pairs of atoms listed in the table below have an unusually short distance. The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centers of the two atoms. 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. 62 CYS ( 62 ) SG -- 126 MET ( 126 ) SD 0.325 3.275 INTRA BF 59 LEU ( 59 ) CG -- 60 TYR ( 60 ) N 0.141 2.959 INTRA BF 104 ARG ( 104 ) CD -- 111 MET ( 111 ) SD 0.080 3.320 INTRA 23 TYR ( 23 ) CG -- 24 GLY ( 24 ) N 0.055 3.045 INTRA BF 105 GLU ( 105 ) N -- 106 ASP ( 106 ) N 0.048 2.552 INTRA BF 52 ARG ( 52 ) NH2 -- 133 GLU ( 133 ) CD 0.045 3.055 INTRA BF 53 PHE ( 53 ) CB -- 62 CYS ( 62 ) SG 0.041 3.359 INTRA BF 107 ASN ( 107 ) N -- 108 SER ( 108 ) N 0.026 2.574 INTRA B3 36 LEU ( 36 ) CG -- 37 ASP ( 37 ) N 0.014 3.086 INTRA BF 35 MET ( 35 ) CE -- 86 ASN ( 86 ) ND2 0.006 3.094 INTRA BF 12 SER ( 12 ) N -- 13 ASP ( 13 ) N 0.001 2.599 INTRA BF # 40 # 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. 170 ARG ( 170 ) -7.15 60 TYR ( 60 ) -7.08 38 ARG ( 38 ) -6.37 68 LYS ( 68 ) -6.33 58 ARG ( 58 ) -6.23 56 LYS ( 56 ) -6.19 2 HIS ( 2 ) -6.19 158 GLN ( 158 ) -5.79 67 GLU ( 67 ) -5.73 160 GLN ( 160 ) -5.60 27 GLN ( 27 ) -5.42 127 PHE ( 127 ) -5.23 # 41 # Warning: Abnormal packing environment for sequential residues A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop, but might also be an indication of misthreading. The table below lists the first and last residue in each stretch found, as well as the average residue score of the series. 158 GLN ( 158 ) --- 160 GLN ( 160 ) -5.24 # 42 # Warning: Structural average packing environment a bit worrysome The structural average quality control value is a bit low. The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average quality of 200 highly refined Xray structures was -0.5+/-0.4 [REF]. Average for range 1 - 173 : -1.419 # 43 # 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 without chain identifier # 44 # Warning: Low packing Z-score for some residues The residues listed in the table below have an unusual packing environment according to the 2nd generation quality check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the "unusual" residues in the structure, so it will be interesting to take a special look at them. 36 LEU ( 36 ) -2.53 # 45 # 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. # 46 # Note: Structural average packing Z-score OK The structural average for the second generation quality control value is within normal ranges. All contacts : Average = -0.511 Z-score = -2.62 BB-BB contacts : Average = -0.333 Z-score = -2.04 BB-SC contacts : Average = -0.344 Z-score = -2.04 SC-BB contacts : Average = -0.533 Z-score = -3.24 SC-SC contacts : Average = -0.349 Z-score = -1.65 # 47 # 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 without chain identifier # 48 # Warning: Backbone oxygen evaluation The residues listed in the table below have an unusual backbone oxygen position. For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some constraints on the neighboring backbone oxygens. In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking! 54 ARG ( 54 ) 3.24 30 4 HIS ( 4 ) 2.85 48 19 ASN ( 19 ) 2.76 38 18 HIS ( 18 ) 2.71 53 17 LEU ( 17 ) 2.70 80 5 HIS ( 5 ) 2.69 47 125 ASP ( 125 ) 2.49 32 51 GLN ( 51 ) 2.46 40 70 GLU ( 70 ) 2.44 26 42 ILE ( 42 ) 2.42 80 90 VAL ( 90 ) 2.29 35 52 ARG ( 52 ) 2.09 80 146 THR ( 146 ) 2.05 19 22 VAL ( 22 ) 2.03 16 147 PHE ( 147 ) 1.97 32 136 LYS ( 136 ) 1.93 77 55 LEU ( 55 ) 1.89 25 153 CYS ( 153 ) 1.81 80 63 ILE ( 63 ) 1.81 80 139 HIS ( 139 ) 1.67 80 144 ILE ( 144 ) 1.64 27 171 GLU ( 171 ) 1.57 17 116 TYR ( 116 ) 1.51 26 # 49 # 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. 96 GLU ( 96 ) 0.39 # 50 # 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! 13 ASP ( 13 ) 0 23 TYR ( 23 ) 0 36 LEU ( 36 ) 0 37 ASP ( 37 ) 0 56 LYS ( 56 ) 0 68 LYS ( 68 ) 0 77 MET ( 77 ) 0 94 GLU ( 94 ) 0 106 ASP ( 106 ) 0 107 ASN ( 107 ) 0 120 ASN ( 120 ) 0 121 LYS ( 121 ) 0 154 LYS ( 154 ) 0 155 LYS ( 155 ) 0 158 GLN ( 158 ) 0 12 SER ( 12 ) 1 16 GLN ( 16 ) 1 58 ARG ( 58 ) 1 60 TYR ( 60 ) 1 156 LYS ( 156 ) 1 164 ASP ( 164 ) 1 10 CYS ( 10 ) 2 15 LEU ( 15 ) 2 25 SER ( 25 ) 2 38 ARG ( 38 ) 2 108 SER ( 108 ) 2 117 MET ( 117 ) 2 127 PHE ( 127 ) 2 # 51 # Error: Backbone conformation Z-score very low A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is very unusual. Backbone conformation Z-score : -9.843 # 52 # Warning: Average B-factor problem 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. Because of the extreme value for the average B-factor, no further analysis of the B-factors is performed. Average B-factor for buried atoms : 39.551 # 53 # 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 without chain identifier # 54 # 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. 5 HIS ( 5 ) 16 GLN ( 16 ) 19 ASN ( 19 ) 93 ASN ( 93 ) # 55 # Note: Histidine type assignments For all complete HIS residues in the structure a tentative assignment to HIS-D (protonated on ND1), HIS-E (protonated on NE2), or HIS-H (protonated on both ND1 and NE2, positively charged) is made based on the hydrogen bond network. A second assignment is made based on which of the Engh and Huber [REF] histidine geometries fits best to the structure. In the table below all normal histidine residues are listed. The assignment based on the geometry of the residue is listed first, together with the RMS Z-score for the fit to the Engh and Huber parameters. For all residues where the H-bond assignment is different, the assignment is listed in the last columns, together with its RMS Z-score to the Engh and Huber parameters. As always, the RMS Z-scores should be close to 1.0 if the residues were restrained to the Engh and Huber parameters during refinement. Please note that because the differences between the geometries of the different types are small it is possible that the geometric assignment given here does not correspond to the type used in refinement. This is especially true if the RMS Z-scores are much higher than 1.0. If the two assignments differ, or the ``geometry'' RMS Z-score is high, it is advisable to verify the hydrogen bond assignment, check the HIS type used during the refinement and possibly adjust it. 2 HIS ( 2 ) HIS-H 0.77 HIS-E 0.82 3 HIS ( 3 ) HIS-H 0.43 HIS-E 0.70 4 HIS ( 4 ) HIS-H 0.43 HIS-E 0.70 5 HIS ( 5 ) HIS-H 0.81 HIS-D 0.97 6 HIS ( 6 ) HIS-H 0.57 HIS-E 0.78 7 HIS ( 7 ) HIS-H 0.79 HIS-E 0.85 18 HIS ( 18 ) HIS-E 0.77 HIS-D 0.97 72 HIS ( 72 ) HIS-H 0.39 HIS-D 0.72 139 HIS ( 139 ) HIS-H 0.59 HIS-E 0.81 167 HIS ( 167 ) HIS-H 0.68 HIS-E 0.78 # 56 # 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. 7 HIS ( 7 ) N 23 TYR ( 23 ) N 24 GLY ( 24 ) N 26 PHE ( 26 ) N 37 ASP ( 37 ) N 38 ARG ( 38 ) N 59 LEU ( 59 ) N 60 TYR ( 60 ) N 63 ILE ( 63 ) N 72 HIS ( 72 ) N 82 ASP ( 82 ) N 104 ARG ( 104 ) NE 107 ASN ( 107 ) N 116 TYR ( 116 ) OH 127 PHE ( 127 ) N 130 TRP ( 130 ) N 158 GLN ( 158 ) N 162 ASN ( 162 ) N 164 ASP ( 164 ) N # 57 # 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. # 58 # Note: Summary report for users of a structure This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations. The second part of the table mostly gives an impression of how well the model conforms to common refinement constraint values. The first part of the table shows a number of constraint-independent quality indicators. Structure Z-scores, positive is better than average: 1st generation packing quality : -2.297 2nd generation packing quality : -2.621 Ramachandran plot appearance : -3.275 (poor) chi-1/chi-2 rotamer normality : -1.377 Backbone conformation : -9.843 (bad) RMS Z-scores, should be close to 1.0: Bond lengths : 0.750 Bond angles : 0.755 Omega angle restraints : 0.618 (tight) Side chain planarity : 0.557 (tight) Improper dihedral distribution : 4.912 (loose) Inside/Outside distribution : 1.136 REFERENCES ========== WHAT IF G.Vriend, WHAT IF: a molecular modelling and drug design program, J. Mol. Graph. 8, 52--56 (1990). WHAT_CHECK (verification routines from WHAT IF) R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola, Errors in protein structures Nature 381, 272 (1996). Bond lengths and angles, protein residues R.Engh and R.Huber, Accurate bond and angle parameters for X-ray protein structure refinement, Acta Crystallogr. A47, 392--400 (1991). Bond lengths and angles, DNA/RNA G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman, New parameters for the refinement of nucleic acid-containing structures Acta Crystallogr. D52, 57--64 (1996). DSSP W.Kabsch and C.Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen bond and geometrical features Biopolymers 22, 2577--2637 (1983). Hydrogen bond networks R.W.W.Hooft, C.Sander and G.Vriend, Positioning hydrogen atoms by optimizing hydrogen bond networks in protein structures PROTEINS, 26, 363--376 (1996). Matthews' Coefficient B.W.Matthews Solvent content of Protein Crystals J. Mol. Biol. 33, 491--497 (1968). Protein side chain planarity R.W.W. Hooft, C. Sander and G. Vriend, Verification of protein structures: side-chain planarity J. Appl. Cryst. 29, 714--716 (1996). Puckering parameters D.Cremer and J.A.Pople, A general definition of ring puckering coordinates J. Am. Chem. Soc. 97, 1354--1358 (1975). Quality Control G.Vriend and C.Sander, Quality control of protein models: directional atomic contact analysis, J. Appl. Cryst. 26, 47--60 (1993). Ramachandran plot G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan, Stereochemistry of Polypeptide Chain Conformations J. Mol. Biol. 7, 95--99 (1963). Symmetry Checks R.W.W.Hooft, C.Sander and G.Vriend, Reconstruction of symmetry related molecules from protein data bank (PDB) files J. Appl. Cryst. 27, 1006--1009 (1994).