************************************************************************ ********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program ********** ************************************************************************ Date : 2011-05-27 This report was created by WHAT IF version 20110504-1335 This document is a WHAT_CHECK-report that holds the findings of the WHAT IF program during the analysis of a PDB-file. Each reported fact has an assigned severity, one of: error : Items marked as errors are considered severe problems requiring immediate attention. warning: Either less severe problems or uncommon structural features. These still need special attention. note : Statistical values, plots, or other verbose results of tests and analyses that have been performed. If alternate conformations are present, only the first is evaluated. Hydrogen atoms are only included if explicitly requested, and even then they are not used in all checks. The software functions less well for non-canonical amino acids and exotic ligands than for the 20 canonical residues and canonical nucleic acids. Some remarks regarding the output: Residues/atoms in tables are normally given in a few parts: A number. This is the internal sequence number of the residue used by WHAT IF. The first residues in the file get number 1, 2, etc. The residue type. Normally this is a three letter amino acid type. The sequence number, between brackets. This is the residue number as it was given in the input file. It can be followed by the insertion code. The chain identifier. A single character. If no chain identifier was given in the input file, this will be a minus sign or a blank. A model number. If no model number exists, like in most X-ray files, this will be a blank or occasionally a minus sign. In case an atom is part of the output, the atom will be listed using the PDB nomenclature for type and identifier. To indicate the normality of a score, the score may be expressed as a Z-value or Z-score. This is just the number of standard deviations that the score deviates from the expected value. A property of Z-values is that the root-mean-square of a group of Z-values (the RMS Z-value) is expected to be 1.0. Z-values above 4.0 and below $-4.0$ are very uncommon. If a Z-score is used in WHAT IF, the accompanying text will explain how the expected value and standard deviation were obtained. The names of nucleic acids are DGUA, DTHY, OCYT, OADE, etc. The first character is a D or O for DNA or RNA respectively. This circumvents ambiguities in the many old PDB files in which DNA and RNA were both called A, C, G, and T. ERROR. C1A ( C1A) does not belong in NAG ( 144) B 0 ERROR. C2A ( C2A) does not belong in NAG ( 144) B 0 ERROR. C3A ( C3A) does not belong in NAG ( 144) B 0 ERROR. C4A ( C4A) does not belong in NAG ( 144) B 0 ERROR. C5A ( C5A) does not belong in NAG ( 144) B 0 ERROR. C6A ( C6A) does not belong in NAG ( 144) B 0 ERROR. C7A ( C7A) does not belong in NAG ( 144) B 0 ERROR. C8A ( C8A) does not belong in NAG ( 144) B 0 ERROR. N2A ( N2A) does not belong in NAG ( 144) B 0 ERROR. O3A ( O3A) does not belong in NAG ( 144) B 0 ERROR. O4A ( O4A) does not belong in NAG ( 144) B 0 ERROR. O5A ( O5A) does not belong in NAG ( 144) B 0 ERROR. O6A ( O6A) does not belong in NAG ( 144) B 0 ERROR. O7A ( O7A) does not belong in NAG ( 144) B 0 ERROR. C1B ( C1B) does not belong in NAG ( 144) B 0 ERROR. C2B ( C2B) does not belong in NAG ( 144) B 0 ERROR. C3B ( C3B) does not belong in NAG ( 144) B 0 ERROR. C4B ( C4B) does not belong in NAG ( 144) B 0 ERROR. C5B ( C5B) does not belong in NAG ( 144) B 0 ERROR. C6B ( C6B) does not belong in NAG ( 144) B 0 ERROR. C7B ( C7B) does not belong in NAG ( 144) B 0 ERROR. C8B ( C8B) does not belong in NAG ( 144) B 0 ERROR. N2B ( N2B) does not belong in NAG ( 144) B 0 ERROR. O3B ( O3B) does not belong in NAG ( 144) B 0 ERROR. O4B ( O4B) does not belong in NAG ( 144) B 0 ERROR. O5B ( O5B) does not belong in NAG ( 144) B 0 ERROR. O6B ( O6B) does not belong in NAG ( 144) B 0 ERROR. O7B ( O7B) does not belong in NAG ( 144) B 0 ERROR. C1C ( C1C) does not belong in NAG ( 144) B 0 ERROR. C2C ( C2C) does not belong in NAG ( 144) B 0 ERROR. C3C ( C3C) does not belong in NAG ( 144) B 0 ERROR. C4C ( C4C) does not belong in NAG ( 144) B 0 ERROR. C5C ( C5C) does not belong in NAG ( 144) B 0 ERROR. C6C ( C6C) does not belong in NAG ( 144) B 0 ERROR. C7C ( C7C) does not belong in NAG ( 144) B 0 ERROR. C8C ( C8C) does not belong in NAG ( 144) B 0 ERROR. OC ( OC ) does not belong in NAG ( 144) B 0 ERROR. O3C ( O3C) does not belong in NAG ( 144) B 0 ERROR. O4C ( O4C) does not belong in NAG ( 144) B 0 ERROR. O6C ( O6C) does not belong in NAG ( 144) B 0 ERROR. O7C ( O7C) does not belong in NAG ( 144) B 0 ERROR. N2C ( N2C) does not belong in NAG ( 144) B 0 ERROR. O1L ( O1L) does not belong in NAG ( 144) B 0 ======================================================================== ==== Compound code /home/whatif/httpd/htdocs/servers/tmp//tmpaklPz0/====L1.fil ======================================================================== # 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. Note: Since neither a valid SCALE matrix, nor a valid CRYST1 card were found, SYMMETRY will be unavailable for this molecule. # 3 # 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. # 4 # Note: No strange inter-chain connections detected No covalent bonds have been detected between molecules with non-identical chain identifiers. # 5 # Note: No duplicate atom names in ligands All atom names in ligands seem adequately unique. # 6 # 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. # 7 # 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 are none). # 8 # 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). # 9 # 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. # 10 # Note: No probable side chain atoms with zero occupancy detected. Either there are no side chain atoms with zero occupancy, or the side chain atoms with zero occupancy were not present in the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy. # 11 # Note: No probable backbone atoms with zero occupancy detected. Either there are no backbone atoms with zero occupancy, or the backbone atoms with zero occupancy were not present in the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy. # 12 # Note: All residues have a complete backbone. No residues have missing backbone atoms. # 13 # Note: No C-alpha only residues There are no residues that consist of only an alpha carbon atom. # 14 # Note: Non-canonicals WHAT IF has not detected any non-canonical residue that it does not understand (or there are no non-canonical residues in the PDB file). # 15 # 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]. 1 1 ( 1) 143 ( 143) A Protein checkset 2 144 ( 144) 144 ( 144) B Sugar checkset 3 145 ( 143) 145 ( 143) A L O2 <- 143 checkset # 16 # Note: Some notes regarding the PDB file contents The numbers and remarks listed below have no explicit validation purpose, they are merely meant for the crystallographer or NMR spectroscopists to perhaps pinpoint something unexpected. See the WHAT_CHECK course [REF] for an explanation of terms like 'poor', 'missing', etcetera (in case those words pop up in the lines underneath this message). The total number of amino acids found is 143. of which 70 have poor or missing atoms. Number of (recognized) sugars 1 of which 1 have poor or missing atoms. # 17 # Note: Ramachandran plot In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands. In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website [REF]. In the TeX file, a plot has been inserted here Chain identifier: A # 18 # 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]. Secondary structure assignment 10 20 30 40 50 60 | | | | | | 1 - 60 MKIPVFLLLLALANAKVFQRCEWARVLKARGMDGYRGISLADWVCLSKWESQYNTNAINH ( 1)-( 60) HHHHHHHHHHHT TT TT HHHHHHHHHHHHTT TT SSS 70 80 90 100 110 120 | | | | | | 61 - 120 NTDGSTDYGIFQINSRWWCNDDRIPTRNACNIKCSALQTDDVTVAINCAKRVVSDPQGIR ( 61)-( 120) TTT SSSTTTTSSTTTTSS TTT TT SS33333TT HHHHHHHHHHHHTTT333 130 140 | | 121 - 143 AWVAWNRHCQNRDLSAYIAGCGL ( 121)-( 143)3 HHHHHHTTTT HHHHTTT # 19 # Note: No rounded coordinates detected No significant rounding of atom coordinates has been detected. # 20 # Note: No artificial side chains detected No artificial side-chain positions characterized by chi-1=0.0 or chi-1=180.0 have been detected. # 21 # Warning: Unexpected atoms encountered While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about. # 22 # Warning: Missing atoms The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'. 144 NAG ( 144-) B - O4 144 NAG ( 144-) B - C4 144 NAG ( 144-) B - C1 144 NAG ( 144-) B - O5 144 NAG ( 144-) B - C5 144 NAG ( 144-) B - C6 144 NAG ( 144-) B - O6 144 NAG ( 144-) B - C3 144 NAG ( 144-) B - O3 144 NAG ( 144-) B - C2 144 NAG ( 144-) B - N2 144 NAG ( 144-) B - C7 144 NAG ( 144-) B - O7 144 NAG ( 144-) B - C8 # 23 # 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. # 24 # 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. # 25 # Note: No OXT found in the middle of chains No OXT groups were found in the middle of protein chains. # 26 # Note: Introduction to the nomenclature section. Nomenclature problems seem, at first, rather unimportant. After all who cares if we call the delta atoms in leucine delta2 and delta1 rather than the other way around. Chemically speaking that is correct. But structures have not been solved and deposited just for chemists to look at them. Most times a structure is used, it is by software in a bioinformatics lab. And if they compare structures in which the one used C delta1 and delta2 and the other uses C delta2 and delta1, then that comparison will fail. Also, we recalculate all structures every so many years to make sure that everybody always can get access to the best coordinates that can be obtained from the (your?) experimental data. These recalculations will be troublesome if there are nomenclature problems. Several Nomenclature problems actually are worse than that. At the WHAT_CHECK website [REF] you can get an overview of the importance of all nomenclature problems that we list. # 27 # Note: Valine nomenclature OK No errors were detected in valine nomenclature. # 28 # Note: Threonine nomenclature OK No errors were detected in threonine nomenclature. # 29 # Note: Isoleucine nomenclature OK No errors were detected in isoleucine nomenclature. # 30 # Note: Leucine nomenclature OK No errors were detected in leucine nomenclature. # 31 # Note: Arginine nomenclature OK No errors were detected in arginine nomenclature. # 32 # Note: Tyrosine torsion conventions OK No errors were detected in tyrosine torsion angle conventions. # 33 # Note: Phenylalanine torsion conventions OK No errors were detected in phenylalanine torsion angle conventions. # 34 # Note: Aspartic acid torsion conventions OK No errors were detected in aspartic acid torsion angle conventions. # 35 # Note: Glutamic acid torsion conventions OK No errors were detected in glutamic acid torsion angle conventions. # 36 # Note: Phosphate group names OK No errors were detected in phosphate group naming conventions. # 37 # 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. # 38 # 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 acids have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]) # 39 # 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: 0.937 RMS-deviation in bond distances: 0.019 # 40 # 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. 6 PHE ( 6-) A - CA CB CG 108.97 -4.8 18 PHE ( 18-) A - CA CB CG 108.60 -5.2 23 TRP ( 23-) A - CB CG CD2 120.60 -4.4 42 ASP ( 42-) A - CA CB CG 107.26 -5.3 50 GLU ( 50-) A - CB CG CD 102.51 -5.9 56 ASN ( 56-) A - CA CB CG 105.29 -7.3 60 HIS ( 60-) A - NE2 CD2 CG 110.57 4.1 61 ASN ( 61-) A - CA CB CG 107.89 -4.7 63 ASP ( 63-) A - -C N CA 129.29 4.2 68 TYR ( 68-) A - C CA CB 101.04 -4.8 71 PHE ( 71-) A - CA CB CG 107.15 -6.6 74 ASN ( 74-) A - CA CB CG 107.77 -4.8 74 ASN ( 74-) A - CB CG ND2 91.51 -16.6 74 ASN ( 74-) A - CB CG OD1 46.34 -37.2 74 ASN ( 74-) A - ND2 CG OD1 137.85 15.3 84 ILE ( 84-) A - -C N CA 114.29 -4.1 87 ARG ( 87-) A - -C N CA 130.93 5.1 88 ASN ( 88-) A - CA CB CG 108.30 -4.3 100 ASP ( 100-) A - CA CB CG 107.62 -5.0 101 ASP ( 101-) A - CA CB CG 108.57 -4.0 107 ASN ( 107-) A - CA CB CG 108.13 -4.5 126 ASN ( 126-) A - CA CB CG 107.88 -4.7 128 HIS ( 128-) A - NE2 CD2 CG 110.58 4.1 131 ASN ( 131-) A - CA CB CG 107.75 -4.8 134 LEU ( 134-) A - -C N CA 129.64 4.4 141 CYS ( 141-) A - CA CB SG 104.83 -4.2 # 41 # Note: Normal bond angle variability Bond angles were found to deviate normally from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. RMS Z-score for bond angles: 1.300 RMS-deviation in bond angles: 2.275 # 42 # 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. # 43 # Note: Chirality OK All protein atoms have proper chirality. The average deviation= 1.139 # 44 # Note: Improper dihedral angle distribution OK The RMS Z-score for all improper dihedrals in the structure is within normal ranges. Improper dihedral RMS Z-score : 1.001 10 20 30 40 50 60 | | | | | | 1 - 60 MKIPVFLLLLALANAKVFQRCEWARVLKARGMDGYRGISLADWVCLSKWESQYNTNAINH ( 1)-( 60) HHHHHHHHHHHT TT TT HHHHHHHHHHHHTT TT SSS 70 80 90 100 110 120 | | | | | | 61 - 120 NTDGSTDYGIFQINSRWWCNDDRIPTRNACNIKCSALQTDDVTVAINCAKRVVSDPQGIR ( 61)-( 120) TTT SSSTTTTSSTTTTSS TTT TT SS33333TT HHHHHHHHHHHHTTT333 130 140 | | 121 - 143 AWVAWNRHCQNRDLSAYIAGCGL ( 121)-( 143)3 HHHHHHTTTT HHHHTTT # 45 # Note: Tau angles OK All of the tau angles of amino acids that actually have a tau angle fall within expected RMS deviations. # 46 # Note: Normal tau angle deviations The RMS Z-score for the tau angles in the structure falls within the normal range that we guess to be 0.5 - 1.5. Be aware, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers. Tau angle RMS Z-score : 1.398 # 47 # Note: Side chain planarity OK All of the side chains of residues that have a planar group are planar within expected RMS deviations. # 48 # Note: Atoms connected to aromatic rings OK All of the atoms that are connected to planar aromatic rings in side chains of amino-acid residues are in the plane within expected RMS deviations. Since there is no DNA and no protein with hydrogens, no uncalibrated planarity check was performed. Ramachandran Z-score : 0.102 # 49 # Note: Ramachandran Z-score OK The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is within expected ranges for well-refined structures. Ramachandran Z-score : 0.102 # 50 # 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. 58 ILE ( 58-) A - -2.2 92 ILE ( 92-) A - -2.2 86 THR ( 86-) A - -2.2 # 51 # Warning: Backbone evaluation reveals unusual conformations The residues listed in the table below have abnormal backbone torsion angles. Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations. 52 GLN ( 52-) A - Poor phi/psi 53 TYR ( 53-) A - Poor phi/psi 72 GLN ( 72-) A - Poor phi/psi 77 TRP ( 77-) A - omega poor 82 ASP ( 82-) A - Poor phi/psi 88 ASN ( 88-) A - Poor phi/psi 91 ASN ( 91-) A - Poor phi/psi 131 ASN ( 131-) A - Poor phi/psi chi-1/chi-2 correlation Z-score : -2.956 # 52 # Note: chi-1/chi-2 angle correlation Z-score OK The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is within expected ranges for well-refined structures. chi-1/chi-2 correlation Z-score : -2.956 # 53 # Note: Rotamers checked OK None of the residues that have a normal backbone environment have abnormal rotamers. # 54 # 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! 30 ARG ( 30-) A - 0 32 MET ( 32-) A - 0 33 ASP ( 33-) A - 0 35 TYR ( 35-) A - 0 36 ARG ( 36-) A - 0 51 SER ( 51-) A - 0 52 GLN ( 52-) A - 0 53 TYR ( 53-) A - 0 57 ALA ( 57-) A - 0 68 TYR ( 68-) A - 0 74 ASN ( 74-) A - 0 76 ARG ( 76-) A - 0 77 TRP ( 77-) A - 0 78 TRP ( 78-) A - 0 81 ASP ( 81-) A - 0 82 ASP ( 82-) A - 0 83 ARG ( 83-) A - 0 84 ILE ( 84-) A - 0 85 PRO ( 85-) A - 0 86 THR ( 86-) A - 0 87 ARG ( 87-) A - 0 88 ASN ( 88-) A - 0 89 ALA ( 89-) A - 0 90 CYS ( 90-) A - 0 91 ASN ( 91-) A - 0 102 VAL ( 102-) A - 0 115 ASP ( 115-) A - 0 117 GLN ( 117-) A - 0 119 ILE ( 119-) A - 0 122 TRP ( 122-) A - 0 127 ARG ( 127-) A - 0 128 HIS ( 128-) A - 0 129 CYS ( 129-) A - 0 130 GLN ( 130-) A - 0 131 ASN ( 131-) A - 0 138 ILE ( 138-) A - 0 139 ALA ( 139-) A - 0 142 GLY ( 142-) A - 0 54 ASN ( 54-) A - 1 62 THR ( 62-) A - 1 63 ASP ( 63-) A - 1 65 SER ( 65-) A - 1 70 ILE ( 70-) A - 1 72 GLN ( 72-) A - 1 79 CYS ( 79-) A - 1 92 ILE ( 92-) A - 1 94 CYS ( 94-) A - 1 95 SER ( 95-) A - 1 100 ASP ( 100-) A - 1 103 THR ( 103-) A - 1 134 LEU ( 134-) A - 1 141 CYS ( 141-) A - 1 14 ASN ( 14-) A - 2 19 GLN ( 19-) A - 2 67 ASP ( 67-) A - 2 71 PHE ( 71-) A - 2 98 GLN ( 98-) A - 2 99 THR ( 99-) A - 2 123 VAL ( 123-) A - 2 132 ARG ( 132-) A - 2 133 ASP ( 133-) A - 2 # 55 # Note: Backbone conformation Z-score OK The backbone conformation analysis gives a score that is normal for well refined protein structures. Backbone conformation Z-score : -1.711 Omega average and std. deviation= 181.477 4.018 # 56 # 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. Standard deviation of omega values : 4.018 # 57 # 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. # 58 # Note: Peptide bond conformations We could not find any peptide bonds that are likely to actually be a cis bond. This check has not yet fully matured... # 59 # Note: PRO puckering amplitude OK Puckering amplitudes for all PRO residues are within normal ranges. # 60 # 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. 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]. 85 PRO ( 85-) A - -128.2 half-chair C-delta/C-gamma (-126 degrees) # 61 # Error: Abnormally short interatomic distances The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction. The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance. The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively. 38 ILE ( 38-) A - CG2 <-> 43 TRP ( 43-) A - NE1 0.32 2.78 INTRA BL 23 TRP ( 23-) A - CH2 <-> 53 TYR ( 53-) A - CA 0.29 2.91 INTRA BF 23 TRP ( 23-) A - CH2 <-> 47 SER ( 47-) A - CB 0.28 2.92 INTRA BF 23 TRP ( 23-) A - CZ3 <-> 47 SER ( 47-) A - CB 0.28 2.92 INTRA BF 75 SER ( 75-) A - C <-> 84 ILE ( 84-) A - CD1 0.27 2.93 INTRA BF 28 LYS ( 28-) A - CD <-> 143 LEU ( 143-) A - CD1 0.27 2.93 INTRA BF 76 ARG ( 76-) A - CA <-> 84 ILE ( 84-) A - CD1 0.27 2.93 INTRA BF 23 TRP ( 23-) A - CZ3 <-> 53 TYR ( 53-) A - CD2 0.26 2.94 INTRA BF 30 ARG ( 30-) A - CD <-> 106 ILE ( 106-) A - CD1 0.26 2.94 INTRA BF 30 ARG ( 30-) A - CD <-> 106 ILE ( 106-) A - CB 0.26 2.94 INTRA BF 18 PHE ( 18-) A - CB <-> 23 TRP ( 23-) A - CD1 0.26 2.94 INTRA BF 66 THR ( 66-) A - CG2 <-> 68 TYR ( 68-) A - CE1 0.26 2.94 INTRA BF 66 THR ( 66-) A - CG2 <-> 68 TYR ( 68-) A - CZ 0.26 2.94 INTRA BF 23 TRP ( 23-) A - CZ2 <-> 53 TYR ( 53-) A - CA 0.26 2.94 INTRA BF 23 TRP ( 23-) A - CZ2 <-> 70 ILE ( 70-) A - CG2 0.26 2.94 INTRA BF 112 VAL ( 112-) A - CG1 <-> 122 TRP ( 122-) A - CH2 0.26 2.94 INTRA BF 23 TRP ( 23-) A - CE3 <-> 53 TYR ( 53-) A - CD2 0.26 2.94 INTRA BF 23 TRP ( 23-) A - CZ2 <-> 70 ILE ( 70-) A - CD1 0.25 2.95 INTRA BF 90 CYS ( 90-) A - CB <-> 92 ILE ( 92-) A - CD1 0.25 2.95 INTRA BF 6 PHE ( 6-) A - CE2 <-> 8 LEU ( 8-) A - CD2 0.25 2.95 INTRA BF 6 PHE ( 6-) A - CZ <-> 8 LEU ( 8-) A - CD2 0.25 2.95 INTRA BF 38 ILE ( 38-) A - CG2 <-> 43 TRP ( 43-) A - CZ2 0.25 2.95 INTRA BL 38 ILE ( 38-) A - CG1 <-> 42 ASP ( 42-) A - CB 0.25 2.95 INTRA BL 38 ILE ( 38-) A - CD1 <-> 119 ILE ( 119-) A - CD1 0.25 2.95 INTRA BF 78 TRP ( 78-) A - CE2 <-> 112 VAL ( 112-) A - CG2 0.24 2.96 INTRA BF 30 ARG ( 30-) A - NE <-> 110 LYS ( 110-) A - CE 0.24 2.86 INTRA BF 71 PHE ( 71-) A - CB <-> 73 ILE ( 73-) A - CD1 0.24 2.96 INTRA BF 30 ARG ( 30-) A - NH1 <-> 106 ILE ( 106-) A - CG1 0.24 2.86 INTRA BF 30 ARG ( 30-) A - NH1 <-> 106 ILE ( 106-) A - CD1 0.23 2.87 INTRA BF 15 ALA ( 15-) A - CB <-> 56 ASN ( 56-) A - ND2 0.23 2.87 INTRA BF 22 GLU ( 22-) A - CA <-> 25 ARG ( 25-) A - NH1 0.23 2.87 INTRA BF 54 ASN ( 54-) A - C <-> 70 ILE ( 70-) A - CD1 0.23 2.97 INTRA BF 117 GLN ( 117-) A - CG <-> 120 ARG ( 120-) A - NE 0.23 2.87 INTRA BF 14 ASN ( 14-) A - CG <-> 100 ASP ( 100-) A - CG 0.23 2.97 INTRA BF 117 GLN ( 117-) A - CD <-> 121 ALA ( 121-) A - CA 0.22 2.98 INTRA BL 78 TRP ( 78-) A - CZ2 <-> 112 VAL ( 112-) A - CG2 0.21 2.99 INTRA BF 68 TYR ( 68-) A - CE1 <-> 94 CYS ( 94-) A - SG 0.21 3.19 INTRA BL 48 LYS ( 48-) A - CG <-> 53 TYR ( 53-) A - CE1 0.21 2.99 INTRA BF 18 PHE ( 18-) A - CG <-> 23 TRP ( 23-) A - CD1 0.21 2.99 INTRA BF 6 PHE ( 6-) A - CE2 <-> 8 LEU ( 8-) A - CG 0.20 3.00 INTRA BF 38 ILE ( 38-) A - CD1 <-> 42 ASP ( 42-) A - CB 0.20 3.00 INTRA BL 117 GLN ( 117-) A - CG <-> 120 ARG ( 120-) A - CB 0.20 3.00 INTRA BF 38 ILE ( 38-) A - CG2 <-> 43 TRP ( 43-) A - CE2 0.19 3.01 INTRA BL 48 LYS ( 48-) A - NZ <-> 49 TRP ( 49-) A - CZ3 0.19 2.91 INTRA BF 16 LYS ( 16-) A - NZ <-> 18 PHE ( 18-) A - CA 0.19 2.91 INTRA BF 78 TRP ( 78-) A - CZ3 <-> 111 ARG ( 111-) A - NH1 0.19 2.91 INTRA BF 28 LYS ( 28-) A - NZ <-> 143 LEU ( 143-) A - CD1 0.19 2.91 INTRA BF 103 THR ( 103-) A - CG2 <-> 104 VAL ( 104-) A - N 0.18 2.82 INTRA BF 58 ILE ( 58-) A - CD1 <-> 59 ASN ( 59-) A - N 0.18 2.82 INTRA BF 132 ARG ( 132-) A - CD <-> 133 ASP ( 133-) A - N 0.17 2.83 INTRA BF 1 MET ( 1-) A - CG <-> 2 LYS ( 2-) A - N 0.17 2.83 INTRA BF 112 VAL ( 112-) A - CG1 <-> 113 VAL ( 113-) A - N 0.17 2.83 INTRA BF 16 LYS ( 16-) A - N <-> 55 THR ( 55-) A - CG2 0.17 2.93 INTRA BF 123 VAL ( 123-) A - CG1 <-> 124 ALA ( 124-) A - N 0.16 2.84 INTRA BL 104 VAL ( 104-) A - CG1 <-> 105 ALA ( 105-) A - N 0.16 2.84 INTRA BL 62 THR ( 62-) A - CG2 <-> 63 ASP ( 63-) A - N 0.16 2.84 INTRA BF 28 LYS ( 28-) A - CB <-> 40 LEU ( 40-) A - CD1 0.15 3.05 INTRA BF 21 CYS ( 21-) A - SG <-> 141 CYS ( 141-) A - CA 0.15 2.85 INTRA BL 76 ARG ( 76-) A - CB <-> 77 TRP ( 77-) A - CE3 0.15 2.95 INTRA BF 23 TRP ( 23-) A - CE3 <-> 53 TYR ( 53-) A - CE2 0.15 3.05 INTRA BF 76 ARG ( 76-) A - NH1 <-> 85 PRO ( 85-) A - CG 0.14 2.96 INTRA BF 76 ARG ( 76-) A - CB <-> 77 TRP ( 77-) A - CZ3 0.14 2.96 INTRA BF 46 LEU ( 46-) A - CD1 <-> 122 TRP ( 122-) A - CD2 0.13 3.07 INTRA BF 30 ARG ( 30-) A - CG <-> 106 ILE ( 106-) A - CD1 0.13 3.07 INTRA BF 132 ARG ( 132-) A - NH1 <-> 133 ASP ( 133-) A - CB 0.13 2.87 INTRA BF 43 TRP ( 43-) A - CH2 <-> 113 VAL ( 113-) A - CG1 0.12 3.08 INTRA BL 117 GLN ( 117-) A - CD <-> 121 ALA ( 121-) A - N 0.11 2.99 INTRA BL 18 PHE ( 18-) A - CD1 <-> 23 TRP ( 23-) A - NE1 0.11 2.99 INTRA BF 10 LEU ( 10-) A - CD2 <-> 11 ALA ( 11-) A - N 0.11 2.89 INTRA BF 53 TYR ( 53-) A - C <-> 70 ILE ( 70-) A - CD1 0.11 3.09 INTRA BF 68 TYR ( 68-) A - CE1 <-> 94 CYS ( 94-) A - CB 0.10 3.10 INTRA BL 45 CYS ( 45-) A - SG <-> 49 TRP ( 49-) A - CD1 0.10 3.30 INTRA BL 55 THR ( 55-) A - N <-> 70 ILE ( 70-) A - CD1 0.10 3.00 INTRA BF 76 ARG ( 76-) A - N <-> 84 ILE ( 84-) A - CD1 0.10 3.00 INTRA BF 115 ASP ( 115-) A - CB <-> 116 PRO ( 116-) A - CD 0.10 3.00 INTRA BF 63 ASP ( 63-) A - CG <-> 76 ARG ( 76-) A - NE 0.09 3.01 INTRA BF 1 MET ( 1-) A - CB <-> 2 LYS ( 2-) A - N 0.09 2.61 INTRA BF 46 LEU ( 46-) A - CD2 <-> 50 GLU ( 50-) A - CD 0.09 3.11 INTRA BF 77 TRP ( 77-) A - CD1 <-> 87 ARG ( 87-) A - NH1 0.09 3.01 INTRA BF 117 GLN ( 117-) A - NE2 <-> 121 ALA ( 121-) A - CA 0.08 3.02 INTRA BL 76 ARG ( 76-) A - NH2 <-> 85 PRO ( 85-) A - CG 0.08 3.02 INTRA BF 63 ASP ( 63-) A - OD1 <-> 65 SER ( 65-) A - N 0.08 2.62 INTRA BF 46 LEU ( 46-) A - CD1 <-> 122 TRP ( 122-) A - CE3 0.08 3.12 INTRA BF 64 GLY ( 64-) A - O <-> 84 ILE ( 84-) A - CG2 0.07 2.73 INTRA BF 15 ALA ( 15-) A - CA <-> 56 ASN ( 56-) A - CG 0.07 3.13 INTRA BF 95 SER ( 95-) A - O <-> 98 GLN ( 98-) A - CG 0.07 2.73 INTRA BF 36 ARG ( 36-) A - CD <-> 113 VAL ( 113-) A - O 0.06 2.74 INTRA BF 46 LEU ( 46-) A - CD2 <-> 50 GLU ( 50-) A - OE2 0.06 2.74 INTRA BF 15 ALA ( 15-) A - CA <-> 56 ASN ( 56-) A - OD1 0.06 2.74 INTRA BF 64 GLY ( 64-) A - N <-> 65 SER ( 65-) A - N 0.06 2.54 INTRA BL 109 ALA ( 109-) A - O <-> 112 VAL ( 112-) A - CG1 0.06 2.74 INTRA BF 21 CYS ( 21-) A - CA <-> 141 CYS ( 141-) A - SG 0.06 2.94 INTRA BL 46 LEU ( 46-) A - O <-> 50 GLU ( 50-) A - CG 0.06 2.74 INTRA BF 7 LEU ( 7-) A - CD1 <-> 8 LEU ( 8-) A - N 0.06 2.94 INTRA BF 35 TYR ( 35-) A - O <-> 38 ILE ( 38-) A - CG2 0.06 2.74 INTRA BL 14 ASN ( 14-) A - ND2 <-> 100 ASP ( 100-) A - CG 0.06 3.04 INTRA BF 117 GLN ( 117-) A - OE1 <-> 120 ARG ( 120-) A - CD 0.06 2.74 INTRA BF 14 ASN ( 14-) A - OD1 <-> 100 ASP ( 100-) A - CG 0.06 2.74 INTRA BF 101 ASP ( 101-) A - OD2 <-> 103 THR ( 103-) A - CG2 0.05 2.75 INTRA BF 51 SER ( 51-) A - CB <-> 70 ILE ( 70-) A - O 0.05 2.75 INTRA BF 21 CYS ( 21-) A - O <-> 25 ARG ( 25-) A - CD 0.05 2.75 INTRA BF 75 SER ( 75-) A - O <-> 84 ILE ( 84-) A - CD1 0.05 2.75 INTRA BF 15 ALA ( 15-) A - C <-> 100 ASP ( 100-) A - OD1 0.05 2.75 INTRA BF 112 VAL ( 112-) A - O <-> 115 ASP ( 115-) A - CG 0.05 2.75 INTRA BF 61 ASN ( 61-) A - N <-> 65 SER ( 65-) A - O 0.05 2.65 INTRA BL 79 CYS ( 79-) A - C <-> 94 CYS ( 94-) A - SG 0.05 3.35 INTRA BL 110 LYS ( 110-) A - O <-> 113 VAL ( 113-) A - CG2 0.05 2.75 INTRA BF 73 ILE ( 73-) A - CG2 <-> 78 TRP ( 78-) A - CB 0.05 3.15 INTRA BF 23 TRP ( 23-) A - CZ3 <-> 53 TYR ( 53-) A - CE2 0.05 3.15 INTRA BF 102 VAL ( 102-) A - O <-> 106 ILE ( 106-) A - CG1 0.05 2.75 INTRA BF 41 ALA ( 41-) A - CB <-> 134 LEU ( 134-) A - CB 0.05 3.15 INTRA BF 51 SER ( 51-) A - OG <-> 54 ASN ( 54-) A - N 0.05 2.65 INTRA BF 18 PHE ( 18-) A - CG <-> 23 TRP ( 23-) A - NE1 0.05 3.05 INTRA BF 20 ARG ( 20-) A - CD <-> 137 TYR ( 137-) A - O 0.04 2.76 INTRA BF 73 ILE ( 73-) A - CG2 <-> 74 ASN ( 74-) A - N 0.04 2.96 INTRA BF 67 ASP ( 67-) A - OD1 <-> 74 ASN ( 74-) A - ND2 0.04 2.66 INTRA BF 16 LYS ( 16-) A - CB <-> 100 ASP ( 100-) A - CG 0.04 3.16 INTRA BF 20 ARG ( 20-) A - NH1 <-> 139 ALA ( 139-) A - O 0.04 2.66 INTRA BF 15 ALA ( 15-) A - CA <-> 56 ASN ( 56-) A - ND2 0.04 3.06 INTRA BF 20 ARG ( 20-) A - NH1 <-> 137 TYR ( 137-) A - O 0.04 2.66 INTRA BF 63 ASP ( 63-) A - OD2 <-> 76 ARG ( 76-) A - NE 0.04 2.66 INTRA BF 126 ASN ( 126-) A - O <-> 130 GLN ( 130-) A - NE2 0.04 2.66 INTRA BL 20 ARG ( 20-) A - NH2 <-> 139 ALA ( 139-) A - O 0.04 2.66 INTRA BF 14 ASN ( 14-) A - ND2 <-> 100 ASP ( 100-) A - OD2 0.04 2.66 INTRA BF 12 LEU ( 12-) A - O <-> 98 GLN ( 98-) A - NE2 0.04 2.66 INTRA BF 3 ILE ( 3-) A - CA <-> 4 PRO ( 4-) A - CD 0.03 2.77 INTRA BL 35 TYR ( 35-) A - CE2 <-> 113 VAL ( 113-) A - CG2 0.03 3.17 INTRA BL 120 ARG ( 120-) A - CG <-> 126 ASN ( 126-) A - ND2 0.03 3.07 INTRA BF 117 GLN ( 117-) A - CD <-> 120 ARG ( 120-) A - C 0.03 3.17 INTRA BF 76 ARG ( 76-) A - NH1 <-> 85 PRO ( 85-) A - O 0.03 2.67 INTRA BF 63 ASP ( 63-) A - O <-> 76 ARG ( 76-) A - NH2 0.02 2.68 INTRA BF 30 ARG ( 30-) A - NE <-> 110 LYS ( 110-) A - NZ 0.02 2.83 INTRA BF 30 ARG ( 30-) A - CD <-> 106 ILE ( 106-) A - CG1 0.02 3.18 INTRA BF 58 ILE ( 58-) A - CD1 <-> 66 THR ( 66-) A - OG1 0.02 2.78 INTRA BF 125 TRP ( 125-) A - CH2 <-> 130 GLN ( 130-) A - CB 0.02 3.18 INTRA BL 78 TRP ( 78-) A - NE1 <-> 112 VAL ( 112-) A - CG2 0.02 3.08 INTRA BF 33 ASP ( 33-) A - CB <-> 40 LEU ( 40-) A - CG 0.02 3.18 INTRA BF 48 LYS ( 48-) A - NZ <-> 49 TRP ( 49-) A - CE3 0.01 3.09 INTRA BF 52 GLN ( 52-) A - C <-> 53 TYR ( 53-) A - CD1 0.01 3.09 INTRA BF 119 ILE ( 119-) A - C <-> 121 ALA ( 121-) A - N 0.01 2.89 INTRA BF 88 ASN ( 88-) A - OD1 <-> 91 ASN ( 91-) A - N 0.01 2.69 INTRA BL 63 ASP ( 63-) A - OD1 <-> 76 ARG ( 76-) A - NE 0.01 2.69 INTRA BF 68 TYR ( 68-) A - OH <-> 81 ASP ( 81-) A - CB 0.01 2.79 INTRA BF 18 PHE ( 18-) A - CB <-> 23 TRP ( 23-) A - NE1 0.01 3.09 INTRA BF 45 CYS ( 45-) A - O <-> 49 TRP ( 49-) A - CD1 0.01 2.79 INTRA BL 14 ASN ( 14-) A - ND2 <-> 15 ALA ( 15-) A - N 0.01 2.74 INTRA BF 48 LYS ( 48-) A - NZ <-> 49 TRP ( 49-) A - CH2 0.01 3.09 INTRA BF 132 ARG ( 132-) A - CG <-> 133 ASP ( 133-) A - N 0.00 3.00 INTRA BF 69 GLY ( 69-) A - O <-> 72 GLN ( 72-) A - NE2 0.00 2.70 INTRA BL 111 ARG ( 111-) A - NH2 <-> 114 SER ( 114-) A - OG 0.00 2.70 INTRA BF 31 GLY ( 31-) A - N <-> 32 MET ( 32-) A - N 0.00 2.60 INTRA BF 66 THR ( 66-) A - CG2 <-> 68 TYR ( 68-) A - OH 0.00 2.80 INTRA BF 78 TRP ( 78-) A - CH2 <-> 115 ASP ( 115-) A - OD2 0.00 2.80 INTRA BF # 62 # 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 : 1.055 # 63 # Note: Inside/Outside RMS Z-score plot The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns. In the TeX file, a plot has been inserted here Chain identifier: A # 64 # 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. 83 ARG ( 83-) A - -7.23 2 LYS ( 2-) A - -6.56 36 ARG ( 36-) A - -5.74 30 ARG ( 30-) A - -5.64 98 GLN ( 98-) A - -5.13 127 ARG ( 127-) A - -5.03 # 65 # 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. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc. The table below lists the first and last residue in each stretch found, as well as the average residue score of the series. 49 TRP ( 49-) A - 51 - SER 51- ( A) - -4.21 # 66 # Warning: Structural average packing environment a bit worrysome The structural average packing score 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 packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF]. Average for range 1 - 144 : -1.457 # 67 # Note: Quality value plot The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing. In the TeX file, a plot has been inserted here Chain identifier: A # 68 # Note: Second generation packing environment OK None of the individual amino acid residues has a bad packing environment. # 69 # Note: No series of residues with abnormal new packing environment There are no stretches of four or more residues each having a packing Z-score worse than -1.75. # 70 # Note: Second generation quality Z-score plot The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing. In the TeX file, a plot has been inserted here Chain identifier: A # 71 # Error: HIS, ASN, GLN side chain flips Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors. 61 ASN ( 61-) A - 126 ASN ( 126-) A - # 72 # 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. 60 HIS ( 60-) A - HIS-D 0.36 HIS-E 1.49 128 HIS ( 128-) A - HIS-D 0.33 # 73 # 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. 2 LYS ( 2-) A - N 22 GLU ( 22-) A - N 30 ARG ( 30-) A - NE 33 ASP ( 33-) A - N 63 ASP ( 63-) A - N 66 THR ( 66-) A - N 71 PHE ( 71-) A - N 77 TRP ( 77-) A - N 79 CYS ( 79-) A - N 103 THR ( 103-) A - N 104 VAL ( 104-) A - N 124 ALA ( 124-) A - N # 74 # Warning: Buried unsatisfied hydrogen bond acceptors The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network. Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here. Waters are not listed by this option. 50 GLU ( 50-) A - OE2 100 ASP ( 100-) A - OD1 115 ASP ( 115-) A - OD2 # 75 # 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. # 76 # 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. Since there are no waters, the water check has been skipped. # 77 # 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]. 1 1 ( 1) 143 ( 143) A Protein checkset 2 144 ( 144) 144 ( 144) B Sugar checkset 3 145 ( 143) 145 ( 143) A L O2 <- 143 checkset # 78 # 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 global quality indicators. Structure Z-scores, positive is better than average: 1st generation packing quality : -2.392 2nd generation packing quality : -2.753 Ramachandran plot appearance : 0.102 chi-1/chi-2 rotamer normality : -2.956 Backbone conformation : -1.711 RMS Z-scores, should be close to 1.0: Bond lengths : 0.937 Bond angles : 1.300 Omega angle restraints : 0.730 Side chain planarity : 0.352 (tight) Improper dihedral distribution : 1.001 Inside/Outside distribution : 1.055 ============== WHAT IF G.Vriend, WHAT IF: a molecular modelling and drug design program, J. Mol. Graph. 8, 52--56 (1990). WHAT_CHECK (verification routines from WHAT IF) R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola, Errors in protein structures Nature 381, 272 (1996). (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra information) 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). R.W.W. Hooft, C.Sander and G.Vriend, Objectively judging the quality of a protein structure from a Ramachandran plot CABIOS (1997), 13, 425--430. Symmetry Checks R.W.W.Hooft, C.Sander and G.Vriend, Reconstruction of symmetry related molecules from protein data bank (PDB) files J. Appl. Cryst. 27, 1006--1009 (1994). Tau angle W.G.Touw and G.Vriend On the complexity of Engh and Huber refinement restraints: the angle tau as example. Acta Crystallogr D 66, 1341--1350 (2010). Ion Checks I.D.Brown and K.K.Wu, Empirical Parameters for Calculating Cation-Oxygen Bond Valences Acta Cryst. B32, 1957--1959 (1975). M.Nayal and E.Di Cera, Valence Screening of Water in Protein Crystals Reveals Potential Na+ Binding Sites J.Mol.Biol. 256 228--234 (1996). P.Mueller, S.Koepke and G.M.Sheldrick, Is the bond-valence method able to identify metal atoms in protein structures? Acta Cryst. D 59 32--37 (2003). Checking checks K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al. Who checks the checkers J.Mol.Biol. (1998) 276,417-436. /home/vriend/whatif/dbdata/pdbout2html After running WHAT IF's WHAT_CHECK option many things have happened to the data structure that might not be optimal for many other options. FULCHK therefore is a so-called terminal option, i.e. after running the validation option, WHAT IF will restart without any coordinates in the soup; so the molecule you just checked got deleted together with anything else you might have had in the SOUP. Option not found, try:%NO For obvious reasons $ commands are not allowed in WWW scripts. WHAT IF detected a $ in a WWW script. The command will be listed below. If this command contains something that is potentially harmful to your environment, please mail G Vriend (Vriend@cmbi.kun.nl) which $ command was detected, and from where you got this script. Option:$/home/vriend/whatif/dbdata/pdbout2html ERROR. Trying to close non-opened log file ============== WHAT IF G.Vriend, WHAT IF: a molecular modelling and drug design program, J. Mol. Graph. 8, 52--56 (1990). WHAT_CHECK (verification routines from WHAT IF) R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola, Errors in protein structures Nature 381, 272 (1996). (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra information) 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). R.W.W. Hooft, C.Sander and G.Vriend, Objectively judging the quality of a protein structure from a Ramachandran plot CABIOS (1997), 13, 425--430. Symmetry Checks R.W.W.Hooft, C.Sander and G.Vriend, Reconstruction of symmetry related molecules from protein data bank (PDB) files J. Appl. Cryst. 27, 1006--1009 (1994). Tau angle W.G.Touw and G.Vriend On the complexity of Engh and Huber refinement restraints: the angle tau as example. Acta Crystallogr D 66, 1341--1350 (2010). Ion Checks I.D.Brown and K.K.Wu, Empirical Parameters for Calculating Cation-Oxygen Bond Valences Acta Cryst. B32, 1957--1959 (1975). M.Nayal and E.Di Cera, Valence Screening of Water in Protein Crystals Reveals Potential Na+ Binding Sites J.Mol.Biol. 256 228--234 (1996). P.Mueller, S.Koepke and G.M.Sheldrick, Is the bond-valence method able to identify metal atoms in protein structures? Acta Cryst. D 59 32--37 (2003). Checking checks K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al. Who checks the checkers J.Mol.Biol. (1998) 276,417-436.