************************************************************************ ********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program ********** ************************************************************************ Date : 2011-09-09 This report was created by WHAT IF version 20110906-2245 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. WARNING. Date error on HEADER card: HEADER DUMMY FOR WHATIF 1 - 10 LYS VAL PHE GLU ARG CYS GLU LEU ALA ARG 11 - 20 THR LEU LYS ARG LEU GLY MET ASP GLY TYR 21 - 30 ARG GLY ILE SER LEU ALA ASN TRP MET CYS 31 - 40 LEU ALA LYS TRP GLU SER GLY TYR ASN THR 41 - 50 ARG ALA THR ASN TYR ASN ALA GLY ASP ARG 51 - 60 SER THR ASP TYR GLY ILE PHE GLN ILE ASN 61 - 70 SER ARG TYR TRP CYS ASN ASP GLY LYS THR 71 - 80 PRO GLY ALA VAL ASN ALA CYS HIS LEU SER 81 - 90 CYS SER ALA LEU LEU GLN ASP ASN ILE ALA 91 - 100 ASP ALA VAL ALA CYS ALA LYS ARG VAL VAL 101 - 110 ARG GLU PRO GLN GLY ILE ARG ALA TRP VAL 111 - 120 ALA TRP ARG ASN ARG CYS GLN ASN ARG ASP 121 - 130 VAL ARG GLN TYR VAL GLN GLY CYS GLY VAL 131 - 132 NAG NAG 136 GAL ( 133-) A - Starting PRODRUG on this drug 136 GAL ( 133-) A - Incomplete TOPOLOGY ********************************************************************** *** *** *** Work to do... *** *** *** ********************************************************************** 136 GAL ( 133-) A - Terminate PRODRUG on USEDD3 error flag 134 GAL ( 131-) A - Starting PRODRUG on this drug 134 GAL ( 131-) A - Incomplete TOPOLOGY ********************************************************************** *** *** *** Work to do... *** *** *** ********************************************************************** 134 GAL ( 131-) A - Terminate PRODRUG on USEDD3 error flag ======================================================================== ==== Compound code /home/whatif/httpd/htdocs/servers/tmp//tmpEti5SI/====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: Chain identifiers OK WHAT CHECK has not detected any serious chain identifier problems. But be aware that WHAT CHECK doesn't care about the chain identifiers of waters. # 4 # Warning: Ligands or residues without topology The entities (non-canonical residues or ligands) in the table below are too complicated for the automatic topology determination. WHAT CHECK uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities. The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'Residue' indicates that WHAT CHECK thinks that this entity is perhaps a non-canonical residue. 'OK' indicates that the automatic topology generation succeeded. 134 GAL ( 131-) A - 136 GAL ( 133-) A - # 5 # Note: No strange inter-chain connections detected No covalent bonds have been detected between molecules with non-identical chain identifiers. # 6 # Note: No duplicate atom names in ligands All atom names in ligands seem adequately unique. # 7 # 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. # 8 # Note: In all cases the primary alternate atom was used WHAT CHECK saw no need to make any alternate atom corrections (which means they are all correct, or there are none). # 9 # 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). # 10 # Warning: Groups attached to potentially hydrogenbonding atoms Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT CHECK is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error. For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day. 35 GLU ( 35-) A - OE2 bound to 137 GOL ( 136-) A - C1 53 ASP ( 53-) A - OD2 bound to 135 GOL ( 135-) A - C1 131 NAG ( 132-) A - O4 bound to 134 GAL ( 131-) A - C1 132 NAG ( 134-) A - O4 bound to 136 GAL ( 133-) A - C1 # 11 # 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. # 12 # 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. # 13 # Note: All residues have a complete backbone. No residues have missing backbone atoms. # 14 # Note: No C-alpha only residues There are no residues that consist of only an alpha carbon atom. # 15 # Note: Non-canonical residues WHAT CHECK has not detected any non-canonical residue(s). Number of NMR MODELs skipped upon reading PDB file: 9 # 16 # Note: Content of the PDB file as interpreted by WHAT CHECK Content of the PDB file as interpreted by WHAT CHECK. WHAT CHECK 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 CHECK output formats can be found at swift.cmbi.umcn.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK web pages. 1 1 ( 1) 130 ( 130) A Protein checkset 2 131 ( 132) 131 ( 132) A Sugar<= checkset 3 132 ( 134) 132 ( 134) A Sugar<= checkset 4 133 ( 130) 133 ( 130) A V O2 <- 130 checkset 5 134 ( 131) 134 ( 131) A GAL <- checkset 6 135 ( 135) 135 ( 135) A GOL <= checkset 7 136 ( 133) 136 ( 133) A GAL <- checkset 8 137 ( 136) 137 ( 136) A GOL <= checkset 9 138 ( HOH ) 138 ( HOH ) A water ( 113) checkset # 17 # 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 130. Number of (recognized) sugars: 2 Number of water molecules: 113 # 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 swift.cmbi.umcn.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 KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQIN ( 1)-( 60) HHHHHHHHHHTT TT TT HHHHHHHHHHHHTT TT SSSSTTTTSSSSTTTTSS 70 80 90 100 110 120 | | | | | | 61 - 120 SRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVREPQGIRAWVAWRNRCQNRD ( 61)-( 120)TTTT T TT TT 33333TT HHHHHHHHHHTTTTT3333 HHHHHHTTTT 130 | 121 - 130 VRQYVQGCGV ( 121)-( 130) 3333TTT # 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 # Note: No missing atoms detected in residues All expected atoms are present in residues. This validation option has not looked at 'things' that can or should be attached to the elemantary building blocks (amino acids, nucleotides). Even the C-terminal oxygens are treated separately. # 22 # Note: All B-factors fall in the range 0.0 - 100.0 All B-factors are larger than zero, and none are observed above 100.0. # 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: C-terminus capping The residues listed in the table below either are pseudo C-terminal residues, or have two groups attached of which neither is the normal C-terminal O. In this table REAL means that the C-terminal residue is likely to be the real C-terminus of its chain; OX means that an incorrect second oxygen (OXT) was detected that should not be there; -O indicates that the 'normal' oxygen (i.e. not the OXT) is missing; OT indicates the detection of any other capping group. C-terminal nitrogen atoms, if any, have already been dealt with in a previous check and are indicated here by -N. PSEUDO means that this is the last visible residue in the chain, but not the real C-terminus, i.e. all residues after this one are missing in this chain. BREAK means that this is the last residue before a chain-break, i.e. the chain continues but after this residue a number of residues is missing. In case a break is observed the number of residues that seems to be missing is shown in brackets. OK means that given the status (REAL, PSEUDO, BREAK), no problems were found. Be aware that we cannot easily see the difference between these errors and errors in the chain and residue numbering schemes. So do not blindly trust the table below. 130 VAL ( 130-) A : Unknown problem # 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 # Warning: Low bond length variability Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures. RMS Z-score for bond lengths: 0.554 RMS-deviation in bond distances: 0.013 # 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. 4 GLU ( 4-) A N CA C 97.07 -5.0 64 TRP ( 64-) A N CA C 125.75 5.2 110 VAL ( 110-) A N CA CB 117.61 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: 0.821 RMS-deviation in bond angles: 1.859 # 42 # Note: Residue hand error(s) No atoms are observed that have the wrong handedness. Be aware, though, that WHAT CHECK might have corrected the handedness of some atoms already. The handedness has not been corrected for any case where the problem is worse than just an administrative discomfort. # 43 # Note: Chirality OK All protein atoms have proper chirality, or there is no intact protein present in the PDB file. The average deviation= 1.171 # 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 : 1.218 # 45 # Error: Tau angle problems The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value. 64 TRP ( 64-) A 5.51 4 GLU ( 4-) A 4.90 36 SER ( 36-) A 4.42 115 ARG ( 115-) A 4.38 # 46 # Warning: High tau angle deviations The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, 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 : 1.751 # 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 # Error: Connections to aromatic rings out of plane The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane. For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures. 63 TYR ( 63-) A OH 12.26 Since there is no DNA and no protein with hydrogens, no uncalibrated planarity check was performed. Ramachandran Z-score : -1.324 # 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 : -1.324 # 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 CHECK 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. 85 LEU ( 85-) A -2.3 38 TYR ( 38-) A -2.3 79 LEU ( 79-) A -2.1 21 ARG ( 21-) A -2.1 # 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. 21 ARG ( 21-) A Poor phi/psi 38 TYR ( 38-) A Poor phi/psi 50 ARG ( 50-) A Poor phi/psi 118 ASN ( 118-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -2.248 # 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 : -2.248 # 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! 15 LEU ( 15-) A 0 17 MET ( 17-) A 0 18 ASP ( 18-) A 0 20 TYR ( 20-) A 0 21 ARG ( 21-) A 0 36 SER ( 36-) A 0 38 TYR ( 38-) A 0 42 ALA ( 42-) A 0 54 TYR ( 54-) A 0 60 ASN ( 60-) A 0 63 TYR ( 63-) A 0 64 TRP ( 64-) A 0 67 ASP ( 67-) A 0 71 PRO ( 71-) A 0 73 ALA ( 73-) A 0 77 CYS ( 77-) A 0 78 HIS ( 78-) A 0 81 CYS ( 81-) A 0 86 GLN ( 86-) A 0 87 ASP ( 87-) A 0 102 GLU ( 102-) A 0 104 GLN ( 104-) A 0 106 ILE ( 106-) A 0 107 ARG ( 107-) A 0 109 TRP ( 109-) A 0 110 VAL ( 110-) A 0 115 ARG ( 115-) A 0 117 GLN ( 117-) A 0 118 ASN ( 118-) A 0 121 VAL ( 121-) A 0 128 CYS ( 128-) A 0 129 GLY ( 129-) A 0 130 VAL ( 130-) A 0 5 ARG ( 5-) A 1 39 ASN ( 39-) A 1 41 ARG ( 41-) A 1 47 ALA ( 47-) A 1 51 SER ( 51-) A 1 58 GLN ( 58-) A 1 65 CYS ( 65-) A 1 69 LYS ( 69-) A 1 74 VAL ( 74-) A 1 75 ASN ( 75-) A 1 76 ALA ( 76-) A 1 82 SER ( 82-) A 1 88 ASN ( 88-) A 1 89 ILE ( 89-) A 1 100 VAL ( 100-) A 1 116 CYS ( 116-) A 1 122 ARG ( 122-) A 1 125 VAL ( 125-) A 1 126 GLN ( 126-) A 1 35 GLU ( 35-) A 2 56 ILE ( 56-) A 2 57 PHE ( 57-) A 2 79 LEU ( 79-) A 2 101 ARG ( 101-) A 2 114 ASN ( 114-) 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 : -0.992 Omega average and std. deviation= 179.739 1.891 Significant deviations from expected 5.5!!! # 56 # Warning: Omega angles too tightly restrained The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees. Standard deviation of omega values : 1.891 # 57 # Note: Backbone oxygen evaluation OK All residues for which the local backbone conformation could be found in the WHAT CHECK database have a normal backbone oxygen position. # 58 # Note: Peptide bond conformations There are not enough (intact) amino acids in the file to analyse peptide bond conformations. # 59 # Note: PRO puckering amplitude OK Puckering amplitudes for all PRO residues are within normal ranges. # 60 # Note: PRO puckering phases OK Puckering phases for all PRO residues are normal # 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. 136 GAL ( 133-) A C5 <-> 138 HOH ( 248 ) A O 0.37 2.43 INTRA 66 ASN ( 66-) A ND2 <-> 138 HOH ( 246 ) A O 0.22 2.48 INTRA 78 HIS ( 78-) A CE1 <-> 138 HOH ( 235 ) A O 0.20 2.60 INTRA 65 CYS ( 65-) A C <-> 81 CYS ( 81-) A SG 0.19 3.21 INTRA BL 62 ARG ( 62-) A NH2 <-> 71 PRO ( 71-) A O 0.17 2.53 INTRA 50 ARG ( 50-) A NH1 <-> 138 HOH ( 217 ) A O 0.14 2.56 INTRA 120 ASP ( 120-) A O <-> 123 GLN ( 123-) A NE2 0.13 2.57 INTRA BL 91 ASP ( 91-) A CB <-> 138 HOH ( 212 ) A O 0.09 2.71 INTRA 49 ASP ( 49-) A O <-> 62 ARG ( 62-) A NH1 0.09 2.61 INTRA 110 VAL ( 110-) A CG1 <-> 113 ARG ( 113-) A NH1 0.08 3.02 INTRA 49 ASP ( 49-) A OD2 <-> 138 HOH ( 244 ) A O 0.07 2.33 INTRA 118 ASN ( 118-) A N <-> 138 HOH ( 147 ) A O 0.07 2.63 INTRA BL 136 GAL ( 133-) A O5 <-> 138 HOH ( 248 ) A O 0.07 2.33 INTRA 132 NAG ( 134-) A C7 <-> 137 GOL ( 136-) A C3 0.07 3.13 INTRA 138 HOH ( 154 ) A O <-> 138 HOH ( 247 ) A O 0.06 2.14 INTRA BL 112 TRP ( 112-) A CD1 <-> 116 CYS ( 116-) A CB 0.05 3.15 INTRA BL 135 GOL ( 135-) A C1 <-> 137 GOL ( 136-) A C3 0.05 3.15 INTRA 132 NAG ( 134-) A O7 <-> 137 GOL ( 136-) A C3 0.04 2.76 INTRA 109 TRP ( 109-) A NE1 <-> 131 NAG ( 132-) A C8 0.04 3.06 INTRA BL 44 ASN ( 44-) A O <-> 53 ASP ( 53-) A N 0.02 2.68 INTRA BL 19 GLY ( 19-) A N <-> 23 ILE ( 23-) A O 0.02 2.68 INTRA BL 136 GAL ( 133-) A C1 <-> 138 HOH ( 248 ) A O 0.02 2.78 INTRA 57 PHE ( 57-) A O <-> 109 TRP ( 109-) A NE1 0.02 2.68 INTRA BL 120 ASP ( 120-) A O <-> 123 GLN ( 123-) A CD 0.02 2.78 INTRA BL 133 VAL ( 130-) A O'' <-> 138 HOH ( 216 ) A O 0.02 2.38 INTRA 129 GLY ( 129-) A N <-> 138 HOH ( 185 ) A O 0.01 2.69 INTRA # 62 # Note: Some notes regarding these bumps The bumps have been binned in 5 categories ranging from 'should deal with' till 'must fix'. Additionally, the integrated sum of all bumps, the squared sum of all bumps, and these latter two values normalized by the number of contacts are listed too for comparison purposes between, for example, small and large proteins. Total bump value: 2.331 Total bump value per residue: 0.197 Total number of bumps: 26 Total squared bump value: 0.383 Total number of bumps in the mildest bin: 25 Total number of bumps in the second bin: 1 Total number of bumps in the middle bin: 0 Total number of bumps in the fourth bin: 0 Total number of bumps in the worst bin: 0 # 63 # 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 : 0.909 14 ARG ( 14) : -5.731 21 ARG ( 21) : -5.443 69 LYS ( 69) : -5.444 78 HIS ( 78) : -5.120 101 ARG ( 101) : -5.950 114 ASN ( 114) : -5.090 118 ASN ( 118) : -5.052 # 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. 101 ARG ( 101-) A -5.95 14 ARG ( 14-) A -5.73 69 LYS ( 69-) A -5.44 21 ARG ( 21-) A -5.44 78 HIS ( 78-) A -5.12 114 ASN ( 114-) A -5.09 118 ASN ( 118-) A -5.05 # 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. 34 TRP ( 34-) A 36 - SER 36- ( A) -4.49 # 66 # Note: Structural average packing environment OK The structural average packing score is within normal ranges. Average for range 1 - 132 : -1.009 -Residue- State AllAll BB-BB BB-SC SC-BB SC-SC - All contacts : Average = -0.172 Z-score = -1.16 BB-BB contacts : Average = -0.208 Z-score = -1.44 BB-SC contacts : Average = -0.031 Z-score = -0.32 SC-BB contacts : Average = -0.105 Z-score = -0.53 SC-SC contacts : Average = -0.114 Z-score = -0.47 # 67 # 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 packing 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. 108 ALA ( 108-) A -2.82 # 68 # 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. # 69 # Note: Structural average packing Z-score OK The structural average for the second generation packing score is within normal ranges. All contacts : Average = -0.172 Z-score = -1.16 BB-BB contacts : Average = -0.208 Z-score = -1.44 BB-SC contacts : Average = -0.031 Z-score = -0.32 SC-BB contacts : Average = -0.105 Z-score = -0.53 SC-SC contacts : Average = -0.114 Z-score = -0.47 # 70 # Note: Water contacts OK All water clusters make at least one contact with a non-water atom. # 71 # Note: Symmetry related water molecules check not performed Since there is no symmetry, the position check for symmetry related water molecules can not be performed # 72 # Error: Water molecules without hydrogen bonds The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file. 138 HOH ( 221 ) A O 138 HOH ( 224 ) A O Number of donors: 356 Number of H-atoms: 525 Number of donor groups: 12 Symmetry related molecules will be taken into account Calculating accessibilities and coordinates The FLIP penalty for 78 HIS ( 78-) A was set to 0.4 Number of positive ions : 0 Finding possible acceptors for all donors... Total number of potential acceptors: 508 Locating affected donors for all ambiguities... Number of donors affected by ambiguities: 343 Initializing group penalty for all donors 356 Fraction of hydrogen network done : 0.000 Fraction of hydrogen network done : 0.070 Fraction of hydrogen network done : 0.270 Fraction of hydrogen network done : 0.298 Fraction of hydrogen network done : 0.337 Fraction of hydrogen network done : 0.361 Fraction of hydrogen network done : 0.386 Fraction of hydrogen network done : 0.410 Fraction of hydrogen network done : 0.488 Fraction of hydrogen network done : 0.496 Fraction of hydrogen network done : 0.505 Fraction of hydrogen network done : 0.533 Fraction of hydrogen network done : 0.535 Fraction of hydrogen network done : 0.539 Fraction of hydrogen network done : 0.630 Fraction of hydrogen network done : 0.639 Fraction of hydrogen network done : 0.644 Fraction of hydrogen network done : 0.645 Fraction of hydrogen network done : 0.649 Fraction of hydrogen network done : 0.661 Fraction of hydrogen network done : 0.676 Fraction of hydrogen network done : 0.695 Fraction of hydrogen network done : 0.712 Fraction of hydrogen network done : 0.737 Fraction of hydrogen network done : 0.754 Fraction of hydrogen network done : 0.774 Fraction of hydrogen network done : 0.779 Fraction of hydrogen network done : 0.794 Fraction of hydrogen network done : 0.863 Fraction of hydrogen network done : 0.870 Fraction of hydrogen network done : 0.878 Fraction of hydrogen network done : 0.893 Fraction of hydrogen network done : 0.901 Fraction of hydrogen network done : 0.908 Fraction of hydrogen network done : 0.924 Fraction of hydrogen network done : 0.931 Fraction of hydrogen network done : 0.939 Fraction of hydrogen network done : 0.947 Fraction of hydrogen network done : 0.954 Fraction of hydrogen network done : 0.962 Fraction of hydrogen network done : 0.969 Fraction of hydrogen network done : 0.977 Fraction of hydrogen network done : 0.992 Fraction of hydrogen network done : 1.000 Total log10 N solved by Cutting.....: 28.528 Total log10 N solved by Treshold Acc: 247.823 Total log10 N solved by Brute Force.: 59.445 Of these only TA is a heuristic method. Total number of positions evaluated 1089125 # 73 # 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. 60 ASN ( 60-) A 78 HIS ( 78-) A # 74 # 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, and if enough (high resolution) data is available. 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. 78 HIS ( 78-) A HIS-H 0.30 HIS-E 0.72 Unsatisfied donor : 21 ARG ( 21-) A NE Unsatisfied donor : 26 ALA ( 26-) A N Unsatisfied donor : 58 GLN ( 58-) A NE2 -Potential acceptor : 44 ASN ( 44-) A OD1 -Potential acceptor : 55 GLY ( 55-) A O Unsatisfied donor : 69 LYS ( 69-) A NZ -Potential acceptor : 52 THR ( 52-) A OG1 -Potential acceptor : 67 ASP ( 67-) A OD2 Unsatisfied donor : 91 ASP ( 91-) A N Unsatisfied donor : 132 NAG ( 134-) A O6 # 75 # 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. 21 ARG ( 21-) A NE 26 ALA ( 26-) A N 58 GLN ( 58-) A NE2 69 LYS ( 69-) A NZ 91 ASP ( 91-) A N 132 NAG ( 134-) A O6 1 LYS ( 1-) A N 2.9615 0.6595 0.0000 1 LYS ( 1-) A O 0.0000 0.0000 0.4332 1 LYS ( 1-) A NZ 8.2609 0.5670 0.0000 2 VAL ( 2-) A N 2.4939 0.0000 0.0000 2 VAL ( 2-) A O 4.4398 0.0000 0.0000 3 PHE ( 3-) A N 0.0000 0.6348 0.0000 3 PHE ( 3-) A O 0.8457 0.0000 0.3694 4 GLU ( 4-) A N 0.0000 0.7507 0.0000 4 GLU ( 4-) A O 0.0000 0.0000 0.3572 4 GLU ( 4-) A OE1 3.5941 0.0000 0.0000 4 GLU ( 4-) A OE2 5.9197 0.0000 0.0000 5 ARG ( 5-) A N 2.1821 0.9491 0.0000 5 ARG ( 5-) A O 0.0000 0.0000 0.3649 5 ARG ( 5-) A NE 4.8319 0.0000 0.0000 5 ARG ( 5-) A NH1 0.0000 0.8422 0.0000 5 ARG ( 5-) A NH2 10.5989 0.4872 0.0000 6 CYS ( 6-) A N 0.9352 1.2045 0.0000 6 CYS ( 6-) A O 0.0000 0.0000 0.4042 6 CYS ( 6-) A SG 3.8832 0.0000 0.0000 7 GLU ( 7-) A N 0.3117 0.4493 0.0000 7 GLU ( 7-) A O 0.3171 0.0000 0.5466 7 GLU ( 7-) A OE1 0.8457 0.0000 0.4168 7 GLU ( 7-) A OE2 5.2854 0.0000 0.6872 8 LEU ( 8-) A N 0.0000 0.6432 0.0000 8 LEU ( 8-) A O 0.0000 0.0000 0.3644 9 ALA ( 9-) A N 0.0000 0.6571 0.0000 9 ALA ( 9-) A O 0.0000 0.0000 0.2879 10 ARG ( 10-) A N 0.0000 0.7280 0.0000 10 ARG ( 10-) A O 0.2114 0.0000 0.3851 10 ARG ( 10-) A NE 4.0525 0.4377 0.0000 10 ARG ( 10-) A NH1 3.2732 0.4690 0.0000 10 ARG ( 10-) A NH2 10.1313 0.7795 0.0000 11 THR ( 11-) A N 0.1559 0.5125 0.0000 11 THR ( 11-) A O 0.0000 0.0000 0.6231 11 THR ( 11-) A OG1 4.0169 0.4719 0.0000 12 LEU ( 12-) A N 0.0000 0.6562 0.0000 12 LEU ( 12-) A O 0.0000 0.0000 0.3510 13 LYS ( 13-) A N 0.0000 0.5185 0.0000 13 LYS ( 13-) A O 2.8541 0.0000 0.8824 13 LYS ( 13-) A NZ 9.6637 1.2464 0.0000 14 ARG ( 14-) A N 0.0000 0.6936 0.0000 14 ARG ( 14-) A O 6.7653 0.0000 0.0000 14 ARG ( 14-) A NE 5.6112 0.3857 0.0000 14 ARG ( 14-) A NH1 8.5726 0.0000 0.0000 14 ARG ( 14-) A NH2 18.5481 0.3467 0.0000 15 LEU ( 15-) A N 0.0000 0.4735 0.0000 15 LEU ( 15-) A O 0.5285 0.0000 0.3092 16 GLY ( 16-) A N 0.6235 0.5072 0.0000 16 GLY ( 16-) A O 2.1142 0.0000 0.4355 17 MET ( 17-) A N 0.0000 0.6321 0.0000 17 MET ( 17-) A O 0.0000 0.0000 0.5849 17 MET ( 17-) A SD 0.0000 0.0000 0.0000 18 ASP ( 18-) A N 0.0000 0.7189 0.0000 18 ASP ( 18-) A O 5.4968 0.0000 0.5184 18 ASP ( 18-) A OD1 3.5941 0.0000 0.0414 18 ASP ( 18-) A OD2 1.6913 0.0000 0.4101 19 GLY ( 19-) A N 0.0000 0.8553 0.0000 19 GLY ( 19-) A O 4.4398 0.0000 0.2811 20 TYR ( 20-) A N 0.0000 0.6216 0.0000 20 TYR ( 20-) A O 0.0000 0.0000 0.3388 20 TYR ( 20-) A OH 2.4313 0.0000 0.3110 21 ARG ( 21-) A N 2.8056 0.7948 0.0000 21 ARG ( 21-) A O 4.7569 0.0000 0.0000 21 ARG ( 21-) A NE 0.0000 0.0000 0.0000 21 ARG ( 21-) A NH1 14.9632 0.0000 0.0000 21 ARG ( 21-) A NH2 8.1050 0.8508 0.0000 22 GLY ( 22-) A N 2.0263 0.5063 0.0000 22 GLY ( 22-) A O 7.5053 0.0000 0.0000 23 ILE ( 23-) A N 0.0000 0.6101 0.0000 23 ILE ( 23-) A O 0.0000 0.0000 0.2903 24 SER ( 24-) A N 0.4676 0.1164 0.0000 24 SER ( 24-) A O 0.0000 0.0000 0.3046 24 SER ( 24-) A OG 0.9514 0.8738 0.5815 25 LEU ( 25-) A N 0.0000 0.0746 0.0000 25 LEU ( 25-) A O 0.0000 0.0000 0.3578 26 ALA ( 26-) A N 0.0000 0.0000 0.0000 26 ALA ( 26-) A O 0.0000 0.0000 0.3723 27 ASN ( 27-) A N 0.0000 0.6943 0.0000 27 ASN ( 27-) A O 0.0000 0.0000 0.3164 27 ASN ( 27-) A OD1 0.7400 0.0000 0.9239 27 ASN ( 27-) A ND2 8.8844 0.9874 0.0000 28 TRP ( 28-) A N 0.0000 0.5678 0.0000 28 TRP ( 28-) A O 0.0000 0.0000 0.3919 28 TRP ( 28-) A NE1 0.0000 0.4319 0.0000 29 MET ( 29-) A N 0.0000 0.6443 0.0000 29 MET ( 29-) A O 0.0000 0.0000 0.3651 29 MET ( 29-) A SD 0.0000 0.0000 0.0000 30 CYS ( 30-) A N 0.0000 0.6705 0.0000 30 CYS ( 30-) A O 0.0000 0.0000 0.3950 30 CYS ( 30-) A SG 0.0000 0.0000 0.0000 31 LEU ( 31-) A N 0.0000 0.5697 0.0000 31 LEU ( 31-) A O 0.0000 0.0000 0.3072 32 ALA ( 32-) A N 0.0000 0.7057 0.0000 32 ALA ( 32-) A O 0.0000 0.0000 0.6635 33 LYS ( 33-) A N 0.0000 0.6576 0.0000 33 LYS ( 33-) A O 1.0571 0.0000 0.4016 33 LYS ( 33-) A NZ 15.8983 0.0000 0.0000 34 TRP ( 34-) A N 0.0000 0.7114 0.0000 34 TRP ( 34-) A O 5.1797 0.0000 0.0000 34 TRP ( 34-) A NE1 0.0000 0.6845 0.0000 35 GLU ( 35-) A N 0.0000 0.5533 0.0000 35 GLU ( 35-) A O 3.9112 0.0000 0.8143 35 GLU ( 35-) A OE1 0.0000 0.0000 0.2021 36 SER ( 36-) A N 0.0000 0.6749 0.0000 36 SER ( 36-) A O 2.2199 0.0000 0.2411 36 SER ( 36-) A OG 0.0000 0.7549 0.1405 37 GLY ( 37-) A N 0.7793 0.8403 0.0000 37 GLY ( 37-) A O 2.3256 0.0000 0.3008 38 TYR ( 38-) A N 0.0000 0.8245 0.0000 38 TYR ( 38-) A O 0.0000 0.0000 0.3525 38 TYR ( 38-) A OH 0.8457 0.9074 0.0000 39 ASN ( 39-) A N 0.0000 0.3992 0.0000 39 ASN ( 39-) A O 0.0000 0.0000 0.3075 39 ASN ( 39-) A OD1 0.1057 0.0000 0.3924 39 ASN ( 39-) A ND2 8.1050 0.6749 0.0000 40 THR ( 40-) A N 0.0000 1.0395 0.0000 40 THR ( 40-) A O 0.0000 0.0000 0.0000 40 THR ( 40-) A OG1 0.0000 0.8167 0.3662 41 ARG ( 41-) A N 0.0000 0.7067 0.0000 41 ARG ( 41-) A O 3.4884 0.0000 0.0000 41 ARG ( 41-) A NE 4.6760 0.0000 0.0000 41 ARG ( 41-) A NH1 7.9492 0.0000 0.0000 41 ARG ( 41-) A NH2 13.7162 0.0000 0.0000 42 ALA ( 42-) A N 0.0000 0.5537 0.0000 42 ALA ( 42-) A O 0.0000 0.0000 0.2678 43 THR ( 43-) A N 1.4028 0.0000 0.0000 43 THR ( 43-) A O 3.6998 0.0000 0.0000 43 THR ( 43-) A OG1 6.7653 0.0000 0.8703 44 ASN ( 44-) A N 0.0000 0.7425 0.0000 44 ASN ( 44-) A O 0.9514 0.0000 0.6339 44 ASN ( 44-) A OD1 3.9112 0.0000 0.1611 44 ASN ( 44-) A ND2 14.1838 0.4681 0.0000 45 TYR ( 45-) A N 2.3380 0.6458 0.0000 45 TYR ( 45-) A O 6.4482 0.0000 0.0000 45 TYR ( 45-) A OH 5.6026 0.6405 0.4255 46 ASN ( 46-) A N 0.0000 0.7569 0.0000 46 ASN ( 46-) A O 0.0000 0.0000 0.2125 46 ASN ( 46-) A OD1 2.8541 0.0000 0.1877 46 ASN ( 46-) A ND2 11.8458 0.0000 0.0000 47 ALA ( 47-) A N 1.8704 0.0000 0.0000 47 ALA ( 47-) A O 3.9112 0.0000 0.0000 48 GLY ( 48-) A N 2.0263 0.9095 0.0000 48 GLY ( 48-) A O 6.7653 0.0000 0.0000 49 ASP ( 49-) A N 0.1559 0.5551 0.0000 49 ASP ( 49-) A O 0.2114 0.0000 0.3841 49 ASP ( 49-) A OD1 0.0000 0.0000 0.6243 49 ASP ( 49-) A OD2 2.7484 0.0000 0.3488 50 ARG ( 50-) A N 0.0000 0.3827 0.0000 50 ARG ( 50-) A O 0.2114 0.0000 0.0000 50 ARG ( 50-) A NE 4.5201 0.0000 0.0000 50 ARG ( 50-) A NH1 12.1576 0.5922 0.0000 50 ARG ( 50-) A NH2 17.6129 0.0000 0.0000 51 SER ( 51-) A N 0.0000 0.8145 0.0000 51 SER ( 51-) A O 0.0000 0.0000 0.4203 51 SER ( 51-) A OG 0.4228 0.6555 0.4957 52 THR ( 52-) A N 0.0000 0.7394 0.0000 52 THR ( 52-) A O 0.0000 0.0000 0.3263 52 THR ( 52-) A OG1 0.4228 0.0000 0.8866 53 ASP ( 53-) A N 0.1559 0.6888 0.0000 53 ASP ( 53-) A O 0.0000 0.0000 0.4123 53 ASP ( 53-) A OD1 0.1057 0.0000 0.1960 54 TYR ( 54-) A N 0.0000 0.7218 0.0000 54 TYR ( 54-) A O 0.3171 0.0000 0.7476 54 TYR ( 54-) A OH 1.6913 0.6591 0.4583 55 GLY ( 55-) A N 0.0000 0.4823 0.0000 55 GLY ( 55-) A O 0.0000 0.0000 0.6177 56 ILE ( 56-) A N 0.0000 0.7075 0.0000 56 ILE ( 56-) A O 0.0000 0.0000 0.2910 57 PHE ( 57-) A N 0.0000 0.6874 0.0000 57 PHE ( 57-) A O 0.0000 0.0000 0.2898 58 GLN ( 58-) A N 0.0000 0.3557 0.0000 58 GLN ( 58-) A O 0.0000 0.0000 0.1122 58 GLN ( 58-) A OE1 0.6343 0.0000 0.0000 58 GLN ( 58-) A NE2 0.0000 0.7690 0.0000 59 ILE ( 59-) A N 0.0000 0.5806 0.0000 59 ILE ( 59-) A O 0.0000 0.0000 0.4008 60 ASN ( 60-) A N 0.0000 0.6129 0.0000 60 ASN ( 60-) A O 0.0000 0.0000 0.5490 60 ASN ( 60-) A OD1 0.0000 0.0000 0.4030 60 ASN ( 60-) A ND2 1.5587 0.9569 0.0000 61 SER ( 61-) A N 0.0000 0.8755 0.0000 61 SER ( 61-) A O 0.0000 0.0000 0.3919 61 SER ( 61-) A OG 0.0000 0.7066 0.4106 62 ARG ( 62-) A N 0.0000 0.7258 0.0000 62 ARG ( 62-) A O 0.0000 0.0000 0.2722 62 ARG ( 62-) A NE 3.4291 0.3427 0.0000 62 ARG ( 62-) A NH1 0.0000 0.5938 0.0000 62 ARG ( 62-) A NH2 2.9615 0.2635 0.0000 63 TYR ( 63-) A N 0.0000 0.1952 0.0000 63 TYR ( 63-) A O 0.0000 0.0000 0.6088 63 TYR ( 63-) A OH 4.9683 0.0000 0.0000 64 TRP ( 64-) A N 0.0000 0.5237 0.0000 64 TRP ( 64-) A O 0.0000 0.0000 0.3512 64 TRP ( 64-) A NE1 0.0000 0.7053 0.0000 65 CYS ( 65-) A N 0.0000 0.4650 0.0000 65 CYS ( 65-) A O 0.0000 0.0000 0.3542 65 CYS ( 65-) A SG 0.0000 0.0000 0.0000 66 ASN ( 66-) A N 0.0000 0.7908 0.0000 66 ASN ( 66-) A O 1.3742 0.0000 0.5863 66 ASN ( 66-) A OD1 6.9768 0.0000 0.0000 66 ASN ( 66-) A ND2 6.5464 1.1601 0.0000 67 ASP ( 67-) A N 0.3117 0.8098 0.0000 67 ASP ( 67-) A O 4.6512 0.0000 0.0000 67 ASP ( 67-) A OD1 0.1057 0.0000 0.7833 67 ASP ( 67-) A OD2 0.0000 0.0000 0.6860 68 GLY ( 68-) A N 0.1559 0.0000 0.0000 68 GLY ( 68-) A O 7.9281 0.0000 0.0000 69 LYS ( 69-) A N 0.0000 0.6635 0.0000 69 LYS ( 69-) A O 4.0169 0.0000 0.0000 69 LYS ( 69-) A NZ 0.0000 1.4798 0.0000 70 THR ( 70-) A N 0.4676 0.3377 0.0000 70 THR ( 70-) A O 2.1142 0.0000 0.5377 70 THR ( 70-) A OG1 0.0000 0.7472 0.3924 71 PRO ( 71-) A O 0.0000 0.0000 0.0000 72 GLY ( 72-) A N 5.1436 0.0000 0.0000 72 GLY ( 72-) A O 3.3827 0.0000 0.0000 73 ALA ( 73-) A N 0.0000 0.4639 0.0000 73 ALA ( 73-) A O 3.8055 0.0000 0.3327 74 VAL ( 74-) A N 0.0000 0.4903 0.0000 74 VAL ( 74-) A O 4.4398 0.0000 0.1742 75 ASN ( 75-) A N 0.0000 0.3844 0.0000 75 ASN ( 75-) A O 0.2114 0.0000 0.1957 75 ASN ( 75-) A OD1 0.0000 0.0000 0.3586 75 ASN ( 75-) A ND2 6.5464 0.6789 0.0000 76 ALA ( 76-) A N 0.0000 0.8463 0.0000 76 ALA ( 76-) A O 0.8457 0.0000 0.3920 77 CYS ( 77-) A N 0.0000 0.6324 0.0000 77 CYS ( 77-) A O 4.2283 0.0000 0.5096 77 CYS ( 77-) A SG 0.4315 0.0000 0.0000 78 HIS ( 78-) A N 0.0000 0.4464 0.0000 78 HIS ( 78-) A O 5.6026 0.0000 0.0000 78 HIS ( 78-) A ND1 3.2732 0.0000 0.0000 78 HIS ( 78-) A NE2 3.7408 0.7005 0.0000 79 LEU ( 79-) A N 0.0000 0.6459 0.0000 79 LEU ( 79-) A O 0.0000 0.0000 0.4391 80 SER ( 80-) A N 2.0263 0.6379 0.0000 80 SER ( 80-) A O 0.0000 0.0000 0.2486 80 SER ( 80-) A OG 3.3827 0.5623 0.8956 81 CYS ( 81-) A N 0.1559 0.6603 0.0000 81 CYS ( 81-) A O 0.0000 0.0000 0.1957 81 CYS ( 81-) A SG 0.0000 0.0000 0.0000 82 SER ( 82-) A N 1.0911 0.7025 0.0000 82 SER ( 82-) A O 0.7400 0.0000 0.6602 82 SER ( 82-) A OG 4.6512 0.9105 0.0000 83 ALA ( 83-) A N 0.3117 0.4477 0.0000 83 ALA ( 83-) A O 0.0000 0.0000 0.1324 84 LEU ( 84-) A N 0.0000 0.3525 0.0000 84 LEU ( 84-) A O 0.4228 0.0000 0.2107 85 LEU ( 85-) A N 0.0000 0.6155 0.0000 85 LEU ( 85-) A O 0.0000 0.0000 0.3328 86 GLN ( 86-) A N 0.0000 0.2384 0.0000 86 GLN ( 86-) A O 0.4228 0.0000 0.3348 86 GLN ( 86-) A OE1 6.2368 0.0000 0.0000 86 GLN ( 86-) A NE2 9.0402 0.0000 0.0000 87 ASP ( 87-) A N 1.5587 0.0000 0.0000 87 ASP ( 87-) A O 0.6343 0.0000 0.0000 87 ASP ( 87-) A OD1 0.3171 0.0000 0.3726 87 ASP ( 87-) A OD2 7.8224 0.0000 0.0000 88 ASN ( 88-) A N 1.2469 0.7060 0.0000 88 ASN ( 88-) A O 0.0000 0.0000 0.0000 88 ASN ( 88-) A OD1 2.9598 0.0000 0.4327 88 ASN ( 88-) A ND2 12.0017 0.0000 0.0000 89 ILE ( 89-) A N 0.6235 0.9893 0.0000 89 ILE ( 89-) A O 0.0000 0.0000 0.3339 90 ALA ( 90-) A N 0.0000 0.6961 0.0000 90 ALA ( 90-) A O 1.0571 0.0000 0.5583 91 ASP ( 91-) A N 0.0000 0.0000 0.0000 91 ASP ( 91-) A O 0.0000 0.0000 0.5081 91 ASP ( 91-) A OD1 2.1142 0.0000 0.0000 91 ASP ( 91-) A OD2 0.2114 0.0000 0.4015 92 ALA ( 92-) A N 0.0000 0.3345 0.0000 92 ALA ( 92-) A O 0.0000 0.0000 0.3723 93 VAL ( 93-) A N 0.0000 0.6013 0.0000 93 VAL ( 93-) A O 0.0000 0.0000 0.3021 94 ALA ( 94-) A N 0.0000 0.6252 0.0000 94 ALA ( 94-) A O 1.5856 0.0000 0.5563 95 CYS ( 95-) A N 0.1559 0.6571 0.0000 95 CYS ( 95-) A O 0.0000 0.0000 0.4329 95 CYS ( 95-) A SG 0.0000 0.0000 0.0000 96 ALA ( 96-) A N 0.0000 0.6705 0.0000 96 ALA ( 96-) A O 0.0000 0.0000 0.3226 97 LYS ( 97-) A N 0.0000 0.5440 0.0000 97 LYS ( 97-) A O 0.0000 0.0000 0.0000 97 LYS ( 97-) A NZ 7.9492 2.3644 0.0000 98 ARG ( 98-) A N 0.0000 0.4941 0.0000 98 ARG ( 98-) A O 0.0000 0.0000 0.6930 98 ARG ( 98-) A NE 3.1173 0.4291 0.0000 98 ARG ( 98-) A NH1 0.6235 1.4941 0.0000 98 ARG ( 98-) A NH2 11.3782 1.1972 0.0000 99 VAL ( 99-) A N 0.0000 0.7796 0.0000 99 VAL ( 99-) A O 0.0000 0.0000 0.5085 100 VAL ( 100-) A N 0.0000 0.5810 0.0000 100 VAL ( 100-) A O 0.4228 0.0000 0.4724 101 ARG ( 101-) A N 0.0000 0.5819 0.0000 101 ARG ( 101-) A O 6.5539 0.0000 0.0000 101 ARG ( 101-) A NE 4.2084 0.7344 0.0000 101 ARG ( 101-) A NH1 1.2469 1.1351 0.0000 101 ARG ( 101-) A NH2 11.0665 0.1667 0.0000 102 GLU ( 102-) A N 0.0000 0.4140 0.0000 102 GLU ( 102-) A O 0.4228 0.0000 0.3121 102 GLU ( 102-) A OE1 2.3256 0.0000 0.0000 102 GLU ( 102-) A OE2 2.7484 0.0000 0.8397 103 PRO ( 103-) A O 7.2939 0.0000 0.0000 104 GLN ( 104-) A N 0.1559 0.8121 0.0000 104 GLN ( 104-) A O 1.2685 0.0000 0.3300 104 GLN ( 104-) A OE1 0.1057 0.0000 0.4694 104 GLN ( 104-) A NE2 2.4939 0.3996 0.0000 105 GLY ( 105-) A N 0.1559 0.5622 0.0000 105 GLY ( 105-) A O 0.0000 0.0000 0.6978 106 ILE ( 106-) A N 0.9352 0.9594 0.0000 106 ILE ( 106-) A O 0.0000 0.0000 0.3694 107 ARG ( 107-) A N 0.0000 0.5944 0.0000 107 ARG ( 107-) A O 0.0000 0.0000 0.4129 107 ARG ( 107-) A NE 2.8056 0.5077 0.0000 107 ARG ( 107-) A NH1 7.7933 0.0000 0.0000 107 ARG ( 107-) A NH2 12.6252 0.0000 0.0000 108 ALA ( 108-) A N 0.0000 0.5588 0.0000 108 ALA ( 108-) A O 0.0000 0.0000 0.3478 109 TRP ( 109-) A N 0.0000 0.6653 0.0000 109 TRP ( 109-) A O 0.0000 0.0000 0.6002 109 TRP ( 109-) A NE1 0.0000 0.5220 0.0000 110 VAL ( 110-) A N 0.0000 0.5373 0.0000 110 VAL ( 110-) A O 0.0000 0.0000 0.3985 111 ALA ( 111-) A N 0.0000 0.3639 0.0000 111 ALA ( 111-) A O 0.0000 0.0000 0.3086 112 TRP ( 112-) A N 0.0000 0.4064 0.0000 112 TRP ( 112-) A O 0.0000 0.0000 0.6209 112 TRP ( 112-) A NE1 0.0000 0.7326 0.0000 113 ARG ( 113-) A N 0.0000 0.6746 0.0000 113 ARG ( 113-) A O 1.7970 0.0000 0.0000 113 ARG ( 113-) A NE 0.0000 0.4639 0.0000 113 ARG ( 113-) A NH1 7.6374 0.5147 0.0000 113 ARG ( 113-) A NH2 0.9352 0.2796 0.0000 114 ASN ( 114-) A N 0.0000 0.7177 0.0000 114 ASN ( 114-) A O 2.8541 0.0000 0.0000 114 ASN ( 114-) A OD1 4.3340 0.0000 0.0000 114 ASN ( 114-) A ND2 13.2486 0.0000 0.0000 115 ARG ( 115-) A N 0.0000 0.5557 0.0000 115 ARG ( 115-) A O 1.9028 0.0000 0.3613 115 ARG ( 115-) A NE 3.4291 0.0000 0.0000 115 ARG ( 115-) A NH1 10.2872 0.7449 0.0000 115 ARG ( 115-) A NH2 15.5866 0.0000 0.0000 116 CYS ( 116-) A N 0.0000 0.5131 0.0000 116 CYS ( 116-) A O 0.4228 0.0000 0.4821 116 CYS ( 116-) A SG 0.0000 0.0000 0.0000 117 GLN ( 117-) A N 0.0000 0.6050 0.0000 117 GLN ( 117-) A O 1.0571 0.0000 0.1310 117 GLN ( 117-) A OE1 3.1713 0.0000 0.3168 117 GLN ( 117-) A NE2 4.3643 0.0000 0.0000 118 ASN ( 118-) A N 2.8056 0.6966 0.0000 118 ASN ( 118-) A O 4.6512 0.0000 0.1632 118 ASN ( 118-) A OD1 7.7167 0.0000 0.3870 118 ASN ( 118-) A ND2 12.3134 0.0000 0.0000 119 ARG ( 119-) A N 0.6235 0.2731 0.0000 119 ARG ( 119-) A O 3.0655 0.0000 0.0000 119 ARG ( 119-) A NE 1.4028 0.0000 0.0000 119 ARG ( 119-) A NH1 14.4956 0.0000 0.0000 119 ARG ( 119-) A NH2 9.6637 0.3511 0.0000 120 ASP ( 120-) A N 1.7145 0.0000 0.0000 120 ASP ( 120-) A O 1.1628 0.0000 0.0000 120 ASP ( 120-) A OD1 1.7970 0.0000 0.3865 120 ASP ( 120-) A OD2 7.7167 0.0000 0.3521 121 VAL ( 121-) A N 0.7793 0.4605 0.0000 121 VAL ( 121-) A O 0.0000 0.0000 0.3666 122 ARG ( 122-) A N 0.0000 0.6961 0.0000 122 ARG ( 122-) A O 0.0000 0.0000 0.3975 122 ARG ( 122-) A NE 0.6235 0.0000 0.0000 122 ARG ( 122-) A NH1 12.7810 0.0000 0.0000 122 ARG ( 122-) A NH2 0.7793 0.0000 0.0000 123 GLN ( 123-) A N 0.0000 0.2727 0.0000 123 GLN ( 123-) A O 2.3256 0.0000 0.0000 123 GLN ( 123-) A OE1 1.1628 0.0000 0.1514 123 GLN ( 123-) A NE2 11.5341 0.7870 0.0000 124 TYR ( 124-) A N 0.0000 0.6603 0.0000 124 TYR ( 124-) A O 0.0000 0.0000 0.1475 124 TYR ( 124-) A OH 3.1713 0.0000 0.3801 125 VAL ( 125-) A N 0.0000 0.4933 0.0000 125 VAL ( 125-) A O 1.3742 0.0000 0.3443 126 GLN ( 126-) A N 0.0000 0.3576 0.0000 126 GLN ( 126-) A O 0.1057 0.0000 0.5907 126 GLN ( 126-) A OE1 0.6343 0.0000 0.1295 126 GLN ( 126-) A NE2 16.3659 0.0000 0.0000 127 GLY ( 127-) A N 1.4028 0.8082 0.0000 127 GLY ( 127-) A O 6.4482 0.0000 0.0000 128 CYS ( 128-) A N 0.0000 0.6200 0.0000 128 CYS ( 128-) A O 0.7400 0.0000 0.2604 128 CYS ( 128-) A SG 0.0000 0.0000 0.0000 129 GLY ( 129-) A N 1.0911 0.6714 0.0000 129 GLY ( 129-) A O 6.6596 0.0000 0.0000 130 VAL ( 130-) A N 0.4676 0.0000 0.0000 130 VAL ( 130-) A O 6.8711 0.0000 0.1472 131 NAG ( 132-) A O5 0.0000 0.0000 0.1768 131 NAG ( 132-) A O6 4.8626 0.0739 0.2340 131 NAG ( 132-) A O3 0.3171 0.7164 0.3916 131 NAG ( 132-) A N2 0.0000 0.6263 0.0000 131 NAG ( 132-) A O7 0.0000 0.0000 0.3403 132 NAG ( 134-) A O5 0.0000 0.0000 0.2983 132 NAG ( 134-) A O6 0.0000 0.0000 0.2219 132 NAG ( 134-) A O3 6.4482 0.0000 0.2839 132 NAG ( 134-) A N2 1.7145 0.5297 0.0000 132 NAG ( 134-) A O7 0.6343 0.0000 0.0000 Acceptor does not accept : 17 MET ( 17-) A SD Acceptor does not accept : 29 MET ( 29-) A SD Acceptor does not accept : 30 CYS ( 30-) A SG Acceptor does not accept : 40 THR ( 40-) A O -Potential donor : 138 HOH ( 169 ) A O Acceptor does not accept : 65 CYS ( 65-) A SG Acceptor does not accept : 81 CYS ( 81-) A SG Acceptor does not accept : 88 ASN ( 88-) A O -Potential donor : 91 ASP ( 91-) A OD1 -Potential donor : 91 ASP ( 91-) A OD2 -Potential donor : 138 HOH ( 138 ) A O Acceptor does not accept : 95 CYS ( 95-) A SG Acceptor does not accept : 97 LYS ( 97-) A O Acceptor does not accept : 116 CYS ( 116-) A SG Acceptor does not accept : 128 CYS ( 128-) A SG Acceptor does not accept : 131 NAG ( 132-) A N2 Acceptor does not accept : 137 GOL ( 136-) A O2 # 76 # 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. # 77 # Note: Some notes regarding these donors and acceptors The donors and acceptors have been counted, also as function of their accessibility. The buried donors and acceptors have been binned in five categories ranging from not forming any hydrogen bond till forming a poor till perfect hydrogen bond. Obviously, the buried donors and acceptors with no or just a poor hydrogen bond should be a topic of concern. Total number of acceptors: 204 of which buried: 88 Total number of donors: 220 of which buried: 106 Total number of donor+acceptors: 23 of which buried: 6 Donors without H-bond: 4 essentially without H-bond: 0 with only a very poor H-bond: 1 with a poor H-bond: 1 with a H-bond: 100 Acceptors without H-bond: 13 essentially without H-bond: 0 with only a very poor H-bond: 0 with a poor H-bond: 6 with a H-bond: 69 # 78 # 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. # 79 # 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. # 80 # Note: Water packing OK All waters seem properly packed, or at least not packed like an ion. This method is experimental. See: swift.cmbi.umcn.nl/teach/theory/ # 81 # Warning: Possible wrong residue type The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue. 91 ASP ( 91-) A H-bonding suggests Asn Number of NMR MODELs skipped upon reading PDB file: 9 # 82 # Note: Content of the PDB file as interpreted by WHAT CHECK Content of the PDB file as interpreted by WHAT CHECK. WHAT CHECK 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 CHECK output formats can be found at swift.cmbi.umcn.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK web pages. 1 1 ( 1) 130 ( 130) A Protein checkset 2 131 ( 132) 131 ( 132) A Sugar<= checkset 3 132 ( 134) 132 ( 134) A Sugar<= checkset 4 133 ( 130) 133 ( 130) A V O2 <- 130 checkset 5 134 ( 131) 134 ( 131) A GAL <- checkset 6 135 ( 135) 135 ( 135) A GOL <= checkset 7 136 ( 133) 136 ( 133) A GAL <- checkset 8 137 ( 136) 137 ( 136) A GOL <= checkset 9 138 ( HOH ) 138 ( HOH ) A water ( 113) checkset # 83 # 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 : -1.271 2nd generation packing quality : -1.162 Ramachandran plot appearance : -1.324 chi-1/chi-2 rotamer normality : -2.248 Backbone conformation : -0.992 RMS Z-scores, should be close to 1.0: Bond lengths : 0.554 (tight) Bond angles : 0.821 Omega angle restraints : 0.344 (tight) Side chain planarity : 0.728 Improper dihedral distribution : 1.218 Inside/Outside distribution : 0.909 # 84 # Note: Introduction to refinement recommendations First, be aware that the recommendations listed below are produced by a computer program that was written by a guy who got his PhD in NMR... We have tried to convert the messages written in this report into a small set of things you can do with your refinement software to get a better structure. The things you should do first are listed first. And in some cases you should first fix that problem, then refine a bit further, and then run WHAT CHECK again before looking at other problems. If, for example, WHAT CHECK has found a problem with the SCALE and CRYST cards, then you must first fix that problem, refine the structure a bit further, and run WHAT CHECK again because errors in the SCALE and or CRYST card can lead to many problems elsewhere in the validation process. It is also important to keep in mind that WHAT CHECK is software and that it occasionally totally misunderstands what is the cause of a problem. But, if WHAT CHECK lists a problem there normally is a problem albeit that it not always is the actual problem that gets listed. # 85 # Note: No crippling problems detected Some problems can be so crippling that they negatively influence the validity of other validation steps. If such a problem is detected, it must be solved and some further refinemnet must be done before you can continue working with a new WHAT CHECK report. In this file such problems were not detected. You can therefore try to fix as many problems in one go as you want. # 86 # Note: No resolution information detected WHAT CHECK needs to know the resolution of your data to provide advice for the refinement process. This resolution information is needed because a Z-score that is very good at 1.0 Angstrom resolution might actually be a sign of over-refinement at 3.5 Angstrom, etcetera. So, take a look at the formats of REMARK 2 and/or REMARK 3 and put the resolution in ether of those 2. An example of a REMARK 2 card is: REMARK 2 RESOLUTION. 4.50 ANGSTROMS. ============== 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.umcn.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.umcn.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.