WHAT IF Check report

This file was created 2011-12-16 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2hzn.ent

Checks that need to be done early-on in validation

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF 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. 'OK' indicates that the automatic topology generation succeeded.

 274 KIN   ( 600-)  A  -

Non-validating, descriptive output paragraph

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.

Chain identifier: A

Coordinate problems, unexpected atoms, B-factor and occupancy checks

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'.

  14 GLU   ( 238-)  A      CD
  14 GLU   ( 238-)  A      OE1
  14 GLU   ( 238-)  A      OE2
  35 LYS   ( 262-)  A      NZ
  36 LYS   ( 263-)  A      CD
  36 LYS   ( 263-)  A      CE
  36 LYS   ( 263-)  A      NZ
  37 TYR   ( 264-)  A      CD1
  37 TYR   ( 264-)  A      CD2
  37 TYR   ( 264-)  A      CE1
  37 TYR   ( 264-)  A      CE2
  37 TYR   ( 264-)  A      CZ
  37 TYR   ( 264-)  A      OH
  52 GLU   ( 281-)  A      CG
  52 GLU   ( 281-)  A      CD
  52 GLU   ( 281-)  A      OE1
  52 GLU   ( 281-)  A      OE2
 127 LYS   ( 356-)  A      NZ
 233 GLU   ( 462-)  A      CG
 233 GLU   ( 462-)  A      CD
 233 GLU   ( 462-)  A      OE1
 233 GLU   ( 462-)  A      OE2
 237 GLU   ( 466-)  A      CG
 237 GLU   ( 466-)  A      CD
 237 GLU   ( 466-)  A      OE1
 237 GLU   ( 466-)  A      OE2

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   2 ASP   ( 226-)  A    High
   5 SER   ( 229-)  A    High
   7 ASN   ( 231-)  A    High
  15 ARG   ( 239-)  A    High
  16 THR   ( 240-)  A    High
  17 ASP   ( 241-)  A    High
  18 ILE   ( 242-)  A    High
  19 THR   ( 243-)  A    High
  20 MET   ( 244-)  A    High
  21 LYS   ( 245-)  A    High
  22 HIS   ( 246-)  A    High
  23 LYS   ( 247-)  A    High
  24 LEU   ( 248-)  A    High
  25 GLY   ( 249-)  A    High
  26 GLY   ( 250-)  A    High
  28 GLU   ( 255-)  A    High
  30 TYR   ( 257-)  A    High
  31 GLU   ( 258-)  A    High
  34 TRP   ( 261-)  A    High
  35 LYS   ( 262-)  A    High
  36 LYS   ( 263-)  A    High
  37 TYR   ( 264-)  A    High
  38 SER   ( 265-)  A    High
  40 THR   ( 267-)  A    High
  45 THR   ( 272-)  A    High
And so on for a total of 92 lines.

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 273 ILE   ( 502-)  A

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) : 94.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Nomenclature related problems

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

  83 TYR   ( 312-)  A
 164 TYR   ( 393-)  A
 206 TYR   ( 435-)  A
 220 TYR   ( 449-)  A

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

  82 PHE   ( 311-)  A
 130 PHE   ( 359-)  A
 153 PHE   ( 382-)  A
 172 PHE   ( 401-)  A
 257 PHE   ( 486-)  A

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 162 ASP   ( 391-)  A

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  87 GLU   ( 316-)  A
 123 GLU   ( 352-)  A
 202 GLU   ( 431-)  A
 221 GLU   ( 450-)  A
 230 GLU   ( 459-)  A
 241 GLU   ( 470-)  A
 259 GLU   ( 488-)  A

Geometric checks

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.

  24 LEU   ( 248-)  A      N    CA   C    97.95   -4.7
 167 HIS   ( 396-)  A      N    CA   C    93.73   -6.2
 167 HIS   ( 396-)  A      CG   ND1  CE1 109.74    4.1

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  87 GLU   ( 316-)  A
 123 GLU   ( 352-)  A
 162 ASP   ( 391-)  A
 202 GLU   ( 431-)  A
 221 GLU   ( 450-)  A
 230 GLU   ( 459-)  A
 241 GLU   ( 470-)  A
 259 GLU   ( 488-)  A

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

   6 PRO   ( 230-)  A      N     -7.7   -27.82    -2.48
 212 PRO   ( 441-)  A      N      8.3    24.62    -2.48
The average deviation= 1.636

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.

 167 HIS   ( 396-)  A    6.95
 158 LEU   ( 387-)  A    5.88
  24 LEU   ( 248-)  A    5.40
 200 LEU   ( 429-)  A    4.71
 183 ALA   ( 412-)  A    4.66
 104 GLN   ( 333-)  A    4.26

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 : 1.666

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 167 HIS   ( 396-)  A    5.34
 123 GLU   ( 352-)  A    5.18
   9 ASP   ( 233-)  A    5.14
 202 GLU   ( 431-)  A    5.04

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.855

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.

  84 ILE   ( 313-)  A    -2.6
 161 GLY   ( 390-)  A    -2.5
  25 GLY   ( 249-)  A    -2.4
  77 THR   ( 306-)  A    -2.4
  38 SER   ( 265-)  A    -2.3
 186 LYS   ( 415-)  A    -2.1
  41 VAL   ( 268-)  A    -2.1
 205 THR   ( 434-)  A    -2.0

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 LYS   ( 245-)  A  Poor phi/psi
  25 GLY   ( 249-)  A  Poor phi/psi
  80 PRO   ( 309-)  A  PRO omega poor
 133 ARG   ( 362-)  A  Poor phi/psi
 136 ALA   ( 365-)  A  Poor phi/psi
 145 ASN   ( 374-)  A  Poor phi/psi
 151 ALA   ( 380-)  A  Poor phi/psi
 160 THR   ( 389-)  A  Poor phi/psi
 161 GLY   ( 390-)  A  Poor phi/psi
 162 ASP   ( 391-)  A  Poor phi/psi
 168 ALA   ( 397-)  A  Poor phi/psi
 170 ALA   ( 399-)  A  Poor phi/psi
 185 ASN   ( 414-)  A  Poor phi/psi
 207 GLY   ( 436-)  A  Poor phi/psi
 226 ASP   ( 455-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.322

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.322

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 120 SER   ( 349-)  A    0.38

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!

  11 TRP   ( 235-)  A      0
  12 GLU   ( 236-)  A      0
  13 MET   ( 237-)  A      0
  15 ARG   ( 239-)  A      0
  21 LYS   ( 245-)  A      0
  22 HIS   ( 246-)  A      0
  24 LEU   ( 248-)  A      0
  25 GLY   ( 249-)  A      0
  26 GLY   ( 250-)  A      0
  27 GLY   ( 254-)  A      0
  28 GLU   ( 255-)  A      0
  34 TRP   ( 261-)  A      0
  37 TYR   ( 264-)  A      0
  45 THR   ( 272-)  A      0
  46 LEU   ( 273-)  A      0
  47 ASP   ( 276-)  A      0
  48 THR   ( 277-)  A      0
  49 MET   ( 278-)  A      0
  50 GLU   ( 279-)  A      0
  65 LYS   ( 294-)  A      0
  66 HIS   ( 295-)  A      0
  68 ASN   ( 297-)  A      0
  75 VAL   ( 304-)  A      0
  76 CYS   ( 305-)  A      0
  77 THR   ( 306-)  A      0
And so on for a total of 106 lines.

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 : 3.064

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 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]

  67 PRO   ( 296-)  A    0.15 LOW

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].

   6 PRO   ( 230-)  A  -154.0 half-chair N/C-delta (-162 degrees)
  81 PRO   ( 310-)  A   -38.6 envelop C-alpha (-36 degrees)
 179 PRO   ( 408-)  A   133.7 half-chair C-beta/C-alpha (126 degrees)
 210 PRO   ( 439-)  A    50.4 half-chair C-delta/C-gamma (54 degrees)
 212 PRO   ( 441-)  A   -36.1 envelop C-alpha (-36 degrees)
 236 PRO   ( 465-)  A  -146.2 envelop C-delta (-144 degrees)
 251 PRO   ( 480-)  A  -135.1 envelop C-delta (-144 degrees)
 255 PRO   ( 484-)  A   -64.6 envelop C-beta (-72 degrees)

Bump checks

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.

  15 ARG   ( 239-)  A      NH2 <->   79 GLU   ( 308-)  A      O      0.45    2.25  INTRA BF
 190 LYS   ( 419-)  A      NZ  <->  254 ARG   ( 483-)  A      O      0.42    2.28  INTRA BF
 211 TYR   ( 440-)  A      N   <->  229 MET   ( 458-)  A      SD     0.37    2.93  INTRA BF
  99 ARG   ( 328-)  A      NE  <->  207 GLY   ( 436-)  A      O      0.36    2.34  INTRA BL
 167 HIS   ( 396-)  A      NE2 <->  174 ILE   ( 403-)  A      CD1    0.34    2.76  INTRA BF
  96 ASP   ( 325-)  A      O   <->   99 ARG   ( 328-)  A      N      0.34    2.36  INTRA BL
  66 HIS   ( 295-)  A      ND1 <->   68 ASN   ( 297-)  A      N      0.31    2.69  INTRA BL
  15 ARG   ( 239-)  A      NH1 <->   81 PRO   ( 310-)  A      CD     0.28    2.82  INTRA BF
 124 TYR   ( 353-)  A      O   <->  127 LYS   ( 356-)  A      N      0.26    2.44  INTRA BL
 165 THR   ( 394-)  A      CG2 <->  166 ALA   ( 395-)  A      N      0.25    2.75  INTRA BF
 155 LEU   ( 384-)  A      O   <->  159 MET   ( 388-)  A      N      0.23    2.47  INTRA BF
 164 TYR   ( 393-)  A      CE1 <->  173 PRO   ( 402-)  A      CG     0.23    2.97  INTRA BF
  45 THR   ( 272-)  A      CG2 <->   46 LEU   ( 273-)  A      N      0.23    2.77  INTRA BF
  32 GLY   ( 259-)  A      O   <->   41 VAL   ( 268-)  A      N      0.22    2.48  INTRA BF
  73 LEU   ( 302-)  A      N   <->   85 ILE   ( 314-)  A      O      0.22    2.48  INTRA BL
   9 ASP   ( 233-)  A      OD1 <->   11 TRP   ( 235-)  A      N      0.22    2.48  INTRA BF
 131 ILE   ( 360-)  A      CD1 <->  188 SER   ( 417-)  A      CA     0.22    2.98  INTRA BL
 231 ARG   ( 460-)  A      CA  <->  240 TYR   ( 469-)  A      CE1    0.21    2.99  INTRA BF
 242 LEU   ( 471-)  A      CD2 <->  264 PHE   ( 493-)  A      CE2    0.21    2.99  INTRA BF
 231 ARG   ( 460-)  A      N   <->  240 TYR   ( 469-)  A      CZ     0.21    2.89  INTRA BF
 236 PRO   ( 465-)  A      CG  <->  239 VAL   ( 468-)  A      CG2    0.20    3.00  INTRA BF
 155 LEU   ( 384-)  A      CD2 <->  159 MET   ( 388-)  A      CE     0.20    3.00  INTRA BF
 172 PHE   ( 401-)  A      O   <->  174 ILE   ( 403-)  A      N      0.20    2.50  INTRA BF
 162 ASP   ( 391-)  A      N   <->  163 THR   ( 392-)  A      N      0.20    2.40  INTRA BF
 109 VAL   ( 338-)  A      CG1 <->  110 VAL   ( 339-)  A      N      0.19    2.81  INTRA BL
And so on for a total of 96 lines.

Packing, accessibility and threading

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.

Chain identifier: A

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.

 231 ARG   ( 460-)  A      -7.18
  78 ARG   ( 307-)  A      -6.60
 211 TYR   ( 440-)  A      -6.22
  49 MET   ( 278-)  A      -6.02
  65 LYS   ( 294-)  A      -6.00
 208 MET   ( 437-)  A      -5.82
 227 TYR   ( 456-)  A      -5.33
 145 ASN   ( 374-)  A      -5.26
 230 GLU   ( 459-)  A      -5.25

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.

 229 MET   ( 458-)  A       231 - ARG    460- ( A)         -5.60

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.

Chain identifier: A

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.

  70 VAL   ( 299-)  A   -2.77
 183 ALA   ( 412-)  A   -2.56

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.

Chain identifier: A

Water, ion, and hydrogenbond related checks

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 ASP   ( 226-)  A      N
   9 ASP   ( 233-)  A      N
  15 ARG   ( 239-)  A      NH1
  45 THR   ( 272-)  A      OG1
  49 MET   ( 278-)  A      N
  50 GLU   ( 279-)  A      N
  89 MET   ( 318-)  A      N
 107 SER   ( 336-)  A      N
 117 GLN   ( 346-)  A      NE2
 136 ALA   ( 365-)  A      N
 138 ARG   ( 367-)  A      N
 138 ARG   ( 367-)  A      NH2
 152 ASP   ( 381-)  A      N
 164 TYR   ( 393-)  A      N
 167 HIS   ( 396-)  A      NE2
 171 LYS   ( 400-)  A      N
 175 LYS   ( 404-)  A      N
 181 SER   ( 410-)  A      N
 188 SER   ( 417-)  A      N
 221 GLU   ( 450-)  A      N
 229 MET   ( 458-)  A      N

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.

  28 GLU   ( 255-)  A      OE1
 202 GLU   ( 431-)  A      OE2

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.

  28 GLU   ( 255-)  A   H-bonding suggests Gln
 241 GLU   ( 470-)  A   H-bonding suggests Gln
 270 GLU   ( 499-)  A   H-bonding suggests Gln

Final summary

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 :  -1.780
  2nd generation packing quality :  -1.572
  Ramachandran plot appearance   :  -3.855 (poor)
  chi-1/chi-2 rotamer normality  :  -4.322 (bad)
  Backbone conformation          :  -0.453

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.467 (tight)
  Bond angles                    :   0.729
  Omega angle restraints         :   0.557 (tight)
  Side chain planarity           :   1.654
  Improper dihedral distribution :   1.380
  B-factor distribution          :   0.796
  Inside/Outside distribution    :   0.998

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

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, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -1.0
  chi-1/chi-2 rotamer normality  :  -1.9
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.467 (tight)
  Bond angles                    :   0.729
  Omega angle restraints         :   0.557 (tight)
  Side chain planarity           :   1.654
  Improper dihedral distribution :   1.380
  B-factor distribution          :   0.796
  Inside/Outside distribution    :   0.998
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
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    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

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,
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

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.