WHAT IF Check report

This file was created 2012-01-12 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 pdb3rpt.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 506 SO4   ( 283-)  A  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 263 SER   (  11-)  A  -
 273 ASN   (  21-)  A  -
 369 ARG   ( 140-)  A  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 263 SER   (  11-)  A  -
 273 ASN   (  21-)  A  -
 369 ARG   ( 140-)  A  -

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 177 SER   ( 200-)  X  -   OG
 194 ASN   ( 217-)  X  -   CG
 194 ASN   ( 217-)  X  -   ND2
 429 SER   ( 200-)  A  -   OG

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 390 GLN   ( 161-)  A  -   O

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: X

Note: Ramachandran plot

Chain identifier: A

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  30 ARG   (  31-)  X    0.97
  52 LEU   (  56-)  X    0.96
 138 GLN   ( 161-)  X    0.97
 157 ARG   ( 180-)  X    0.69
 171 SER   ( 194-)  X    0.82
 177 SER   ( 200-)  X    0.97
 194 ASN   ( 217-)  X    0.81
 216 MET   ( 239-)  X    0.85
 283 ARG   (  31-)  A    0.96
 305 LEU   (  56-)  A    0.92
 390 GLN   ( 161-)  A    0.46
 423 SER   ( 194-)  A    0.68
 429 SER   ( 200-)  A    0.87
 446 ASN   ( 217-)  A    0.76
 468 MET   ( 239-)  A    0.94

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) :200.000

Note: B-factor plot

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

Chain identifier: X

Note: B-factor plot

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

   4 TYR   (   5-)  X
 156 TYR   ( 179-)  X
 408 TYR   ( 179-)  A

Warning: Phenylalanine convention problem

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

  71 PHE   (  83-)  X

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.

 347 ASP   ( 107-)  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.

  73 GLU   (  85-)  X
  80 GLU   (  92-)  X
 195 GLU   ( 218-)  X

Geometric checks

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: 0.470
RMS-deviation in bond distances: 0.011

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  1.000092 -0.000058  0.001226|
 | -0.000058  0.997766  0.002115|
 |  0.001226  0.002115  1.001185|
Proposed new scale matrix

 |  0.021801 -0.012053 -0.001363|
 |  0.000006  0.024763 -0.003774|
 | -0.000020 -0.000035  0.016386|
With corresponding cell

    A    =  45.872  B   =  46.160  C    =  62.411
    Alpha=  78.328  Beta=  81.677  Gamma=  61.059

The CRYST1 cell dimensions

    A    =  45.867  B   =  46.240  C    =  62.282
    Alpha=  78.570  Beta=  81.800  Gamma=  61.110

Variance: 37.238
(Under-)estimated Z-score: 4.497

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.

 124 HIS   ( 147-)  X      CG   ND1  CE1 109.62    4.0

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the 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. 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 angles: 0.643
RMS-deviation in bond angles: 1.300

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.

  73 GLU   (  85-)  X
  80 GLU   (  92-)  X
 195 GLU   ( 218-)  X
 347 ASP   ( 107-)  A

Torsion-related checks

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.

 209 THR   ( 232-)  X    -2.4
 191 PRO   ( 214-)  X    -2.3
 461 THR   ( 232-)  A    -2.1

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.

  44 GLN   (  48-)  X  omega poor
  87 ASN   (  99-)  X  Poor phi/psi
 126 ALA   ( 149-)  X  Poor phi/psi
 127 TRP   ( 150-)  X  Poor phi/psi
 152 ASN   ( 175-)  X  Poor phi/psi
 154 SER   ( 177-)  X  Poor phi/psi
 155 ASN   ( 178-)  X  omega poor
 180 ALA   ( 203-)  X  omega poor
 219 ALA   ( 242-)  X  omega poor
 221 LEU   ( 244-)  X  omega poor
 223 ILE   ( 246-)  X  omega poor
 231 GLY   ( 254-)  X  Poor phi/psi
 320 VAL   (  71-)  A  omega poor
 339 ASN   (  99-)  A  Poor phi/psi
 342 ALA   ( 102-)  A  Poor phi/psi, omega poor
 378 ALA   ( 149-)  A  Poor phi/psi
 379 TRP   ( 150-)  A  Poor phi/psi
 393 ASP   ( 164-)  A  Poor phi/psi
 404 ASN   ( 175-)  A  Poor phi/psi
 406 SER   ( 177-)  A  Poor phi/psi
 407 ASN   ( 178-)  A  omega poor
 471 ALA   ( 242-)  A  omega poor
 473 LEU   ( 244-)  A  omega poor
 chi-1/chi-2 correlation Z-score : 0.518

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!

  24 THR   (  25-)  X      0
  30 ARG   (  31-)  X      0
  41 ASN   (  42-)  X      0
  42 GLN   (  43-)  X      0
  43 GLY   (  47-)  X      0
  44 GLN   (  48-)  X      0
  68 ASN   (  72-)  X      0
  69 PRO   (  73-)  X      0
  70 ASP   (  74-)  X      0
  71 PHE   (  83-)  X      0
  72 GLU   (  84-)  X      0
  85 LEU   (  97-)  X      0
  86 LYS   (  98-)  X      0
  87 ASN   (  99-)  X      0
  89 PRO   ( 101-)  X      0
  90 ALA   ( 102-)  X      0
  95 ASP   ( 107-)  X      0
  96 PRO   ( 108-)  X      0
  97 ALA   ( 120-)  X      0
  98 ALA   ( 121-)  X      0
 113 SER   ( 136-)  X      0
 122 ALA   ( 145-)  X      0
 125 SER   ( 148-)  X      0
 126 ALA   ( 149-)  X      0
 127 TRP   ( 150-)  X      0
And so on for a total of 206 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 123 GLY   ( 146-)  X   2.15   22
 375 GLY   ( 146-)  A   2.15   19

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]

   7 PRO   (   8-)  X    0.07 LOW
 176 PRO   ( 199-)  X    0.18 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].

   2 PRO   (   3-)  X     0.0 envelop N (0 degrees)
 382 PRO   ( 153-)  A   102.5 envelop C-beta (108 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.

  13 GLU   (  14-)  X      CD  <->   16 ARG   (  17-)  X      NH2    0.46    2.64  INTRA
 323 PHE   (  83-)  A      CE2 <->  327 LYS   (  87-)  A      CE     0.25    2.95  INTRA BF
  68 ASN   (  72-)  X      N   <->   69 PRO   (  73-)  X      CD     0.22    2.78  INTRA
 132 GLN   ( 155-)  X      NE2 <->  507 HOH   ( 331 )  X      O      0.16    2.54  INTRA BF
 114 SER   ( 137-)  X      OG  <->  507 HOH   ( 435 )  X      O      0.15    2.25  INTRA BF
 266 GLU   (  14-)  A      CD  <->  269 ARG   (  17-)  A      NH2    0.15    2.95  INTRA
  87 ASN   (  99-)  X      CG  <->  507 HOH   ( 435 )  X      O      0.14    2.66  INTRA BF
 263 SER   (  11-)  A    A OG  <->  508 HOH   ( 360 )  A      O      0.12    2.28  INTRA BL
 370 ILE   ( 141-)  A      N   <->  399 HIS   ( 170-)  A      ND1    0.11    2.89  INTRA
  13 GLU   (  14-)  X      OE1 <->   16 ARG   (  17-)  X      NH2    0.09    2.61  INTRA
 118 ILE   ( 141-)  X      N   <->  147 HIS   ( 170-)  X      ND1    0.09    2.91  INTRA
 323 PHE   (  83-)  A      CE2 <->  327 LYS   (  87-)  A      NZ     0.05    3.05  INTRA BF
  28 ARG   (  29-)  X      NH2 <->  507 HOH   ( 291 )  X      O      0.05    2.65  INTRA
 450 ASP   ( 221-)  A      N   <->  451 PRO   ( 222-)  A      CD     0.04    2.96  INTRA
  87 ASN   (  99-)  X      CB  <->  507 HOH   ( 435 )  X      O      0.04    2.76  INTRA BF
 271 ASN   (  19-)  A      N   <->  272 PRO   (  20-)  A      CD     0.03    2.97  INTRA BL
  18 ASN   (  19-)  X      N   <->   19 PRO   (  20-)  X      CD     0.02    2.98  INTRA
 198 ASP   ( 221-)  X      N   <->  230 ASP   ( 253-)  X      OD2    0.02    2.68  INTRA BL
 479 GLY   ( 250-)  A      N   <->  499 MET   ( 270-)  A      CE     0.02    3.08  INTRA
 399 HIS   ( 170-)  A      N   <->  400 GLY   ( 171-)  A      N      0.01    2.59  INTRA BL
 508 HOH   ( 340 )  A      O   <->  508 HOH   ( 427 )  A      O      0.01    2.19  INTRA

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: X

Note: Inside/Outside RMS Z-score plot

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.

 295 GLN   (  43-)  A      -6.42
 504 LEU   ( 275-)  A      -6.29
 380 HIS   ( 151-)  A      -5.72
 270 ASN   (  18-)  A      -5.40
  17 ASN   (  18-)  X      -5.31
 128 HIS   ( 151-)  X      -5.27

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: X

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: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

   3 PHE   (   4-)  X     -    6 ASN   (   7-)  X        -1.84

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: X

Note: Second generation quality Z-score plot

Chain identifier: A

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 508 HOH   ( 307 )  A      O    -15.29    8.60   19.12
 508 HOH   ( 434 )  A      O     14.00  -13.58  -16.13
 508 HOH   ( 450 )  A      O     13.10  -17.91   42.39

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.

   8 ASN   (   9-)  X
  20 ASN   (  21-)  X
  41 ASN   (  42-)  X
  68 ASN   (  72-)  X
 128 HIS   ( 151-)  X
 211 ASN   ( 234-)  X
 321 ASN   (  72-)  A

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.

  99 TRP   ( 122-)  X      N
 225 LEU   ( 248-)  X      N
 234 ALA   ( 257-)  X      N
 254 SER   (   2-)  A      N
 289 GLN   (  37-)  A      N
 295 GLN   (  43-)  A      N
 325 GLU   (  85-)  A      N
 410 TRP   ( 181-)  A      NE1
 477 LEU   ( 248-)  A      N
 486 ALA   ( 257-)  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.

  13 GLU   (  14-)  X      OE1
  57 GLN   (  61-)  X      OE1
 301 GLN   (  52-)  A      OE1
 367 GLN   ( 138-)  A      OE1

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.

  79 ASP   (  91-)  X   H-bonding suggests Asn
 183 ASP   ( 206-)  X   H-bonding suggests Asn; but Alt-Rotamer
 331 ASP   (  91-)  A   H-bonding suggests Asn; but Alt-Rotamer
 435 ASP   ( 206-)  A   H-bonding suggests Asn; but Alt-Rotamer
 447 GLU   ( 218-)  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 :   0.080
  2nd generation packing quality :  -0.413
  Ramachandran plot appearance   :   0.292
  chi-1/chi-2 rotamer normality  :   0.518
  Backbone conformation          :   0.340

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.470 (tight)
  Bond angles                    :   0.643 (tight)
  Omega angle restraints         :   0.992
  Side chain planarity           :   0.834
  Improper dihedral distribution :   0.853
  B-factor distribution          :   0.908
  Inside/Outside distribution    :   0.972

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 : 1.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -0.0
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.470 (tight)
  Bond angles                    :   0.643 (tight)
  Omega angle restraints         :   0.992
  Side chain planarity           :   0.834
  Improper dihedral distribution :   0.853
  B-factor distribution          :   0.908
  Inside/Outside distribution    :   0.972
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra 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,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

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

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

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

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

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.