WHAT IF Check report

This file was created 2012-01-13 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 pdb1wdr.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.

 496 MAL   ( 496-)  A  -
 504 MAL   ( 498-)  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.

 168 GLU   ( 170-)  A  -
 242 SER   ( 244-)  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.

 168 GLU   ( 170-)  A  -
 242 SER   ( 244-)  A  -
Delete overlapping entity  504 MAL  ( 498-) A  -

Warning: Overlapping residues or molecules

This molecule contains residues or molecules that overlap too much while not being (administrated as) alternate atom/residue pairs. The residues or molecules listed in the table below have been removed before the validation continued.

Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.

 504 MAL   ( 498-)  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: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

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.

   1 SER   (   3-)  A    High
   2 ASP   (   4-)  A    High
   3 SER   (   5-)  A    High
 493 GLY   ( 495-)  A    High

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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

Crystal temperature (K) :298.000

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: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  41 ARG   (  43-)  A
 124 ARG   ( 126-)  A
 383 ARG   ( 385-)  A
 418 ARG   ( 420-)  A

Warning: Tyrosine convention problem

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

  70 TYR   (  72-)  A
 155 TYR   ( 157-)  A
 301 TYR   ( 303-)  A
 315 TYR   ( 317-)  A

Warning: Phenylalanine convention problem

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

 159 PHE   ( 161-)  A
 259 PHE   ( 261-)  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.

  46 ASP   (  48-)  A
  99 ASP   ( 101-)  A
 174 ASP   ( 176-)  A
 352 ASP   ( 354-)  A
 422 ASP   ( 424-)  A
 444 ASP   ( 446-)  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.

  35 GLU   (  37-)  A
 114 GLU   ( 116-)  A
 131 GLU   ( 133-)  A
 176 GLU   ( 178-)  A
 197 GLU   ( 199-)  A
 359 GLU   ( 361-)  A
 469 GLU   ( 471-)  A
 473 GLU   ( 475-)  A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 197 GLU   ( 199-)  A      N    CA    1.38   -4.3
 332 ARG   ( 334-)  A      CD   NE    1.37   -4.8

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: 0.653
RMS-deviation in bond distances: 0.014

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

 |  1.000412  0.000986  0.000334|
 |  0.000986  1.002293  0.000369|
 |  0.000334  0.000369  0.997183|
Proposed new scale matrix

 |  0.011736  0.006755 -0.000006|
 | -0.000013  0.013533 -0.000005|
 | -0.000002 -0.000003  0.006984|
With corresponding cell

    A    =  85.163  B   =  85.212  C    = 143.191
    Alpha=  89.982  Beta=  89.962  Gamma= 119.868

The CRYST1 cell dimensions

    A    =  85.128  B   =  85.128  C    = 143.598
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 35.649
(Under-)estimated Z-score: 4.400

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   2 ASP   (   4-)  A     -C    N    CA  132.99    6.3
   4 ASN   (   6-)  A     -O   -C    N   114.58   -5.3
   9 TYR   (  11-)  A      CA   CB   CG  130.98    9.1
  23 VAL   (  25-)  A      C    CA   CB  118.04    4.2
  27 PHE   (  29-)  A      CA   CB   CG  118.58    4.8
  41 ARG   (  43-)  A      CD   NE   CZ  130.68    5.0
  85 GLN   (  87-)  A      CG   CD   NE2 105.05   -7.6
  85 GLN   (  87-)  A      NE2  CD   OE1 134.86   12.3
  96 ASN   (  98-)  A     -O   -C    N   116.34   -4.2
 115 SER   ( 117-)  A     -C    N    CA  129.87    4.5
 116 ASN   ( 118-)  A      ND2  CG   OD1 116.94   -5.7
 144 HIS   ( 146-)  A      CG   ND1  CE1 111.14    5.5
 150 GLU   ( 152-)  A     -O   -C    N   114.80   -5.1
 155 TYR   ( 157-)  A      CA   CB   CG  121.67    4.2
 160 ARG   ( 162-)  A      CD   NE   CZ  129.34    4.2
 165 ASP   ( 167-)  A      CA   CB   CG  118.08    5.5
 173 ILE   ( 175-)  A      CB   CG1  CD1 103.30   -5.0
 174 ASP   ( 176-)  A      CA   CB   CG  118.28    5.7
 186 ARG   ( 188-)  A      CG   CD   NE  119.81    5.5
 197 GLU   ( 199-)  A     -O   -C    N   116.15   -4.3
 197 GLU   ( 199-)  A     -CA  -C    N   124.81    4.3
 197 GLU   ( 199-)  A     -C    N    CA  139.58    9.9
 199 PRO   ( 201-)  A      N    CA   CB   98.30   -4.3
 207 TYR   ( 209-)  A      CB   CG   CD2 127.66    4.6
 214 ASP   ( 216-)  A      CA   CB   CG  122.22    9.6
And so on for a total of 81 lines.

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.

  35 GLU   (  37-)  A
  41 ARG   (  43-)  A
  46 ASP   (  48-)  A
  99 ASP   ( 101-)  A
 114 GLU   ( 116-)  A
 124 ARG   ( 126-)  A
 131 GLU   ( 133-)  A
 174 ASP   ( 176-)  A
 176 GLU   ( 178-)  A
 197 GLU   ( 199-)  A
 352 ASP   ( 354-)  A
 359 GLU   ( 361-)  A
 383 ARG   ( 385-)  A
 418 ARG   ( 420-)  A
 422 ASP   ( 424-)  A
 444 ASP   ( 446-)  A
 469 GLU   ( 471-)  A
 473 GLU   ( 475-)  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.

 199 PRO   ( 201-)  A    -3.0
 141 PRO   ( 143-)  A    -2.4
 339 PHE   ( 341-)  A    -2.3
 191 PRO   ( 193-)  A    -2.2
 173 ILE   ( 175-)  A    -2.1
 315 TYR   ( 317-)  A    -2.1
 135 VAL   ( 137-)  A    -2.1
 356 GLY   ( 358-)  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.

  20 VAL   (  22-)  A  omega poor
  25 ASN   (  27-)  A  Poor phi/psi
  52 VAL   (  54-)  A  omega poor
  63 LYS   (  65-)  A  Poor phi/psi
 182 ALA   ( 184-)  A  Poor phi/psi
 188 PRO   ( 190-)  A  Poor phi/psi
 198 PHE   ( 200-)  A  PRO omega poor
 249 ASN   ( 251-)  A  Poor phi/psi
 300 TRP   ( 302-)  A  Poor phi/psi
 306 HIS   ( 308-)  A  omega poor
 334 HIS   ( 336-)  A  Poor phi/psi
 341 CYS   ( 343-)  A  Poor phi/psi
 343 GLU   ( 345-)  A  omega poor
 372 ASP   ( 374-)  A  Poor phi/psi
 378 GLU   ( 380-)  A  omega poor
 417 LEU   ( 419-)  A  omega poor
 441 ALA   ( 443-)  A  Poor phi/psi
 442 ASP   ( 444-)  A  Poor phi/psi
 453 ASN   ( 455-)  A  Poor phi/psi
 492 ASP   ( 494-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : 0.507

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.

 366 SER   ( 368-)  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!

  18 LEU   (  20-)  A      0
  21 VAL   (  23-)  A      0
  25 ASN   (  27-)  A      0
  28 GLU   (  30-)  A      0
  29 ASP   (  31-)  A      0
  46 ASP   (  48-)  A      0
  53 TRP   (  55-)  A      0
  54 TRP   (  56-)  A      0
  58 GLU   (  60-)  A      0
  59 LEU   (  61-)  A      0
  62 PRO   (  64-)  A      0
  63 LYS   (  65-)  A      0
  65 TYR   (  67-)  A      0
  67 TRP   (  69-)  A      0
  80 CYS   (  82-)  A      0
  89 SER   (  91-)  A      0
  90 PHE   (  92-)  A      0
  91 HIS   (  93-)  A      0
  93 CYS   (  95-)  A      0
  97 VAL   (  99-)  A      0
 105 ILE   ( 107-)  A      0
 115 SER   ( 117-)  A      0
 117 HIS   ( 119-)  A      0
 118 ASP   ( 120-)  A      0
 119 ILE   ( 121-)  A      0
And so on for a total of 170 lines.

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]

  30 PRO   (  32-)  A    0.19 LOW
 240 PRO   ( 242-)  A    0.05 LOW
 350 PRO   ( 352-)  A    0.08 LOW
 398 PRO   ( 400-)  A    0.13 LOW
 406 PRO   ( 408-)  A    0.06 LOW
 449 PRO   ( 451-)  A    0.47 HIGH
 467 PRO   ( 469-)  A    0.07 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].

 199 PRO   ( 201-)  A   -57.3 half-chair C-beta/C-alpha (-54 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.

 280 ASN   ( 282-)  A    A ND2 <->  502 HOH   (1231 )  A      O      0.24    2.46  INTRA
 374 ARG   ( 376-)  A      NH1 <->  502 HOH   ( 982 )  A      O      0.22    2.48  INTRA
 334 HIS   ( 336-)  A      ND1 <->  502 HOH   ( 985 )  A      O      0.21    2.49  INTRA
 124 ARG   ( 126-)  A    A NH1 <->  502 HOH   ( 741 )  A      O      0.21    2.49  INTRA
 212 LYS   ( 214-)  A    A NZ  <->  502 HOH   (1192 )  A      O      0.21    2.49  INTRA BF
 157 LYS   ( 159-)  A    A NZ  <->  502 HOH   (1299 )  A      O      0.21    2.49  INTRA BF
 289 LYS   ( 291-)  A      NZ  <->  502 HOH   ( 993 )  A      O      0.21    2.49  INTRA
 212 LYS   ( 214-)  A    A NZ  <->  502 HOH   ( 787 )  A      O      0.21    2.49  INTRA
 270 ASN   ( 272-)  A      ND2 <->  502 HOH   ( 904 )  A      O      0.20    2.50  INTRA
 409 LEU   ( 411-)  A      N   <->  502 HOH   (1065 )  A      O      0.20    2.50  INTRA
 214 ASP   ( 216-)  A      OD2 <->  267 LYS   ( 269-)  A      NZ     0.19    2.51  INTRA
 408 LYS   ( 410-)  A      NZ  <->  502 HOH   (1302 )  A      O      0.16    2.54  INTRA BF
  95 GLY   (  97-)  A      N   <->  502 HOH   ( 890 )  A      O      0.15    2.55  INTRA
 362 GLN   ( 364-)  A    A NE2 <->  502 HOH   (1356 )  A      O      0.13    2.57  INTRA BF
 497 SO4   (2001-)  A      O1  <->  502 HOH   (1053 )  A      O      0.11    2.29  INTRA BF
  28 GLU   (  30-)  A      OE1 <->  502 HOH   (1213 )  A      O      0.11    2.29  INTRA BF
   1 SER   (   3-)  A      O   <->    5 MET   (   7-)  A      N      0.10    2.60  INTRA BF
 496 SO4   (2000-)  A      O3  <->  502 HOH   ( 954 )  A      O      0.10    2.30  INTRA BF
 495 MAL   ( 496-)  A    A O1' <->  502 HOH   (1030 )  A      O      0.10    2.30  INTRA
  24 ASP   (  26-)  A      OD2 <->  502 HOH   (1246 )  A      O      0.10    2.30  INTRA BF
 332 ARG   ( 334-)  A      N   <->  502 HOH   (1123 )  A      O      0.10    2.60  INTRA
 117 HIS   ( 119-)  A      ND1 <->  497 SO4   (2001-)  A      S      0.09    3.21  INTRA
 444 ASP   ( 446-)  A      OD1 <->  502 HOH   (1271 )  A      O      0.09    2.31  INTRA
 216 LYS   ( 218-)  A      NZ  <->  227 TRP   ( 229-)  A      O      0.08    2.62  INTRA
 138 ASP   ( 140-)  A      OD2 <->  271 HIS   ( 273-)  A      ND1    0.08    2.62  INTRA BL
And so on for a total of 52 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.

 124 ARG   ( 126-)  A      -7.38
 465 LYS   ( 467-)  A      -6.57
 198 PHE   ( 200-)  A      -6.38
 221 ARG   ( 223-)  A      -5.73
 194 GLN   ( 196-)  A      -5.62
 384 TYR   ( 386-)  A      -5.35
  60 LYS   (  62-)  A      -5.24
 190 TYR   ( 192-)  A      -5.13
 100 ILE   ( 102-)  A      -5.00
 348 GLU   ( 350-)  A      -5.00

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

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: 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.

 502 HOH   ( 500 )  A      O     28.07   42.15   30.92
 502 HOH   ( 513 )  A      O     14.22   55.62   29.00
 502 HOH   ( 523 )  A      O     13.62   34.50   -3.17
 502 HOH   ( 593 )  A      O     10.83   33.39   60.30
 502 HOH   ( 600 )  A      O      5.08   33.04   -4.27
 502 HOH   ( 609 )  A      O     23.28   32.66   52.39
 502 HOH   ( 660 )  A      O      1.46   53.03   42.21
 502 HOH   ( 708 )  A      O     28.65   35.86   38.49
 502 HOH   ( 739 )  A      O     19.13   52.54   22.61
 502 HOH   ( 746 )  A      O     13.82   39.29   -3.73
 502 HOH   ( 753 )  A      O     -5.86   36.50   45.93
 502 HOH   ( 782 )  A      O      7.40   53.58   23.94
 502 HOH   ( 801 )  A      O    -22.55   31.10   12.80
 502 HOH   ( 807 )  A      O    -19.52   32.37   22.82
 502 HOH   ( 834 )  A      O     -0.36   43.40   43.34
 502 HOH   ( 835 )  A      O     -4.18   46.21   43.25
 502 HOH   ( 857 )  A      O    -21.98   40.44   24.62
 502 HOH   ( 858 )  A      O    -18.24   30.54   22.35
 502 HOH   ( 866 )  A      O    -18.65   38.51    8.94
 502 HOH   ( 892 )  A      O    -20.04   35.42   11.16
 502 HOH   ( 945 )  A      O     17.41   55.45   32.39
 502 HOH   ( 973 )  A      O     16.29   54.55   25.83
 502 HOH   ( 976 )  A      O     -2.50   66.22   15.80
 502 HOH   ( 977 )  A      O     -0.12   51.10    2.02
 502 HOH   ( 984 )  A      O    -16.74   40.07   38.82
And so on for a total of 57 lines.

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.

 502 HOH   (1212 )  A      O
 502 HOH   (1274 )  A      O

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.

 116 ASN   ( 118-)  A
 194 GLN   ( 196-)  A
 205 GLN   ( 207-)  A
 237 ASN   ( 239-)  A
 266 ASN   ( 268-)  A
 280 ASN   ( 282-)  A
 305 ASN   ( 307-)  A
 338 ASN   ( 340-)  A
 391 GLN   ( 393-)  A
 399 GLN   ( 401-)  A
 403 ASN   ( 405-)  A
 453 ASN   ( 455-)  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.

  61 GLY   (  63-)  A      N
  85 GLN   (  87-)  A      NE2
  91 HIS   (  93-)  A      N
 101 VAL   ( 103-)  A      N
 152 TYR   ( 154-)  A      OH
 180 GLY   ( 182-)  A      N
 280 ASN   ( 282-)  A    A ND2
 299 TRP   ( 301-)  A      N
 305 ASN   ( 307-)  A      N
 308 ALA   ( 310-)  A      N
 340 SER   ( 342-)  A      N
 355 SER   ( 357-)  A    A OG
 413 GLY   ( 415-)  A      N
 420 SER   ( 422-)  A      N
 486 GLU   ( 488-)  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.

  91 HIS   (  93-)  A      NE2
 174 ASP   ( 176-)  A      OD1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 502 HOH   ( 505 )  A      O  1.04  K  4
 502 HOH   ( 594 )  A      O  0.90  K  5
 502 HOH   ( 626 )  A      O  0.97  K  5
 502 HOH   ( 636 )  A      O  0.97  K  4
 502 HOH   ( 644 )  A      O  0.95  K  4
 502 HOH   ( 651 )  A      O  0.92  K  5 Ion-B
 502 HOH   ( 675 )  A      O  0.79 NA  4 *2
 502 HOH   ( 684 )  A      O  0.81 NA  4 *2 Ion-B
 502 HOH   ( 829 )  A      O  0.92  K  4
 502 HOH   ( 849 )  A      O  0.92  K  5
 502 HOH   ( 984 )  A      O  0.85  K  5 Ion-B
 502 HOH   ( 995 )  A      O  0.86  K  4
 502 HOH   (1060 )  A      O  1.02  K  4
 502 HOH   (1081 )  A      O  0.88 NA  5 *2 Ion-B
 502 HOH   (1109 )  A      O  0.87  K  4
 502 HOH   (1169 )  A      O  0.81 NA  6 *2 Ion-B
 502 HOH   (1198 )  A      O  0.96  K  7 Ion-B
 502 HOH   (1269 )  A      O  0.78 NA  7 *2 Ion-B
 502 HOH   (1318 )  A      O  1.02  K  4 Ion-B
 502 HOH   (1349 )  A      O  1.04  K  4 ION-B

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.

 492 ASP   ( 494-)  A   H-bonding suggests Asn

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 :  -0.455
  2nd generation packing quality :   0.244
  Ramachandran plot appearance   :   0.258
  chi-1/chi-2 rotamer normality  :   0.507
  Backbone conformation          :  -0.072

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.653 (tight)
  Bond angles                    :   1.315
  Omega angle restraints         :   1.032
  Side chain planarity           :   0.868
  Improper dihedral distribution :   0.770
  B-factor distribution          :   0.919
  Inside/Outside distribution    :   0.967

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 : 1.35


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -0.0
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.653 (tight)
  Bond angles                    :   1.315
  Omega angle restraints         :   1.032
  Side chain planarity           :   0.868
  Improper dihedral distribution :   0.770
  B-factor distribution          :   0.919
  Inside/Outside distribution    :   0.967
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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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
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      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.