WHAT IF Check report

This file was created 2012-01-31 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 pdb2okj.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.669
CA-only RMS fit for the two chains : 0.562

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

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.

1006 ABU   (1001-)  A  -
1007 PLZ   (2001-)  B  -
1008 ABU   (1002-)  B  -

Administrative problems that can generate validation failures

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.

1007 PLZ   (2001-)  B  -

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

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. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 557 LEU   ( 148-)  B  -

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

Note: Ramachandran plot

Chain identifier: B

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 313 LLP   ( 405-)  A
 814 LLP   ( 405-)  B

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'.

   1 THR   (  93-)  A      OG1
   1 THR   (  93-)  A      CG2
   4 SER   (  96-)  A      OG
  15 LYS   ( 107-)  A      CG
  15 LYS   ( 107-)  A      CD
  15 LYS   ( 107-)  A      CE
  15 LYS   ( 107-)  A      NZ
  19 GLU   ( 111-)  A      CB
  19 GLU   ( 111-)  A      CG
  19 GLU   ( 111-)  A      CD
  19 GLU   ( 111-)  A      OE1
  19 GLU   ( 111-)  A      OE2
  38 LYS   ( 130-)  A      CD
  38 LYS   ( 130-)  A      CE
  38 LYS   ( 130-)  A      NZ
  45 LYS   ( 137-)  A      CE
  45 LYS   ( 137-)  A      NZ
  60 GLU   ( 152-)  A      CD
  60 GLU   ( 152-)  A      OE1
  60 GLU   ( 152-)  A      OE2
 242 LYS   ( 334-)  A      CD
 242 LYS   ( 334-)  A      CE
 242 LYS   ( 334-)  A      NZ
 272 GLU   ( 364-)  A      CD
 272 GLU   ( 364-)  A      OE1
And so on for a total of 115 lines.

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.

 814 LLP   ( 405-)  B    0.50

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) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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.

  37 ARG   ( 129-)  A
 431 ARG   ( 523-)  A
 475 ARG   ( 567-)  A
 538 ARG   ( 129-)  B
 932 ARG   ( 523-)  B
 976 ARG   ( 567-)  B

Warning: Tyrosine convention problem

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

 173 TYR   ( 265-)  A
 175 TYR   ( 267-)  A
 244 TYR   ( 336-)  A
 258 TYR   ( 350-)  A
 350 TYR   ( 442-)  A
 397 TYR   ( 489-)  A
 399 TYR   ( 491-)  A
 425 TYR   ( 517-)  A
 464 TYR   ( 556-)  A
 674 TYR   ( 265-)  B
 745 TYR   ( 336-)  B
 759 TYR   ( 350-)  B
 851 TYR   ( 442-)  B
 898 TYR   ( 489-)  B
 900 TYR   ( 491-)  B
 926 TYR   ( 517-)  B
 965 TYR   ( 556-)  B

Warning: Phenylalanine convention problem

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

   3 PHE   (  95-)  A
   7 PHE   (  99-)  A
  96 PHE   ( 188-)  A
 122 PHE   ( 214-)  A
 193 PHE   ( 285-)  A
 211 PHE   ( 303-)  A
 232 PHE   ( 324-)  A
 247 PHE   ( 339-)  A
 344 PHE   ( 436-)  A
 384 PHE   ( 476-)  A
 408 PHE   ( 500-)  A
 423 PHE   ( 515-)  A
 473 PHE   ( 565-)  A
 504 PHE   (  95-)  B
 508 PHE   (  99-)  B
 563 PHE   ( 154-)  B
 597 PHE   ( 188-)  B
 623 PHE   ( 214-)  B
 712 PHE   ( 303-)  B
 733 PHE   ( 324-)  B
 748 PHE   ( 339-)  B
 885 PHE   ( 476-)  B
 909 PHE   ( 500-)  B
 924 PHE   ( 515-)  B
 974 PHE   ( 565-)  B

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.

  82 ASP   ( 174-)  A
 583 ASP   ( 174-)  B

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.

  27 GLU   ( 119-)  A
 125 GLU   ( 217-)  A
 143 GLU   ( 235-)  A
 223 GLU   ( 315-)  A
 233 GLU   ( 325-)  A
 302 GLU   ( 394-)  A
 328 GLU   ( 420-)  A
 396 GLU   ( 488-)  A
 409 GLU   ( 501-)  A
 417 GLU   ( 509-)  A
 493 GLU   ( 585-)  A
 494 GLU   ( 586-)  A
 528 GLU   ( 119-)  B
 626 GLU   ( 217-)  B
 644 GLU   ( 235-)  B
 724 GLU   ( 315-)  B
 734 GLU   ( 325-)  B
 773 GLU   ( 364-)  B
 803 GLU   ( 394-)  B
 829 GLU   ( 420-)  B
 897 GLU   ( 488-)  B
 910 GLU   ( 501-)  B
 918 GLU   ( 509-)  B
 995 GLU   ( 586-)  B

Geometric checks

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

 |  0.996962  0.000060  0.000376|
 |  0.000060  0.997487  0.000165|
 |  0.000376  0.000165  0.996850|
Proposed new scale matrix

 |  0.011933 -0.000001  0.003573|
 |  0.000000  0.015979 -0.000003|
 | -0.000004 -0.000002  0.010334|
With corresponding cell

    A    =  83.792  B   =  62.582  C    = 101.005
    Alpha=  89.983  Beta= 106.646  Gamma=  89.997

The CRYST1 cell dimensions

    A    =  84.048  B   =  62.739  C    = 101.346
    Alpha=  90.000  Beta= 106.680  Gamma=  90.000

Variance: 277.973
(Under-)estimated Z-score: 12.288

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.

 230 ALA   ( 322-)  A      N    CA   C   123.47    4.4
 231 ASP   ( 323-)  A     -C    N    CA  132.09    5.8
 231 ASP   ( 323-)  A      N    CA   CB  119.82    5.5
 253 ALA   ( 345-)  A     -C    N    CA  130.19    4.7
 344 PHE   ( 436-)  A     -C    N    CA  131.85    5.6
 344 PHE   ( 436-)  A      N    CA   C   122.70    4.1
 345 GLN   ( 437-)  A     -C    N    CA  129.24    4.2
 754 ALA   ( 345-)  B     -C    N    CA  130.01    4.6
 846 GLN   ( 437-)  B     -C    N    CA  129.73    4.5

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.

  27 GLU   ( 119-)  A
  37 ARG   ( 129-)  A
  82 ASP   ( 174-)  A
 125 GLU   ( 217-)  A
 143 GLU   ( 235-)  A
 223 GLU   ( 315-)  A
 233 GLU   ( 325-)  A
 302 GLU   ( 394-)  A
 328 GLU   ( 420-)  A
 396 GLU   ( 488-)  A
 409 GLU   ( 501-)  A
 417 GLU   ( 509-)  A
 431 ARG   ( 523-)  A
 475 ARG   ( 567-)  A
 493 GLU   ( 585-)  A
 494 GLU   ( 586-)  A
 528 GLU   ( 119-)  B
 538 ARG   ( 129-)  B
 583 ASP   ( 174-)  B
 626 GLU   ( 217-)  B
 644 GLU   ( 235-)  B
 724 GLU   ( 315-)  B
 734 GLU   ( 325-)  B
 773 GLU   ( 364-)  B
 803 GLU   ( 394-)  B
 829 GLU   ( 420-)  B
 897 GLU   ( 488-)  B
 910 GLU   ( 501-)  B
 918 GLU   ( 509-)  B
 932 ARG   ( 523-)  B
 976 ARG   ( 567-)  B
 995 GLU   ( 586-)  B

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.

 231 ASP   ( 323-)  A      CA    -7.8    18.15    33.73
The average deviation= 0.582

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.

 230 ALA   ( 322-)  A    8.35
 344 PHE   ( 436-)  A    4.42

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.

 935 PRO   ( 526-)  B    -3.0
 344 PHE   ( 436-)  A    -2.5
 361 ILE   ( 453-)  A    -2.4
 862 ILE   ( 453-)  B    -2.4
 341 GLY   ( 433-)  A    -2.4
 967 PRO   ( 558-)  B    -2.4
 961 THR   ( 552-)  B    -2.3
 126 ILE   ( 218-)  A    -2.3
 627 ILE   ( 218-)  B    -2.3
 434 PRO   ( 526-)  A    -2.3
 466 PRO   ( 558-)  A    -2.3
 500 GLN   ( 592-)  A    -2.3
 231 ASP   ( 323-)  A    -2.3
 842 GLY   ( 433-)  B    -2.3
 342 TYR   ( 434-)  A    -2.3
 460 THR   ( 552-)  A    -2.2
 820 LEU   ( 411-)  B    -2.2
 194 THR   ( 286-)  A    -2.2
 978 VAL   ( 569-)  B    -2.2
 695 THR   ( 286-)  B    -2.1
 477 VAL   ( 569-)  A    -2.1
 847 PRO   ( 438-)  B    -2.1
 432 GLY   ( 524-)  A    -2.1
 240 LYS   ( 332-)  A    -2.1
 895 LEU   ( 486-)  B    -2.0
 339 CYS   ( 431-)  A    -2.0
 394 LEU   ( 486-)  A    -2.0
 418 HIS   ( 510-)  A    -2.0
 919 HIS   ( 510-)  B    -2.0
 247 PHE   ( 339-)  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.

   2 ASP   (  94-)  A  Poor phi/psi
  12 LEU   ( 104-)  A  PRO omega poor
  57 GLU   ( 149-)  A  Poor phi/psi
  58 GLY   ( 150-)  A  omega poor
 151 ASP   ( 243-)  A  Poor phi/psi
 158 PRO   ( 250-)  A  Poor phi/psi
 189 LYS   ( 281-)  A  omega poor
 229 PRO   ( 321-)  A  omega poor
 230 ALA   ( 322-)  A  omega poor
 231 ASP   ( 323-)  A  Poor phi/psi
 247 PHE   ( 339-)  A  Poor phi/psi
 252 THR   ( 344-)  A  omega poor
 253 ALA   ( 345-)  A  Poor phi/psi
 319 LEU   ( 411-)  A  omega poor
 323 ALA   ( 415-)  A  omega poor
 340 ALA   ( 432-)  A  omega poor
 341 GLY   ( 433-)  A  Poor phi/psi, omega poor
 342 TYR   ( 434-)  A  Poor phi/psi, omega poor
 343 LEU   ( 435-)  A  omega poor
 344 PHE   ( 436-)  A  Poor phi/psi, omega poor
 345 GLN   ( 437-)  A  Poor phi/psi
 363 CYS   ( 455-)  A  Poor phi/psi
 418 HIS   ( 510-)  A  Poor phi/psi
 424 TRP   ( 516-)  A  omega poor
 431 ARG   ( 523-)  A  omega poor
 432 GLY   ( 524-)  A  omega poor
 433 VAL   ( 525-)  A  Poor phi/psi, PRO omega poor
 503 ASP   (  94-)  B  Poor phi/psi
 513 LEU   ( 104-)  B  PRO omega poor
 560 MET   ( 151-)  B  omega poor
 561 GLU   ( 152-)  B  omega poor
 748 PHE   ( 339-)  B  Poor phi/psi
 753 THR   ( 344-)  B  omega poor
 754 ALA   ( 345-)  B  Poor phi/psi
 776 ASN   ( 367-)  B  Poor phi/psi
 820 LEU   ( 411-)  B  omega poor
 824 ALA   ( 415-)  B  omega poor
 842 GLY   ( 433-)  B  Poor phi/psi, omega poor
 843 TYR   ( 434-)  B  Poor phi/psi
 845 PHE   ( 436-)  B  omega poor
 846 GLN   ( 437-)  B  Poor phi/psi
 864 CYS   ( 455-)  B  Poor phi/psi
 919 HIS   ( 510-)  B  Poor phi/psi
 925 TRP   ( 516-)  B  omega poor
 934 VAL   ( 525-)  B  PRO omega poor
 935 PRO   ( 526-)  B  Poor phi/psi
WARNING: Attached group deleted: 1007
 chi-1/chi-2 correlation Z-score : -1.624

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.

 307 VAL   ( 399-)  A    0.36
 808 VAL   ( 399-)  B    0.36
WARNING: Attached group deleted: 1007

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!

   3 PHE   (  95-)  A      0
   4 SER   (  96-)  A      0
  12 LEU   ( 104-)  A      0
  13 PRO   ( 105-)  A      0
  14 ALA   ( 106-)  A      0
  15 LYS   ( 107-)  A      0
  19 GLU   ( 111-)  A      0
  42 ARG   ( 134-)  A      0
  46 VAL   ( 138-)  A      0
  47 LEU   ( 139-)  A      0
  49 PHE   ( 141-)  A      0
  57 GLU   ( 149-)  A      0
  59 MET   ( 151-)  A      0
  60 GLU   ( 152-)  A      0
  64 LEU   ( 156-)  A      0
  68 ASP   ( 160-)  A      0
  89 ARG   ( 181-)  A      0
  94 ARG   ( 186-)  A      0
  95 PHE   ( 187-)  A      0
  96 PHE   ( 188-)  A      0
  97 ASN   ( 189-)  A      0
 100 SER   ( 192-)  A      0
 101 THR   ( 193-)  A      0
 117 ALA   ( 209-)  A      0
 118 ASN   ( 210-)  A      0
And so on for a total of 396 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!

 933 GLY   ( 524-)  B   1.60   24

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].

 346 PRO   ( 438-)  A    22.2 half-chair N/C-delta (18 degrees)
 434 PRO   ( 526-)  A    15.3 half-chair N/C-delta (18 degrees)
 448 PRO   ( 540-)  A  -112.0 envelop C-gamma (-108 degrees)
 466 PRO   ( 558-)  A   -57.5 half-chair C-beta/C-alpha (-54 degrees)
 847 PRO   ( 438-)  B   -42.0 envelop C-alpha (-36 degrees)
 935 PRO   ( 526-)  B   -24.4 half-chair C-alpha/N (-18 degrees)
 967 PRO   ( 558-)  B   -52.8 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.

 814 LLP   ( 405-)  B    A C2' <-> 1007 PLZ   (2001-)  B      C2A    3.09    0.11  INTRA BL
 814 LLP   ( 405-)  B    A C6  <-> 1007 PLZ   (2001-)  B      C16    3.07    0.13  INTRA BL
 814 LLP   ( 405-)  B    A P   <-> 1007 PLZ   (2001-)  B      P      2.58    0.12  INTRA BL
 814 LLP   ( 405-)  B    A OP4 <-> 1007 PLZ   (2001-)  B      O4P    2.32    0.08  INTRA BL
 814 LLP   ( 405-)  B    A C2  <-> 1007 PLZ   (2001-)  B      C12    2.21    0.09  INTRA BL
 814 LLP   ( 405-)  B    A OP2 <-> 1007 PLZ   (2001-)  B      O2P    2.16    0.24  INTRA BL
 814 LLP   ( 405-)  B    A OP1 <-> 1007 PLZ   (2001-)  B      O1P    2.14    0.26  INTRA BL
 814 LLP   ( 405-)  B    A C5  <-> 1007 PLZ   (2001-)  B      C15    2.11    0.19  INTRA BL
 814 LLP   ( 405-)  B    A C3  <-> 1007 PLZ   (2001-)  B      C13    2.11    0.19  INTRA BL
 814 LLP   ( 405-)  B    A C5' <-> 1007 PLZ   (2001-)  B      C5M    2.05    0.25  INTRA BL
 814 LLP   ( 405-)  B    A C4  <-> 1007 PLZ   (2001-)  B      C19    2.04    0.26  INTRA BL
 814 LLP   ( 405-)  B    A N1  <-> 1007 PLZ   (2001-)  B      N1     1.94    0.16  INTRA BL
 814 LLP   ( 405-)  B    A C4' <-> 1007 PLZ   (2001-)  B      C4A    1.87    0.43  INTRA BL
 814 LLP   ( 405-)  B    A C5  <-> 1007 PLZ   (2001-)  B      C16    1.80    1.40  INTRA BL
 814 LLP   ( 405-)  B    A N1  <-> 1007 PLZ   (2001-)  B      C16    1.65    1.45  INTRA BL
 814 LLP   ( 405-)  B    A C4  <-> 1007 PLZ   (2001-)  B      C13    1.47    1.33  INTRA BL
 814 LLP   ( 405-)  B    A C5  <-> 1007 PLZ   (2001-)  B      C19    1.46    1.34  INTRA BL
 814 LLP   ( 405-)  B    A P   <-> 1007 PLZ   (2001-)  B      O2P    1.43    1.57  INTRA BL
 814 LLP   ( 405-)  B    A P   <-> 1007 PLZ   (2001-)  B      O1P    1.42    1.58  INTRA BL
 814 LLP   ( 405-)  B    A C5' <-> 1007 PLZ   (2001-)  B      O4P    1.42    1.38  INTRA BL
 814 LLP   ( 405-)  B    A OP3 <-> 1007 PLZ   (2001-)  B      O3P    1.41    0.09  INTRA BL
 814 LLP   ( 405-)  B    A C6  <-> 1007 PLZ   (2001-)  B      C15    1.41    1.39  INTRA BL
 814 LLP   ( 405-)  B    A P   <-> 1007 PLZ   (2001-)  B      O4P    1.41    1.59  INTRA BL
 814 LLP   ( 405-)  B    A N1  <-> 1007 PLZ   (2001-)  B      C12    1.40    1.30  INTRA BL
 814 LLP   ( 405-)  B    A C3  <-> 1007 PLZ   (2001-)  B      C12    1.39    1.41  INTRA BL
And so on for a total of 142 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 431 ARG   ( 523-)  A      -6.84
1004 HIS   ( 595-)  B      -6.74
 500 GLN   ( 592-)  A      -6.51
 560 MET   ( 151-)  B      -6.45
 342 TYR   ( 434-)  A      -6.16
 150 LYS   ( 242-)  A      -6.10
 850 GLN   ( 441-)  B      -5.76
 241 GLN   ( 333-)  A      -5.68
 932 ARG   ( 523-)  B      -5.67
 349 GLN   ( 441-)  A      -5.66
 651 LYS   ( 242-)  B      -5.65
 404 ASN   ( 496-)  A      -5.35
  59 MET   ( 151-)  A      -5.35
 905 ASN   ( 496-)  B      -5.32
 303 ARG   ( 395-)  A      -5.31
 570 HIS   ( 161-)  B      -5.29
  69 HIS   ( 161-)  A      -5.28
 804 ARG   ( 395-)  B      -5.28
 506 ASN   (  97-)  B      -5.19
1001 GLN   ( 592-)  B      -5.17
 336 ASN   ( 428-)  A      -5.11
 837 ASN   ( 428-)  B      -5.10
 339 CYS   ( 431-)  A      -5.03
 913 PHE   ( 504-)  B      -5.00

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.

 336 ASN   ( 428-)  A       339 - CYS    431- ( A)         -4.70
 837 ASN   ( 428-)  B       840 - CYS    431- ( B)         -4.50
 932 ARG   ( 523-)  B       934 - VAL    525- ( B)         -4.89

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: 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: B

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.

 516 LYS   ( 107-)  B   -3.42
 319 LEU   ( 411-)  A   -3.36
 186 ALA   ( 278-)  A   -3.12
 343 LEU   ( 435-)  A   -2.93
 844 LEU   ( 435-)  B   -2.81
 867 HIS   ( 458-)  B   -2.76
 366 HIS   ( 458-)  A   -2.53

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.

 842 GLY   ( 433-)  B     -  846 GLN   ( 437-)  B        -1.99
WARNING: Attached group deleted: 1007

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

Note: Second generation quality Z-score plot

Chain identifier: B

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.

1009 HOH   (2041 )  B      O    -56.48  -16.05  -16.11

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.

1008 HOH   (1149 )  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.

  69 HIS   ( 161-)  A
 118 ASN   ( 210-)  A
 164 ASN   ( 256-)  A
 296 HIS   ( 388-)  A
 310 ASN   ( 402-)  A
 312 HIS   ( 404-)  A
 337 GLN   ( 429-)  A
 362 GLN   ( 454-)  A
 366 HIS   ( 458-)  A
 472 ASN   ( 564-)  A
 480 ASN   ( 572-)  A
 506 ASN   (  97-)  B
 551 HIS   ( 142-)  B
 554 HIS   ( 145-)  B
 570 HIS   ( 161-)  B
 619 ASN   ( 210-)  B
 665 ASN   ( 256-)  B
 797 HIS   ( 388-)  B
 811 ASN   ( 402-)  B
 838 GLN   ( 429-)  B
 863 GLN   ( 454-)  B
 929 GLN   ( 520-)  B
 973 ASN   ( 564-)  B
 981 ASN   ( 572-)  B

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.

  47 LEU   ( 139-)  A      N
  51 HIS   ( 143-)  A      N
  59 MET   ( 151-)  A      N
  97 ASN   ( 189-)  A      N
  98 GLN   ( 190-)  A      N
  99 LEU   ( 191-)  A      N
 100 SER   ( 192-)  A      N
 122 PHE   ( 214-)  A      N
 123 THR   ( 215-)  A      N
 156 PHE   ( 248-)  A      N
 160 GLY   ( 252-)  A      N
 161 ALA   ( 253-)  A      N
 247 PHE   ( 339-)  A      N
 248 TYR   ( 340-)  A      N
 255 THR   ( 347-)  A      OG1
 310 ASN   ( 402-)  A      ND2
 318 LEU   ( 410-)  A      N
 342 TYR   ( 434-)  A      N
 343 LEU   ( 435-)  A      N
 348 LYS   ( 440-)  A      N
 350 TYR   ( 442-)  A      N
 362 GLN   ( 454-)  A      N
 364 GLY   ( 456-)  A      N
 379 LYS   ( 471-)  A      NZ
 389 ASN   ( 481-)  A      ND2
And so on for a total of 68 lines.

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.

  71 GLU   ( 163-)  A      OE1
  79 ASP   ( 171-)  A      OD2
  82 ASP   ( 174-)  A      OD2
 250 ASN   ( 342-)  A      OD1
 310 ASN   ( 402-)  A      OD1
 465 GLN   ( 557-)  A      OE1
 572 GLU   ( 163-)  B      OE1
 580 ASP   ( 171-)  B      OD2
 751 ASN   ( 342-)  B      OD1
 811 ASN   ( 402-)  B      OD1
 813 HIS   ( 404-)  B      NE2
 966 GLN   ( 557-)  B      OE1

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.

1008 HOH   (1033 )  A      O  1.05  K  4
1008 HOH   (1146 )  A      O  0.88  K  6 Ion-B
1009 HOH   (2073 )  B      O  0.89  K  4
1009 HOH   (2163 )  B      O  1.12  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.

  79 ASP   ( 171-)  A   H-bonding suggests Asn; but Alt-Rotamer
 214 ASP   ( 306-)  A   H-bonding suggests Asn
 262 ASP   ( 354-)  A   H-bonding suggests Asn; but Alt-Rotamer
 368 ASP   ( 460-)  A   H-bonding suggests Asn; but Alt-Rotamer
 580 ASP   ( 171-)  B   H-bonding suggests Asn; but Alt-Rotamer
 715 ASP   ( 306-)  B   H-bonding suggests Asn
 763 ASP   ( 354-)  B   H-bonding suggests Asn; but Alt-Rotamer
 869 ASP   ( 460-)  B   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.624
  2nd generation packing quality :  -1.857
  Ramachandran plot appearance   :  -0.512
  chi-1/chi-2 rotamer normality  :  -1.624
  Backbone conformation          :  -0.543

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.360 (tight)
  Bond angles                    :   0.575 (tight)
  Omega angle restraints         :   0.899
  Side chain planarity           :   0.286 (tight)
  Improper dihedral distribution :   0.551
  B-factor distribution          :   0.458
  Inside/Outside distribution    :   0.975

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.360 (tight)
  Bond angles                    :   0.575 (tight)
  Omega angle restraints         :   0.899
  Side chain planarity           :   0.286 (tight)
  Improper dihedral distribution :   0.551
  B-factor distribution          :   0.458
  Inside/Outside distribution    :   0.975
==============

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.