WHAT IF Check report

This file was created 2011-12-18 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 pdb1wcq.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 : 0.601
CA-only RMS fit for the two chains : 0.465

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.

1807 DAN   (1651-)  A  -
1812 DAN   (1652-)  B  -
1817 DAN   (1651-)  C  -

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

Note: Ramachandran plot

Chain identifier: C

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.

  67 GLU   ( 113-)  A    0.50
 257 ARG   ( 303-)  A    0.50
 405 GLN   ( 451-)  A    0.10
 462 ARG   ( 508-)  A    0.50
 603 GLU   (  48-)  B    0.50
 664 ARG   ( 109-)  B    0.50
 801 ARG   ( 246-)  B    0.50
 998 ASP   ( 443-)  B    0.50
1034 ARG   ( 479-)  B    0.50
1063 ARG   ( 508-)  B    0.50
1099 ARG   ( 544-)  B    0.50
1150 ASP   ( 595-)  B    0.50
1201 GLN   ( 646-)  B    0.50
1615 ARG   ( 461-)  C    0.50
1620 GLN   ( 466-)  C    0.10
1641 ARG   ( 487-)  C    0.50
1643 SER   ( 489-)  C    0.50
1800 GLN   ( 646-)  C    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: 9

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

Note: B-factor plot

Chain identifier: C

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

   5 TYR   (  51-)  A
  88 TYR   ( 134-)  A
 194 TYR   ( 240-)  A
 250 TYR   ( 296-)  A
 335 TYR   ( 381-)  A
 434 TYR   ( 480-)  A
 504 TYR   ( 550-)  A
 523 TYR   ( 569-)  A
 540 TYR   ( 586-)  A
 575 TYR   ( 621-)  A
 606 TYR   (  51-)  B
 639 TYR   (  84-)  B
 689 TYR   ( 134-)  B
 851 TYR   ( 296-)  B
 940 TYR   ( 385-)  B
1035 TYR   ( 480-)  B
1105 TYR   ( 550-)  B
1141 TYR   ( 586-)  B
1176 TYR   ( 621-)  B
1205 TYR   (  51-)  C
1238 TYR   (  84-)  C
1288 TYR   ( 134-)  C
1394 TYR   ( 240-)  C
1450 TYR   ( 296-)  C
1634 TYR   ( 480-)  C
1704 TYR   ( 550-)  C
1737 TYR   ( 583-)  C
1740 TYR   ( 586-)  C
1775 TYR   ( 621-)  C

Warning: Phenylalanine convention problem

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

  98 PHE   ( 144-)  A
 100 PHE   ( 146-)  A
 157 PHE   ( 203-)  A
 350 PHE   ( 396-)  A
 362 PHE   ( 408-)  A
 451 PHE   ( 497-)  A
 568 PHE   ( 614-)  A
 619 PHE   (  64-)  B
 758 PHE   ( 203-)  B
 951 PHE   ( 396-)  B
 963 PHE   ( 408-)  B
1052 PHE   ( 497-)  B
1169 PHE   ( 614-)  B
1218 PHE   (  64-)  C
1357 PHE   ( 203-)  C
1550 PHE   ( 396-)  C
1562 PHE   ( 408-)  C
1651 PHE   ( 497-)  C

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.

 261 ASP   ( 307-)  A
 718 ASP   ( 163-)  B
 862 ASP   ( 307-)  B
1597 ASP   ( 443-)  C

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.

  67 GLU   ( 113-)  A
 206 GLU   ( 252-)  A
 608 GLU   (  53-)  B
1267 GLU   ( 113-)  C

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.

 128 VAL   ( 174-)  A      CA   CB    1.61    4.0
 143 ILE   ( 189-)  A      CG1  CD1   1.68    4.3
 181 ILE   ( 227-)  A      CA   CB    1.61    4.1
 405 GLN   ( 451-)  A      CG   CD    1.66    5.6
 405 GLN   ( 451-)  A      CD   OE1   1.10   -6.6
 405 GLN   ( 451-)  A      CD   NE2   1.75   20.1
 681 ILE   ( 126-)  B      CA   CB    1.61    4.2
 870 ILE   ( 315-)  B      CA   CB    1.61    4.2
 929 THR   ( 374-)  B      CA   CB    1.61    4.2
1150 ASP   ( 595-)  B      CB   CG    1.69    7.1
1150 ASP   ( 595-)  B      CG   OD1   1.73   25.5
1150 ASP   ( 595-)  B      CG   OD2   1.16   -4.6
1172 ARG   ( 617-)  B      NE   CZ    1.39    4.2
1172 ARG   ( 617-)  B      CZ   NH1   1.41    4.7
1526 THR   ( 372-)  C      CA   CB    1.63    4.8
1572 GLY   ( 418-)  C      C    O     1.32    4.3
1573 GLN   ( 419-)  C      CG   CD    1.67    6.0
1573 GLN   ( 419-)  C      CD   OE1   1.40    8.6
1679 ARG   ( 525-)  C      N    CA    1.54    4.4

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

 |  0.995807  0.000965  0.000197|
 |  0.000965  0.994927  0.000530|
 |  0.000197  0.000530  0.994865|
Proposed new scale matrix

 |  0.007005  0.004044 -0.000004|
 | -0.000008  0.008101 -0.000004|
 | -0.000001 -0.000003  0.006272|
With corresponding cell

    A    = 142.666  B   = 142.449  C    = 159.434
    Alpha=  89.958  Beta=  89.977  Gamma= 119.939

The CRYST1 cell dimensions

    A    = 143.258  B   = 143.258  C    = 160.250
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 1376.510
(Under-)estimated Z-score: 27.344

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.

  31 ASP   (  77-)  A      C    CA   CB  102.19   -4.2
 234 ARG   ( 280-)  A      CG   CD   NE  101.63   -5.2
 405 GLN   ( 451-)  A      CG   CD   NE2  95.52  -13.9
 405 GLN   ( 451-)  A      NE2  CD   OE1 135.38   12.8
 462 ARG   ( 508-)  A      CG   CD   NE  120.09    5.6
 640 ASP   (  85-)  B      C    CA   CB   99.92   -5.4
 741 HIS   ( 186-)  B      CG   ND1  CE1 109.95    4.4
 742 ARG   ( 187-)  B      CB   CG   CD  105.79   -4.2
 768 ARG   ( 213-)  B      CG   CD   NE  103.34   -4.2
 772 HIS   ( 217-)  B      CG   ND1  CE1 109.65    4.0
 835 ARG   ( 280-)  B      CG   CD   NE  103.67   -4.0
1094 HIS   ( 539-)  B      CG   ND1  CE1 109.68    4.1
1150 ASP   ( 595-)  B      CB   CG   OD2 133.04    6.4
1150 ASP   ( 595-)  B      CB   CG   OD1  93.00  -11.0
1207 GLU   (  53-)  C      C    CA   CB  101.46   -4.5
1239 ASP   (  85-)  C      C    CA   CB  102.45   -4.0
1356 ARG   ( 202-)  C      CB   CG   CD  104.67   -4.7
1573 GLN   ( 419-)  C      CB   CG   CD  102.11   -6.2
1573 GLN   ( 419-)  C      CG   CD   NE2 109.37   -4.7

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.

  67 GLU   ( 113-)  A
 206 GLU   ( 252-)  A
 261 ASP   ( 307-)  A
 608 GLU   (  53-)  B
 718 ASP   ( 163-)  B
 862 ASP   ( 307-)  B
1267 GLU   ( 113-)  C
1597 ASP   ( 443-)  C

Error: Side chain planarity problems

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

1150 ASP   ( 595-)  B   12.95
 405 GLN   ( 451-)  A    7.85

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.

 263 THR   ( 309-)  A    -3.4
1248 PRO   (  94-)  C    -2.9
 863 PRO   ( 308-)  B    -2.8
 262 PRO   ( 308-)  A    -2.8
1649 THR   ( 495-)  C    -2.8
1462 PRO   ( 308-)  C    -2.8
1223 ILE   (  69-)  C    -2.8
1569 LEU   ( 415-)  C    -2.7
1463 THR   ( 309-)  C    -2.7
  23 ILE   (  69-)  A    -2.7
 624 ILE   (  69-)  B    -2.7
 757 ARG   ( 202-)  B    -2.6
1541 PRO   ( 387-)  C    -2.6
  48 PRO   (  94-)  A    -2.6
 449 THR   ( 495-)  A    -2.6
 628 THR   (  73-)  B    -2.6
1591 LYS   ( 437-)  C    -2.6
1050 THR   ( 495-)  B    -2.5
 156 ARG   ( 202-)  A    -2.5
1227 THR   (  73-)  C    -2.5
1528 THR   ( 374-)  C    -2.4
 369 LEU   ( 415-)  A    -2.4
 391 LYS   ( 437-)  A    -2.4
1356 ARG   ( 202-)  C    -2.4
  27 THR   (  73-)  A    -2.3
And so on for a total of 67 lines.

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.

   4 LEU   (  50-)  A  omega poor
  16 GLU   (  62-)  A  Poor phi/psi, omega poor
  23 ILE   (  69-)  A  Poor phi/psi
  31 ASP   (  77-)  A  omega poor
  39 ASP   (  85-)  A  omega poor
  47 ALA   (  93-)  A  PRO omega poor
  50 PRO   (  96-)  A  Poor phi/psi
  52 SER   (  98-)  A  omega poor
  78 ALA   ( 124-)  A  PRO omega poor
  83 PHE   ( 129-)  A  omega poor
  85 ASP   ( 131-)  A  Poor phi/psi
  90 VAL   ( 136-)  A  omega poor
 102 VAL   ( 148-)  A  omega poor
 105 GLN   ( 151-)  A  Poor phi/psi
 137 THR   ( 183-)  A  omega poor
 156 ARG   ( 202-)  A  omega poor
 164 ILE   ( 210-)  A  omega poor
 168 TYR   ( 214-)  A  omega poor
 193 VAL   ( 239-)  A  omega poor
 198 HIS   ( 244-)  A  Poor phi/psi
 228 ASN   ( 274-)  A  omega poor
 233 ALA   ( 279-)  A  omega poor
 234 ARG   ( 280-)  A  Poor phi/psi
 263 THR   ( 309-)  A  Poor phi/psi
 299 GLY   ( 345-)  A  omega poor
And so on for a total of 111 lines.

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.

 792 VAL   ( 237-)  B    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!

  13 ASN   (  59-)  A      0
  15 ARG   (  61-)  A      0
  16 GLU   (  62-)  A      0
  18 PHE   (  64-)  A      0
  19 PRO   (  65-)  A      0
  20 ASN   (  66-)  A      0
  22 ARG   (  68-)  A      0
  23 ILE   (  69-)  A      0
  24 PRO   (  70-)  A      0
  31 ASP   (  77-)  A      0
  37 SER   (  83-)  A      0
  43 THR   (  89-)  A      0
  46 ASP   (  92-)  A      0
  47 ALA   (  93-)  A      0
  48 PRO   (  94-)  A      0
  50 PRO   (  96-)  A      0
  51 ASN   (  97-)  A      0
  60 ASP   ( 106-)  A      0
  63 ARG   ( 109-)  A      0
  64 THR   ( 110-)  A      0
  67 GLU   ( 113-)  A      0
  71 VAL   ( 117-)  A      0
  77 THR   ( 123-)  A      0
  78 ALA   ( 124-)  A      0
  80 ILE   ( 126-)  A      0
And so on for a total of 816 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!

 344 GLY   ( 390-)  A   1.63   16
1544 GLY   ( 390-)  C   1.57   14
 205 GLY   ( 251-)  A   1.57   11
 945 GLY   ( 390-)  B   1.54   17

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   (  76-)  A    0.47 HIGH
 505 PRO   ( 551-)  A    0.46 HIGH
 551 PRO   ( 597-)  A    0.14 LOW
 569 PRO   ( 615-)  A    0.46 HIGH
 631 PRO   (  76-)  B    0.46 HIGH
 771 PRO   ( 216-)  B    0.14 LOW
 874 PRO   ( 319-)  B    0.14 LOW
 920 PRO   ( 365-)  B    0.11 LOW
1170 PRO   ( 615-)  B    0.08 LOW
1230 PRO   (  76-)  C    0.45 HIGH
1279 PRO   ( 125-)  C    0.46 HIGH
1351 PRO   ( 197-)  C    0.16 LOW
1460 PRO   ( 306-)  C    0.12 LOW
1473 PRO   ( 319-)  C    0.12 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].

  48 PRO   (  94-)  A   -57.4 half-chair C-beta/C-alpha (-54 degrees)
 276 PRO   ( 322-)  A   -63.5 envelop C-beta (-72 degrees)
 331 PRO   ( 377-)  A   102.0 envelop C-beta (108 degrees)
 413 PRO   ( 459-)  A  -112.8 envelop C-gamma (-108 degrees)
 853 PRO   ( 298-)  B    50.3 half-chair C-delta/C-gamma (54 degrees)
 863 PRO   ( 308-)  B   -56.9 half-chair C-beta/C-alpha (-54 degrees)
1248 PRO   (  94-)  C   -54.8 half-chair C-beta/C-alpha (-54 degrees)
1462 PRO   ( 308-)  C   -59.6 half-chair C-beta/C-alpha (-54 degrees)
1578 PRO   ( 424-)  C   -38.7 envelop C-alpha (-36 degrees)
1610 PRO   ( 456-)  C   105.4 envelop C-beta (108 degrees)
1631 PRO   ( 477-)  C    99.2 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.

1117 HIS   ( 562-)  B      CE1 <-> 1819 HOH   (2354 )  B      O      0.49    2.31  INTRA
1064 MET   ( 509-)  B      CE  <-> 1113 LEU   ( 558-)  B      CD2    0.45    2.75  INTRA
 664 ARG   ( 109-)  B      NH1 <-> 1819 HOH   (2058 )  B      O      0.45    2.25  INTRA
1567 VAL   ( 413-)  C      CG1 <-> 1577 VAL   ( 423-)  C      CG1    0.44    2.76  INTRA BF
 237 TYR   ( 283-)  A      CZ  <->  293 GLN   ( 339-)  A      NE2    0.42    2.68  INTRA
 664 ARG   ( 109-)  B      NH2 <-> 1819 HOH   (2059 )  B      O      0.41    2.29  INTRA
1794 GLU   ( 640-)  C      CB  <-> 1820 HOH   (2355 )  C      O      0.40    2.40  INTRA BF
1744 ASN   ( 590-)  C      ND2 <-> 1747 THR   ( 593-)  C      CG2    0.35    2.75  INTRA
 737 LEU   ( 182-)  B      CD1 <-> 1819 HOH   (2122 )  B      O      0.35    2.45  INTRA
 433 ARG   ( 479-)  A      NH1 <->  596 GLU   ( 642-)  A      CD     0.33    2.77  INTRA BF
1153 VAL   ( 598-)  B      CG1 <-> 1172 ARG   ( 617-)  B    A NH1    0.31    2.79  INTRA BL
1820 HOH   (2063 )  C      O   <-> 1820 HOH   (2125 )  C      O      0.31    1.89  INTRA
 433 ARG   ( 479-)  A      NH1 <->  596 GLU   ( 642-)  A      OE2    0.31    2.39  INTRA BF
1356 ARG   ( 202-)  C      CD  <-> 1820 HOH   (2123 )  C      O      0.30    2.50  INTRA
1034 ARG   ( 479-)  B      NE  <-> 1197 GLU   ( 642-)  B      OE2    0.22    2.48  INTRA
 237 TYR   ( 283-)  A      CE1 <->  293 GLN   ( 339-)  A      NE2    0.21    2.89  INTRA
 614 ASN   (  59-)  B      O   <-> 1819 HOH   (2007 )  B      O      0.21    2.19  INTRA
1088 ASN   ( 533-)  B      ND2 <-> 1819 HOH   (2340 )  B      O      0.19    2.51  INTRA
 692 ASP   ( 137-)  B      OD2 <->  799 HIS   ( 244-)  B      ND1    0.19    2.51  INTRA BL
 755 ARG   ( 200-)  B      NE  <-> 1819 HOH   (2139 )  B      O      0.19    2.51  INTRA
1509 GLN   ( 355-)  C      CG  <-> 1820 HOH   (2228 )  C      O      0.18    2.62  INTRA
1034 ARG   ( 479-)  B      CD  <-> 1819 HOH   (2312 )  B      O      0.18    2.62  INTRA BF
1356 ARG   ( 202-)  C      NH2 <-> 1820 HOH   (2130 )  C      O      0.18    2.52  INTRA BL
1707 ARG   ( 553-)  C      NH2 <-> 1820 HOH   (2312 )  C      O      0.18    2.52  INTRA
  70 VAL   ( 116-)  A      N   <-> 1818 HOH   (2039 )  A      O      0.17    2.53  INTRA
And so on for a total of 147 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

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.

1306 ARG   ( 152-)  C      -7.66
 106 ARG   ( 152-)  A      -7.59
 707 ARG   ( 152-)  B      -7.51
1215 ARG   (  61-)  C      -6.49
1367 ARG   ( 213-)  C      -6.45
 768 ARG   ( 213-)  B      -6.42
  15 ARG   (  61-)  A      -6.41
 616 ARG   (  61-)  B      -6.36
1313 ARG   ( 159-)  C      -6.33
 113 ARG   ( 159-)  A      -6.32
 167 ARG   ( 213-)  A      -6.29
1400 ARG   ( 246-)  C      -6.28
 714 ARG   ( 159-)  B      -6.12
 200 ARG   ( 246-)  A      -6.08
1371 HIS   ( 217-)  C      -6.02
 412 MET   ( 458-)  A      -6.02
1201 GLN   ( 646-)  B      -5.93
 664 ARG   ( 109-)  B      -5.90
 835 ARG   ( 280-)  B      -5.86
 462 ARG   ( 508-)  A      -5.83
1076 ARG   ( 521-)  B      -5.77
1063 ARG   ( 508-)  B      -5.74
 234 ARG   ( 280-)  A      -5.74
  63 ARG   ( 109-)  A      -5.70
 600 GLN   ( 646-)  A      -5.68
1662 ARG   ( 508-)  C      -5.64
1263 ARG   ( 109-)  C      -5.61
1434 ARG   ( 280-)  C      -5.59
1013 MET   ( 458-)  B      -5.55
1612 MET   ( 458-)  C      -5.55
 475 ARG   ( 521-)  A      -5.41
1591 LYS   ( 437-)  C      -5.36
1800 GLN   ( 646-)  C      -5.35
 801 ARG   ( 246-)  B      -5.31
 737 LEU   ( 182-)  B      -5.27
1675 ARG   ( 521-)  C      -5.27
 561 LEU   ( 607-)  A      -5.26
 136 LEU   ( 182-)  A      -5.23
 894 GLN   ( 339-)  B      -5.23
1743 LEU   ( 589-)  C      -5.21
1036 ARG   ( 481-)  B      -5.19
1162 LEU   ( 607-)  B      -5.15
 910 GLN   ( 355-)  B      -5.10
 257 ARG   ( 303-)  A      -5.03

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

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: C

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.

 562 ALA   ( 608-)  A   -3.06
1762 ALA   ( 608-)  C   -3.02

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

Note: Second generation quality Z-score plot

Chain identifier: C

Water, ion, and hydrogenbond related checks

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.

1818 HOH   (2221 )  A      O
1818 HOH   (2240 )  A      O
1819 HOH   (2227 )  B      O
1820 HOH   (2198 )  C      O
1820 HOH   (2256 )  C      O
1820 HOH   (2262 )  C      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.

  75 GLN   ( 121-)  A
 215 ASN   ( 261-)  A
 309 GLN   ( 355-)  A
 349 ASN   ( 395-)  A
 516 HIS   ( 562-)  A
 527 GLN   ( 573-)  A
 772 HIS   ( 217-)  B
 816 ASN   ( 261-)  B
 910 GLN   ( 355-)  B
 950 ASN   ( 395-)  B
1117 HIS   ( 562-)  B
1128 GLN   ( 573-)  B
1415 ASN   ( 261-)  C
1549 ASN   ( 395-)  C
1727 GLN   ( 573-)  C

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.

  20 ASN   (  66-)  A      N
  22 ARG   (  68-)  A      NH2
  26 LEU   (  72-)  A      N
  57 ARG   ( 103-)  A      NH2
  99 ASN   ( 145-)  A      ND2
 105 GLN   ( 151-)  A      NE2
 150 ASP   ( 196-)  A      N
 155 SER   ( 201-)  A      N
 156 ARG   ( 202-)  A      N
 215 ASN   ( 261-)  A      N
 230 ARG   ( 276-)  A      NE
 230 ARG   ( 276-)  A      NH1
 238 ARG   ( 284-)  A      NH1
 292 SER   ( 338-)  A      N
 302 ARG   ( 348-)  A      NH2
 470 SER   ( 516-)  A      N
 476 GLU   ( 522-)  A      N
 498 ARG   ( 544-)  A      N
 514 GLY   ( 560-)  A      N
 520 GLY   ( 566-)  A      N
 525 ARG   ( 571-)  A      NH2
 529 SER   ( 575-)  A      N
 577 ARG   ( 623-)  A      NH2
 621 ASN   (  66-)  B      N
 623 ARG   (  68-)  B      NH2
And so on for a total of 62 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.

  85 ASP   ( 131-)  A      OD1
 213 ASP   ( 259-)  A      OD2
 471 GLU   ( 517-)  A      OE2
1072 GLU   ( 517-)  B      OE2
1285 ASP   ( 131-)  C      OD1
1377 GLN   ( 223-)  C      OE1
1671 GLU   ( 517-)  C      OE2

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1813  NA   (1648-)  C     1.28   1.04 Scores about as good as CA

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.

1818 HOH   (2102 )  A      O  0.94  K  4
1818 HOH   (2137 )  A      O  0.92  K  4
1818 HOH   (2253 )  A      O  1.13  K  5 ION-B
1819 HOH   (2086 )  B      O  0.88  K  4 Ion-B
1819 HOH   (2109 )  B      O  1.12  K  4
1819 HOH   (2150 )  B      O  1.00  K  4 NCS 1/1
1820 HOH   (2139 )  C      O  0.90  K  4
1820 HOH   (2175 )  C      O  0.99  K  4
1820 HOH   (2240 )  C      O  1.03  K  4

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.

  60 ASP   ( 106-)  A   H-bonding suggests Asn
  67 GLU   ( 113-)  A   H-bonding suggests Gln
 133 ASP   ( 179-)  A   H-bonding suggests Asn
 162 GLU   ( 208-)  A   H-bonding suggests Gln
 197 ASP   ( 243-)  A   H-bonding suggests Asn; but Alt-Rotamer
 245 ASP   ( 291-)  A   H-bonding suggests Asn; but Alt-Rotamer
 594 GLU   ( 640-)  A   H-bonding suggests Gln; but Alt-Rotamer
 661 ASP   ( 106-)  B   H-bonding suggests Asn
 763 GLU   ( 208-)  B   H-bonding suggests Gln
 798 ASP   ( 243-)  B   H-bonding suggests Asn; but Alt-Rotamer
 846 ASP   ( 291-)  B   H-bonding suggests Asn; but Alt-Rotamer
 907 ASP   ( 352-)  B   H-bonding suggests Asn; but Alt-Rotamer
 998 ASP   ( 443-)  B   H-bonding suggests Asn
1070 ASP   ( 515-)  B   H-bonding suggests Asn
1150 ASP   ( 595-)  B   H-bonding suggests Asn
1184 GLU   ( 629-)  B   H-bonding suggests Gln
1195 GLU   ( 640-)  B   H-bonding suggests Gln; but Alt-Rotamer
1362 GLU   ( 208-)  C   H-bonding suggests Gln
1397 ASP   ( 243-)  C   H-bonding suggests Asn
1445 ASP   ( 291-)  C   H-bonding suggests Asn; but Alt-Rotamer
1669 ASP   ( 515-)  C   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 :  -0.269
  2nd generation packing quality :  -0.861
  Ramachandran plot appearance   :  -0.709
  chi-1/chi-2 rotamer normality  :  -2.055
  Backbone conformation          :   0.156

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.913
  Bond angles                    :   0.889
  Omega angle restraints         :   1.254
  Side chain planarity           :   1.112
  Improper dihedral distribution :   0.969
  B-factor distribution          :   0.542
  Inside/Outside distribution    :   0.977

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.913
  Bond angles                    :   0.889
  Omega angle restraints         :   1.254
  Side chain planarity           :   1.112
  Improper dihedral distribution :   0.969
  B-factor distribution          :   0.542
  Inside/Outside distribution    :   0.977
==============

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.