WHAT IF Check report

This file was created 2011-12-13 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 pdb2bzd.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 : 1.079
CA-only RMS fit for the two chains : 0.961

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

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: B and C

All-atom RMS fit for the two chains : 1.251
CA-only RMS fit for the two chains : 1.155

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: B and C

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 GAL   (1649-)  A  -
1809 GAL   (1649-)  B  -
1814 GAL   (1649-)  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
 395 GLN   ( 441-)  A    0.50
 412 MET   ( 458-)  A    0.50
 462 ARG   ( 508-)  A    0.50
 463 MET   ( 509-)  A    0.50
 481 SER   ( 527-)  A    0.50
 603 GLU   (  48-)  B    0.50
 647 ASP   (  92-)  B    0.50
 664 ARG   ( 109-)  B    0.50
 801 ARG   ( 246-)  B    0.50
 858 ARG   ( 303-)  B    0.50
 896 SER   ( 341-)  B    0.50
 996 GLN   ( 441-)  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
1247 ASP   (  92-)  C    0.50
1616 ARG   ( 461-)  C    0.50
1642 ARG   ( 487-)  C    0.50
1644 SER   ( 489-)  C    0.50
1801 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: 6

Crystal temperature (K) :100.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 5.73

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
 324 TYR   ( 370-)  A
 335 TYR   ( 381-)  A
 339 TYR   ( 385-)  A
 434 TYR   ( 480-)  A
 504 TYR   ( 550-)  A
 540 TYR   ( 586-)  A
 575 TYR   ( 621-)  A
 606 TYR   (  51-)  B
 689 TYR   ( 134-)  B
 795 TYR   ( 240-)  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
1206 TYR   (  51-)  C
1239 TYR   (  84-)  C
1289 TYR   ( 134-)  C
1395 TYR   ( 240-)  C
1451 TYR   ( 296-)  C
1525 TYR   ( 370-)  C
1635 TYR   ( 480-)  C
1705 TYR   ( 550-)  C
1741 TYR   ( 586-)  C
1776 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.

  18 PHE   (  64-)  A
 100 PHE   ( 146-)  A
 157 PHE   ( 203-)  A
 350 PHE   ( 396-)  A
 362 PHE   ( 408-)  A
 451 PHE   ( 497-)  A
 701 PHE   ( 146-)  B
 758 PHE   ( 203-)  B
 963 PHE   ( 408-)  B
1052 PHE   ( 497-)  B
1301 PHE   ( 146-)  C
1358 PHE   ( 203-)  C
1563 PHE   ( 408-)  C
1652 PHE   ( 497-)  C
1769 PHE   ( 614-)  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.

   9 ASP   (  55-)  A
 647 ASP   (  92-)  B
 718 ASP   ( 163-)  B
1598 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.

   7 GLU   (  53-)  A
  67 GLU   ( 113-)  A
 206 GLU   ( 252-)  A
 603 GLU   (  48-)  B
 608 GLU   (  53-)  B
1195 GLU   ( 640-)  B
1268 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.

 218 VAL   ( 264-)  A      CA   CB    1.61    4.2
 422 THR   ( 468-)  A      C    O     1.34    5.4
 870 ILE   ( 315-)  B      CA   CB    1.61    4.1

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

 |  0.996265 -0.000998 -0.000365|
 | -0.000998  0.995675  0.000650|
 | -0.000365  0.000650  0.996017|
Proposed new scale matrix

 |  0.007100  0.004106  0.000000|
 |  0.000008  0.008198 -0.000005|
 |  0.000002 -0.000004  0.006319|
With corresponding cell

    A    = 140.934  B   = 140.984  C    = 158.249
    Alpha=  89.914  Beta=  90.043  Gamma= 120.099

The CRYST1 cell dimensions

    A    = 141.457  B   = 141.457  C    = 158.880
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 972.609
(Under-)estimated Z-score: 22.985

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.

 125 HIS   ( 171-)  A      CG   ND1  CE1 109.61    4.0
1094 HIS   ( 539-)  B      CG   ND1  CE1 109.82    4.2
1107 HIS   ( 552-)  B      CG   ND1  CE1 109.84    4.2
1144 LEU   ( 589-)  B      CA   CB   CG   99.78   -4.7
1247 ASP   (  92-)  C      CA   CB   CG  116.61    4.0
1717 HIS   ( 562-)  C      CG   ND1  CE1 109.62    4.0
1788 HIS   ( 633-)  C      CG   ND1  CE1 109.63    4.0

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.

   7 GLU   (  53-)  A
   9 ASP   (  55-)  A
  67 GLU   ( 113-)  A
 206 GLU   ( 252-)  A
 603 GLU   (  48-)  B
 608 GLU   (  53-)  B
 647 ASP   (  92-)  B
 718 ASP   ( 163-)  B
1195 GLU   ( 640-)  B
1268 GLU   ( 113-)  C
1598 ASP   ( 443-)  C

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    -3.1
  48 PRO   (  94-)  A    -3.0
1249 PRO   (  94-)  C    -2.9
1463 PRO   ( 308-)  C    -2.9
1050 THR   ( 495-)  B    -2.9
 863 PRO   ( 308-)  B    -2.8
 864 THR   ( 309-)  B    -2.8
 234 ARG   ( 280-)  A    -2.7
1228 THR   (  73-)  C    -2.7
1650 THR   ( 495-)  C    -2.7
 628 THR   (  73-)  B    -2.7
 624 ILE   (  69-)  B    -2.6
 649 PRO   (  94-)  B    -2.6
1224 ILE   (  69-)  C    -2.6
1592 LYS   ( 437-)  C    -2.6
 929 THR   ( 374-)  B    -2.5
  23 ILE   (  69-)  A    -2.5
 382 THR   ( 428-)  A    -2.5
1542 PRO   ( 387-)  C    -2.5
1034 ARG   ( 479-)  B    -2.5
 156 ARG   ( 202-)  A    -2.5
1357 ARG   ( 202-)  C    -2.5
 757 ARG   ( 202-)  B    -2.5
1708 ARG   ( 553-)  C    -2.4
 262 PRO   ( 308-)  A    -2.4
And so on for a total of 78 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
   6 THR   (  52-)  A  omega poor
  16 GLU   (  62-)  A  Poor phi/psi
  23 ILE   (  69-)  A  Poor phi/psi
  25 ALA   (  71-)  A  omega poor
  38 TYR   (  84-)  A  Poor phi/psi
  39 ASP   (  85-)  A  omega poor
  47 ALA   (  93-)  A  PRO omega poor
  50 PRO   (  96-)  A  Poor phi/psi
  78 ALA   ( 124-)  A  PRO 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
 138 TRP   ( 184-)  A  omega poor
 168 TYR   ( 214-)  A  omega poor
 179 TYR   ( 225-)  A  omega poor
 192 SER   ( 238-)  A  omega poor
 198 HIS   ( 244-)  A  Poor phi/psi
 209 GLY   ( 255-)  A  omega poor
 213 ASP   ( 259-)  A  Poor phi/psi
 228 ASN   ( 274-)  A  omega poor
 229 SER   ( 275-)  A  omega poor
 234 ARG   ( 280-)  A  Poor phi/psi
 258 ASP   ( 304-)  A  omega poor
And so on for a total of 114 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    0.36
 729 VAL   ( 174-)  B    0.38
 218 VAL   ( 264-)  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!

   8 GLN   (  54-)  A      0
  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
  26 LEU   (  72-)  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
  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
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!

 945 GLY   ( 390-)  B   1.63   20
1545 GLY   ( 390-)  C   1.53   21

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]

 341 PRO   ( 387-)  A    0.20 LOW
 502 PRO   ( 548-)  A    0.11 LOW
 687 PRO   ( 132-)  B    0.19 LOW
 972 PRO   ( 417-)  B    0.11 LOW
1170 PRO   ( 615-)  B    0.08 LOW
1352 PRO   ( 197-)  C    0.13 LOW
1703 PRO   ( 548-)  C    0.13 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].

   3 PRO   (  49-)  A  -122.4 half-chair C-delta/C-gamma (-126 degrees)
  48 PRO   (  94-)  A   -58.0 half-chair C-beta/C-alpha (-54 degrees)
  86 PRO   ( 132-)  A   -61.8 half-chair C-beta/C-alpha (-54 degrees)
 114 PRO   ( 160-)  A  -112.9 envelop C-gamma (-108 degrees)
 121 PRO   ( 167-)  A   -49.1 half-chair C-beta/C-alpha (-54 degrees)
 149 PRO   ( 195-)  A   -47.4 half-chair C-beta/C-alpha (-54 degrees)
 262 PRO   ( 308-)  A   -46.6 half-chair C-beta/C-alpha (-54 degrees)
 378 PRO   ( 424-)  A    49.8 half-chair C-delta/C-gamma (54 degrees)
 390 PRO   ( 436-)  A  -121.1 half-chair C-delta/C-gamma (-126 degrees)
 413 PRO   ( 459-)  A  -112.2 envelop C-gamma (-108 degrees)
 569 PRO   ( 615-)  A   100.7 envelop C-beta (108 degrees)
 649 PRO   (  94-)  B     4.4 envelop N (0 degrees)
 771 PRO   ( 216-)  B  -115.6 envelop C-gamma (-108 degrees)
 863 PRO   ( 308-)  B   -42.6 envelop C-alpha (-36 degrees)
 874 PRO   ( 319-)  B    51.5 half-chair C-delta/C-gamma (54 degrees)
 942 PRO   ( 387-)  B   -64.3 envelop C-beta (-72 degrees)
 979 PRO   ( 424-)  B   -60.7 half-chair C-beta/C-alpha (-54 degrees)
1001 PRO   ( 446-)  B   127.3 half-chair C-beta/C-alpha (126 degrees)
1011 PRO   ( 456-)  B  -129.8 half-chair C-delta/C-gamma (-126 degrees)
1249 PRO   (  94-)  C   -51.6 half-chair C-beta/C-alpha (-54 degrees)
1453 PRO   ( 298-)  C  -115.6 envelop C-gamma (-108 degrees)
1463 PRO   ( 308-)  C   -58.2 half-chair C-beta/C-alpha (-54 degrees)
1542 PRO   ( 387-)  C   -64.3 envelop C-beta (-72 degrees)
1579 PRO   ( 424-)  C    -9.1 half-chair C-alpha/N (-18 degrees)
1764 PRO   ( 609-)  C   102.4 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.

1431 ARG   ( 276-)  C      NH1 <-> 1813 GOL   (1650-)  C      O3     0.57    2.13  INTRA
 146 ASP   ( 192-)  A      CB  <-> 1815 HOH   (2149 )  A      O      0.46    2.34  INTRA
 996 GLN   ( 441-)  B      OE1 <-> 1042 ARG   ( 487-)  B      NH1    0.44    2.26  INTRA
1368 ARG   ( 213-)  C      NH2 <-> 1817 HOH   (2283 )  C      O      0.38    2.32  INTRA
1664 MET   ( 509-)  C    A CE  <-> 1685 ILE   ( 530-)  C      CG2    0.34    2.86  INTRA
1401 ARG   ( 246-)  C      NH2 <-> 1817 HOH   (2320 )  C      O      0.33    2.37  INTRA
 779 GLN   ( 224-)  B      NE2 <->  816 ASN   ( 261-)  B      ND2    0.33    2.52  INTRA BL
  91 ASP   ( 137-)  A      O   <->   95 GLY   ( 141-)  A      N      0.32    2.38  INTRA
  90 VAL   ( 136-)  A      CG2 <-> 1815 HOH   (2050 )  A      O      0.31    2.49  INTRA
1766 ARG   ( 611-)  C      NE  <-> 1799 GLU   ( 644-)  C      OE2    0.30    2.40  INTRA
 207 ALA   ( 253-)  A      CB  <-> 1815 HOH   (2136 )  A      O      0.30    2.50  INTRA
   2 GLU   (  48-)  A      N   <-> 1815 HOH   (2003 )  A      O      0.30    2.40  INTRA
1757 ARG   ( 602-)  C      NE  <-> 1817 HOH   (2609 )  C      O      0.30    2.40  INTRA
1749 TRP   ( 594-)  C      NE1 <-> 1817 HOH   (2603 )  C      O      0.29    2.41  INTRA
1789 LYS   ( 634-)  C      NZ  <-> 1817 HOH   (2636 )  C      O      0.29    2.41  INTRA
 171 HIS   ( 217-)  A      NE2 <-> 1815 HOH   (2127 )  A      O      0.28    2.42  INTRA
1668 ASP   ( 513-)  C      OD2 <-> 1778 ARG   ( 623-)  C      NH2    0.27    2.43  INTRA
 291 ALA   ( 337-)  A      C   <-> 1815 HOH   (2210 )  A      O      0.26    2.54  INTRA
  41 ARG   (  87-)  A      NH1 <->   46 ASP   (  92-)  A    A OD1    0.26    2.44  INTRA BL
 168 TYR   ( 214-)  A      OH  <->  270 ARG   ( 316-)  A      NH2    0.25    2.45  INTRA
1278 THR   ( 123-)  C      CG2 <-> 1817 HOH   (2158 )  C      O      0.25    2.55  INTRA
  41 ARG   (  87-)  A      NH1 <->   46 ASP   (  92-)  A    A CG     0.25    2.85  INTRA
1088 ASN   ( 533-)  B      ND2 <-> 1816 HOH   (2379 )  B      O      0.25    2.45  INTRA
 130 THR   ( 176-)  A      N   <->  139 SER   ( 185-)  A      O      0.24    2.46  INTRA BL
  23 ILE   (  69-)  A      N   <->  340 GLU   ( 386-)  A      OE2    0.23    2.47  INTRA BL
And so on for a total of 268 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.

 106 ARG   ( 152-)  A      -7.66
1307 ARG   ( 152-)  C      -7.60
 707 ARG   ( 152-)  B      -7.55
1368 ARG   ( 213-)  C      -6.57
 412 MET   ( 458-)  A      -6.53
1216 ARG   (  61-)  C      -6.46
 616 ARG   (  61-)  B      -6.43
 435 ARG   ( 481-)  A      -6.32
 714 ARG   ( 159-)  B      -6.25
  15 ARG   (  61-)  A      -6.24
 167 ARG   ( 213-)  A      -6.22
 768 ARG   ( 213-)  B      -6.17
 200 ARG   ( 246-)  A      -6.15
 664 ARG   ( 109-)  B      -6.15
1314 ARG   ( 159-)  C      -6.14
 835 ARG   ( 280-)  B      -5.94
  63 ARG   ( 109-)  A      -5.86
1401 ARG   ( 246-)  C      -5.84
 171 HIS   ( 217-)  A      -5.83
 600 GLN   ( 646-)  A      -5.78
 462 ARG   ( 508-)  A      -5.76
1636 ARG   ( 481-)  C      -5.74
1676 ARG   ( 521-)  C      -5.71
1663 ARG   ( 508-)  C      -5.69
1063 ARG   ( 508-)  B      -5.69
1201 GLN   ( 646-)  B      -5.69
 475 ARG   ( 521-)  A      -5.57
 113 ARG   ( 159-)  A      -5.54
 234 ARG   ( 280-)  A      -5.53
1435 ARG   ( 280-)  C      -5.50
1613 MET   ( 458-)  C      -5.49
1264 ARG   ( 109-)  C      -5.45
1801 GLN   ( 646-)  C      -5.44
1013 MET   ( 458-)  B      -5.42
1744 LEU   ( 589-)  C      -5.42
1036 ARG   ( 481-)  B      -5.39
1762 LEU   ( 607-)  C      -5.27
1510 GLN   ( 355-)  C      -5.27
1076 ARG   ( 521-)  B      -5.26
1592 LYS   ( 437-)  C      -5.23
1337 LEU   ( 182-)  C      -5.17
 737 LEU   ( 182-)  B      -5.13
 257 ARG   ( 303-)  A      -5.07
 293 GLN   ( 339-)  A      -5.06
 801 ARG   ( 246-)  B      -5.05

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.

1163 ALA   ( 608-)  B   -3.07
1763 ALA   ( 608-)  C   -2.67

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

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.

1815 HOH   (2004 )  A      O     27.11   15.44   65.38
1815 HOH   (2309 )  A      O    -45.11   46.18   74.75
1815 HOH   (2349 )  A      O    -33.97   59.73   46.50
1817 HOH   (2058 )  C      O     11.65   13.72   72.70
1817 HOH   (2077 )  C      O      6.70   22.91   73.35
1817 HOH   (2229 )  C      O     18.41   -9.65   25.91

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.

1815 HOH   (2009 )  A      O
1815 HOH   (2033 )  A      O
1815 HOH   (2052 )  A      O
1815 HOH   (2067 )  A      O
1815 HOH   (2078 )  A      O
1815 HOH   (2123 )  A      O
1815 HOH   (2171 )  A      O
1816 HOH   (2179 )  B      O
1816 HOH   (2223 )  B      O
1816 HOH   (2331 )  B      O
1816 HOH   (2480 )  B      O
1816 HOH   (2484 )  B      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.

 215 ASN   ( 261-)  A
 349 ASN   ( 395-)  A
 516 HIS   ( 562-)  A
 527 GLN   ( 573-)  A
 621 ASN   (  66-)  B
 816 ASN   ( 261-)  B
 910 GLN   ( 355-)  B
 950 ASN   ( 395-)  B
1117 HIS   ( 562-)  B
1128 GLN   ( 573-)  B
1341 HIS   ( 186-)  C
1416 ASN   ( 261-)  C
1510 GLN   ( 355-)  C
1550 ASN   ( 395-)  C
1717 HIS   ( 562-)  C
1728 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
  51 ASN   (  97-)  A      ND2
  99 ASN   ( 145-)  A      ND2
 112 SER   ( 158-)  A      N
 150 ASP   ( 196-)  A      N
 155 SER   ( 201-)  A      N
 180 THR   ( 226-)  A      OG1
 213 ASP   ( 259-)  A      N
 215 ASN   ( 261-)  A      N
 265 ASN   ( 311-)  A      N
 270 ARG   ( 316-)  A      NH2
 292 SER   ( 338-)  A      N
 401 ASP   ( 447-)  A      N
 433 ARG   ( 479-)  A      NH1
 457 LEU   ( 503-)  A      N
 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
 526 ARG   ( 572-)  A      NH1
 529 SER   ( 575-)  A      N
 577 ARG   ( 623-)  A      NH1
 582 SER   ( 628-)  A      OG
And so on for a total of 70 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.

  20 ASN   (  66-)  A      OD1
  85 ASP   ( 131-)  A      OD1
 264 ASN   ( 310-)  A      OD1
 384 GLN   ( 430-)  A      OE1
 471 GLU   ( 517-)  A      OE2
 493 HIS   ( 539-)  A      NE2
 778 GLN   ( 223-)  B      OE1
1072 GLU   ( 517-)  B      OE2
1094 HIS   ( 539-)  B      NE2
1195 GLU   ( 640-)  B    A OE1
1197 GLU   ( 642-)  B      OE2
1378 GLN   ( 223-)  C      OE1
1694 HIS   ( 539-)  C      NE2

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.

1815 HOH   (2165 )  A      O  0.98  K  5 Ion-B
1815 HOH   (2285 )  A      O  0.92  K  4 ION-B
1817 HOH   (2084 )  C      O  1.15  K  4
1817 HOH   (2279 )  C      O  0.99  K  4
1817 HOH   (2357 )  C      O  1.00  K  4 Ion-B
1817 HOH   (2448 )  C      O  0.97  K  4 NCS 1/1
1817 HOH   (2455 )  C      O  0.98  K  4
1817 HOH   (2631 )  C      O  0.98  K  5

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.

   9 ASP   (  55-)  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
 261 ASP   ( 307-)  A   H-bonding suggests Asn; but Alt-Rotamer
 306 ASP   ( 352-)  A   H-bonding suggests Asn
 370 GLU   ( 416-)  A   H-bonding suggests Gln
 469 ASP   ( 515-)  A   H-bonding suggests Asn
 594 GLU   ( 640-)  A   H-bonding suggests Gln; but Alt-Rotamer
 661 ASP   ( 106-)  B   H-bonding suggests Asn; but Alt-Rotamer
 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
 862 ASP   ( 307-)  B   H-bonding suggests Asn; but Alt-Rotamer
1070 ASP   ( 515-)  B   H-bonding suggests Asn
1334 ASP   ( 179-)  C   H-bonding suggests Asn; but Alt-Rotamer
1363 GLU   ( 208-)  C   H-bonding suggests Gln
1446 ASP   ( 291-)  C   H-bonding suggests Asn; but Alt-Rotamer
1784 GLU   ( 629-)  C   H-bonding suggests Gln
1795 GLU   ( 640-)  C   H-bonding suggests Gln; 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 :  -0.416
  2nd generation packing quality :  -1.197
  Ramachandran plot appearance   :  -1.256
  chi-1/chi-2 rotamer normality  :  -2.746
  Backbone conformation          :   0.090

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.721
  Bond angles                    :   0.791
  Omega angle restraints         :   1.236
  Side chain planarity           :   0.726
  Improper dihedral distribution :   0.841
  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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.721
  Bond angles                    :   0.791
  Omega angle restraints         :   1.236
  Side chain planarity           :   0.726
  Improper dihedral distribution :   0.841
  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.