WHAT IF Check report

This file was created 2011-12-17 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 pdb3qh0.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 : 0.543
CA-only RMS fit for the two chains : 0.280

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: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

1120 AKR   (   2-)  A  -         OK
1121 COH   ( 626-)  A  -         Atom types
1136 COH   ( 627-)  B  -         Atom types
1138 NDG   ( 662-)  B  -         OK
1139 BOG   ( 703-)  A  -         OK
1140 MAN   ( 673-)  A  -         OK
1141 HSQ   ( 661-)  A  -         OK
1142 AKR   (   3-)  A  -         OK
1143 PLM   ( 625-)  A  -         OK

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

1105 NAG   ( 671-)  A  -   O4  bound to 1106 NAG   ( 672-)  A  -   C1
1106 NAG   ( 672-)  A  -   O4  bound to 1140 MAN   ( 673-)  A  -   C1
1108 NAG   ( 661-)  B  -   O4  bound to 1138 NDG   ( 662-)  B  -   C1
1109 NAG   ( 671-)  B  -   O4  bound to 1110 NAG   ( 672-)  B  -   C1

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: 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'.

  22 GLN   (  54-)  A      CD
  22 GLN   (  54-)  A      OE1
  22 GLN   (  54-)  A      NE2
  24 LYS   (  56-)  A      CE
  24 LYS   (  56-)  A      NZ
  43 LEU   (  75-)  A      CD1
  43 LEU   (  75-)  A      CD2
  46 ILE   (  78-)  A      CD1
  47 LYS   (  79-)  A      NZ
  48 LEU   (  80-)  A      CD1
  49 LEU   (  81-)  A      CG
  49 LEU   (  81-)  A      CD1
  49 LEU   (  81-)  A      CD2
  51 LYS   (  83-)  A      CG
  51 LYS   (  83-)  A      CD
  51 LYS   (  83-)  A      CE
  51 LYS   (  83-)  A      NZ
  65 LYS   (  97-)  A      CD
  65 LYS   (  97-)  A      CE
  65 LYS   (  97-)  A      NZ
  74 ILE   ( 105-)  A      CD1
 138 LYS   ( 169-)  A      CD
 138 LYS   ( 169-)  A      CE
 138 LYS   ( 169-)  A      NZ
 144 LYS   ( 175-)  A      NZ
And so on for a total of 120 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.

 500 LEU   ( 531-)  A    0.87

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: 24

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: Tyrosine convention problem

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

  33 TYR   (  65-)  A
 105 TYR   ( 136-)  A
 223 TYR   ( 254-)  A
 244 TYR   ( 275-)  A
 270 TYR   ( 301-)  A
 354 TYR   ( 385-)  A
 378 TYR   ( 409-)  A
 435 TYR   ( 466-)  A
 585 TYR   (  65-)  B
 611 TYR   (  91-)  B
 657 TYR   ( 136-)  B
 668 TYR   ( 147-)  B
 775 TYR   ( 254-)  B
 822 TYR   ( 301-)  B
 906 TYR   ( 385-)  B
1016 TYR   ( 495-)  B

Warning: Phenylalanine convention problem

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

  32 PHE   (  64-)  A
  64 PHE   (  96-)  A
 167 PHE   ( 198-)  A
 170 PHE   ( 201-)  A
 179 PHE   ( 210-)  A
 373 PHE   ( 404-)  A
 439 PHE   ( 470-)  A
 546 PHE   ( 577-)  A
 549 PHE   ( 580-)  A
 584 PHE   (  64-)  B
 616 PHE   (  96-)  B
 722 PHE   ( 201-)  B
 730 PHE   ( 209-)  B
 741 PHE   ( 220-)  B
 991 PHE   ( 470-)  B
1098 PHE   ( 577-)  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.

  26 ASP   (  58-)  A
 142 ASP   ( 173-)  A
 679 ASP   ( 158-)  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.

  35 GLU   (  67-)  A
 139 GLU   ( 170-)  A
 155 GLU   ( 186-)  A
 367 GLU   ( 398-)  A
 449 GLU   ( 480-)  A
 455 GLU   ( 486-)  A
 587 GLU   (  67-)  B
 811 GLU   ( 290-)  B
 840 GLU   ( 319-)  B
 860 GLU   ( 339-)  B
 937 GLU   ( 416-)  B
 978 GLU   ( 457-)  B
1001 GLU   ( 480-)  B
1011 GLU   ( 490-)  B
1023 GLU   ( 502-)  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

 |  0.995969  0.000170  0.000039|
 |  0.000170  0.996291  0.000121|
 |  0.000039  0.000121  0.996069|
Proposed new scale matrix

 |  0.008236 -0.000001  0.000000|
 | -0.000001  0.007668  0.000000|
 |  0.000000  0.000000  0.005579|
With corresponding cell

    A    = 121.415  B   = 130.405  C    = 179.246
    Alpha=  90.002  Beta=  90.002  Gamma=  89.980

The CRYST1 cell dimensions

    A    = 121.906  B   = 130.888  C    = 179.968
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 571.528
(Under-)estimated Z-score: 17.619

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.

 211 HIS   ( 242-)  A      CG   ND1  CE1 109.60    4.0
 907 HIS   ( 386-)  B      CG   ND1  CE1 109.63    4.0
1103 VAL   ( 582-)  B     -C    N    CA  130.94    5.1
1103 VAL   ( 582-)  B      N    CA   CB  119.38    5.2

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.

  26 ASP   (  58-)  A
  35 GLU   (  67-)  A
 139 GLU   ( 170-)  A
 142 ASP   ( 173-)  A
 155 GLU   ( 186-)  A
 367 GLU   ( 398-)  A
 449 GLU   ( 480-)  A
 455 GLU   ( 486-)  A
 587 GLU   (  67-)  B
 679 ASP   ( 158-)  B
 811 GLU   ( 290-)  B
 840 GLU   ( 319-)  B
 860 GLU   ( 339-)  B
 937 GLU   ( 416-)  B
 978 GLU   ( 457-)  B
1001 GLU   ( 480-)  B
1011 GLU   ( 490-)  B
1023 GLU   ( 502-)  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.

1103 VAL   ( 582-)  B      CA    -6.9    23.24    33.23
The average deviation= 0.830

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.

 440 SER   ( 471-)  A    -2.6
1099 THR   ( 578-)  B    -2.4
 453 GLU   ( 484-)  A    -2.4
  64 PHE   (  96-)  A    -2.3
1005 GLU   ( 484-)  B    -2.3
 616 PHE   (  96-)  B    -2.3
 564 ARG   (  44-)  B    -2.3
 906 TYR   ( 385-)  B    -2.3
 354 TYR   ( 385-)  A    -2.3
 751 LEU   ( 230-)  B    -2.2
 685 GLY   ( 164-)  B    -2.2
 547 THR   ( 578-)  A    -2.2
 133 GLY   ( 164-)  A    -2.2
 199 LEU   ( 230-)  A    -2.2
 548 SER   ( 579-)  A    -2.2
  37 CYS   (  69-)  A    -2.2
1019 ILE   ( 498-)  B    -2.1
 135 LYS   ( 166-)  A    -2.1
 589 CYS   (  69-)  B    -2.1
 467 ILE   ( 498-)  A    -2.1
  12 ARG   (  44-)  A    -2.0
 130 THR   ( 161-)  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.

  11 ASN   (  43-)  A  Poor phi/psi
  12 ARG   (  44-)  A  Poor phi/psi
  29 ARG   (  61-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
  98 THR   ( 129-)  A  Poor phi/psi
 111 PHE   ( 142-)  A  omega poor
 116 TYR   ( 147-)  A  omega poor
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 219 GLY   ( 250-)  A  omega poor
 239 GLN   ( 270-)  A  Poor phi/psi
 367 GLU   ( 398-)  A  Poor phi/psi
 465 SER   ( 496-)  A  Poor phi/psi
 481 PRO   ( 512-)  A  omega poor
 484 ASP   ( 515-)  A  Poor phi/psi
 548 SER   ( 579-)  A  Poor phi/psi
 563 ASN   (  43-)  B  Poor phi/psi
 564 ARG   (  44-)  B  Poor phi/psi
 581 ARG   (  61-)  B  Poor phi/psi
 616 PHE   (  96-)  B  Poor phi/psi
 647 SER   ( 126-)  B  PRO omega poor
 650 THR   ( 129-)  B  Poor phi/psi
 663 PHE   ( 142-)  B  omega poor
 668 TYR   ( 147-)  B  omega poor
 706 ARG   ( 185-)  B  Poor phi/psi
 730 PHE   ( 209-)  B  omega poor
 751 LEU   ( 230-)  B  Poor phi/psi
 768 PHE   ( 247-)  B  Poor phi/psi
 770 ASP   ( 249-)  B  Poor phi/psi
 771 GLY   ( 250-)  B  omega poor
 791 GLN   ( 270-)  B  Poor phi/psi
 908 TRP   ( 387-)  B  Poor phi/psi
 919 GLU   ( 398-)  B  Poor phi/psi
 930 TYR   ( 409-)  B  Poor phi/psi
 980 LYS   ( 459-)  B  Poor phi/psi
 992 SER   ( 471-)  B  Poor phi/psi
1017 SER   ( 496-)  B  Poor phi/psi
1036 ASP   ( 515-)  B  Poor phi/psi
1100 SER   ( 579-)  B  Poor phi/psi
1102 ASN   ( 581-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -0.783

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.

 420 SER   ( 451-)  A    0.35
 631 SER   ( 110-)  B    0.37
 976 SER   ( 455-)  B    0.37
 972 SER   ( 451-)  B    0.37
 424 SER   ( 455-)  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 PRO   (  40-)  A      0
   9 CYS   (  41-)  A      0
  10 GLN   (  42-)  A      0
  11 ASN   (  43-)  A      0
  12 ARG   (  44-)  A      0
  18 THR   (  50-)  A      0
  21 ASP   (  53-)  A      0
  22 GLN   (  54-)  A      0
  27 CYS   (  59-)  A      0
  28 THR   (  60-)  A      0
  29 ARG   (  61-)  A      0
  30 THR   (  62-)  A      0
  32 PHE   (  64-)  A      0
  33 TYR   (  65-)  A      0
  35 GLU   (  67-)  A      0
  37 CYS   (  69-)  A      0
  38 THR   (  70-)  A      0
  62 THR   (  94-)  A      0
  63 HIS   (  95-)  A      0
  64 PHE   (  96-)  A      0
  94 ASP   ( 125-)  A      0
  95 SER   ( 126-)  A      0
  96 PRO   ( 127-)  A      0
  97 PRO   ( 128-)  A      0
  98 THR   ( 129-)  A      0
And so on for a total of 420 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!

 683 PRO   ( 162-)  B   1.73   13
1057 GLY   ( 536-)  B   1.72   11
  54 PRO   (  86-)  A   1.58   10

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]

 410 PRO   ( 441-)  A    0.19 LOW
 516 PRO   ( 547-)  A    0.11 LOW
 712 PRO   ( 191-)  B    0.18 LOW
1063 PRO   ( 542-)  B    0.16 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].

 245 PRO   ( 276-)  A  -114.7 envelop C-gamma (-108 degrees)
 246 PRO   ( 277-)  A  -126.9 half-chair C-delta/C-gamma (-126 degrees)
 497 PRO   ( 528-)  A   100.6 envelop C-beta (108 degrees)
 507 PRO   ( 538-)  A  -115.9 envelop C-gamma (-108 degrees)
 606 PRO   (  86-)  B   101.0 envelop C-beta (108 degrees)
 693 PRO   ( 172-)  B  -123.9 half-chair C-delta/C-gamma (-126 degrees)
1033 PRO   ( 512-)  B    46.6 half-chair C-delta/C-gamma (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.

  36 ASN   (  68-)  A      ND2 <-> 1141 HSQ   ( 661-)  A      C1     1.26    1.44  INTRA B3
1106 NAG   ( 672-)  A      O4  <-> 1140 MAN   ( 673-)  A      C1     0.94    1.46  INTRA B3
1108 NAG   ( 661-)  B      O4  <-> 1138 NDG   ( 662-)  B      C1     0.94    1.46  INTRA BF
1106 NAG   ( 672-)  A      C4  <-> 1140 MAN   ( 673-)  A      C1     0.80    2.40  INTRA
1108 NAG   ( 661-)  B      C4  <-> 1138 NDG   ( 662-)  B      C1     0.72    2.48  INTRA
  36 ASN   (  68-)  A      CG  <-> 1141 HSQ   ( 661-)  A      C1     0.71    2.49  INTRA
 737 ARG   ( 216-)  B      NH1 <-> 1110 NAG   ( 672-)  B      C8     0.48    2.62  INTRA
 185 ARG   ( 216-)  A      NH1 <-> 1106 NAG   ( 672-)  A      C8     0.36    2.74  INTRA BF
 357 HIS   ( 388-)  A    A CE1 <-> 1121 COH   ( 626-)  A     CO      0.34    2.86  INTRA BF
1106 NAG   ( 672-)  A      C4  <-> 1140 MAN   ( 673-)  A      C2     0.31    2.89  INTRA
 959 ARG   ( 438-)  B      NH1 <-> 1007 GLU   ( 486-)  B      OE2    0.28    2.42  INTRA BF
 354 TYR   ( 385-)  A      OH  <-> 1143 PLM   ( 625-)  A      CD     0.27    2.53  INTRA
 130 THR   ( 161-)  A      CG2 <->  135 LYS   ( 166-)  A      O      0.26    2.54  INTRA
 658 LYS   ( 137-)  B      NZ  <-> 1145 HOH   ( 824 )  B      O      0.24    2.46  INTRA
 461 LYS   ( 492-)  A      NZ  <->  465 SER   ( 496-)  A      O      0.18    2.52  INTRA
 371 TYR   ( 402-)  A      OH  <->  386 HIS   ( 417-)  A      NE2    0.18    2.52  INTRA
1144 HOH   ( 863 )  A      O   <-> 1145 HOH   ( 981 )  B      O      0.15    2.25  INTRA
 425 ARG   ( 456-)  A      CD  <->  471 GLU   ( 502-)  A      OE1    0.13    2.67  INTRA
 165 MET   ( 196-)  A      CE  <->  400 ALA   ( 431-)  A      CB     0.12    3.08  INTRA
 793 GLU   ( 272-)  B      N   <-> 1129 EDO   ( 619-)  B      O2     0.12    2.58  INTRA
 929 LEU   ( 408-)  B      O   <-> 1145 HOH   ( 861 )  B      O      0.11    2.29  INTRA
 641 ARG   ( 120-)  B      NH1 <-> 1145 HOH   ( 905 )  B      O      0.11    2.59  INTRA BF
 445 THR   ( 476-)  A      N   <->  449 GLU   ( 480-)  A      OE1    0.11    2.59  INTRA
 137 ASN   ( 168-)  A      ND2 <-> 1144 HOH   ( 700 )  A      O      0.11    2.59  INTRA
1078 LYS   ( 557-)  B      NZ  <-> 1145 HOH   ( 789 )  B      O      0.11    2.59  INTRA
And so on for a total of 78 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.

  20 PHE   (  52-)  A      -6.94
 572 PHE   (  52-)  B      -6.78
1098 PHE   ( 577-)  B      -6.78
 799 HIS   ( 278-)  B      -6.59
 247 HIS   ( 278-)  A      -6.51
  29 ARG   (  61-)  A      -6.45
 581 ARG   (  61-)  B      -6.42
 546 PHE   ( 577-)  A      -5.93
  45 ARG   (  77-)  A      -5.87
 154 ARG   ( 185-)  A      -5.86
 689 ASN   ( 168-)  B      -5.74
 185 ARG   ( 216-)  A      -5.63
 737 ARG   ( 216-)  B      -5.63
 706 ARG   ( 185-)  B      -5.58
 339 GLN   ( 370-)  A      -5.43
 397 ARG   ( 428-)  A      -5.41
  73 ASN   ( 105-)  A      -5.40
 708 PHE   ( 187-)  B      -5.39
 938 HIS   ( 417-)  B      -5.36
 386 HIS   ( 417-)  A      -5.35
 156 PHE   ( 187-)  A      -5.31
 239 GLN   ( 270-)  A      -5.24
 705 ARG   ( 184-)  B      -5.23
 891 GLN   ( 370-)  B      -5.21
 768 PHE   ( 247-)  B      -5.20
 139 GLU   ( 170-)  A      -5.17
 585 TYR   (  65-)  B      -5.09
 753 HIS   ( 232-)  B      -5.08
 201 HIS   ( 232-)  A      -5.05
 540 ASN   ( 571-)  A      -5.05
1092 ASN   ( 571-)  B      -5.05
 183 HIS   ( 214-)  A      -5.00

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: 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.

 746 GLY   ( 225-)  B   -2.93
 886 LEU   ( 365-)  B   -2.65
 334 LEU   ( 365-)  A   -2.60
  51 LYS   (  83-)  A   -2.57
 184 LYS   ( 215-)  A   -2.52

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.

1144 HOH   ( 957 )  A      O      0.24   47.70   30.07
1144 HOH   ( 969 )  A      O     24.19   62.49   27.15
1144 HOH   (1019 )  A      O     13.84   59.88   18.67
1145 HOH   ( 882 )  B      O     62.29   27.30   69.27
1145 HOH   ( 973 )  B      O     -7.67   34.13   51.14
1145 HOH   (1039 )  B      O     -6.66   31.72   51.28

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.

1144 HOH   ( 868 )  A      O
1144 HOH   ( 940 )  A      O
1145 HOH   ( 860 )  B      O
1145 HOH   ( 886 )  B      O
1145 HOH   ( 929 )  B      O
Bound group on Asn; dont flip   36 ASN  (  68-) A
Bound to: 1141 HSQ  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 1105 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to: 1107 NAG  ( 681-) A
Bound group on Asn; dont flip  588 ASN  (  68-) B
Bound to: 1108 NAG  ( 661-) B
Bound group on Asn; dont flip  665 ASN  ( 144-) B
Bound to: 1109 NAG  ( 671-) B
Bound group on Asn; dont flip  931 ASN  ( 410-) B
Bound to: 1111 NAG  ( 681-) B
Metal-coordinating Histidine residue 357 fixed to   2
Metal-coordinating Histidine residue 909 fixed to   1

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.

 247 HIS   ( 278-)  A
 357 HIS   ( 388-)  A
 559 ASN   (  39-)  B
 625 ASN   ( 105-)  B
 689 ASN   ( 168-)  B
 728 HIS   ( 207-)  B
 776 GLN   ( 255-)  B
 791 GLN   ( 270-)  B
 839 GLN   ( 318-)  B
1064 GLN   ( 543-)  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.

  22 GLN   (  54-)  A      N
 100 ASN   ( 131-)  A      ND2
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      OG
 117 TYR   ( 148-)  A      OH
 154 ARG   ( 185-)  A      NE
 154 ARG   ( 185-)  A      NH2
 176 HIS   ( 207-)  A      NE2
 177 GLN   ( 208-)  A      NE2
 217 LYS   ( 248-)  A      N
 247 HIS   ( 278-)  A      N
 266 GLY   ( 297-)  A      N
 317 TYR   ( 348-)  A      OH
 326 PHE   ( 357-)  A      N
 329 LYS   ( 360-)  A      N
 357 HIS   ( 388-)  A      N
 357 HIS   ( 388-)  A    A ND1
 383 LEU   ( 414-)  A      N
 407 ARG   ( 438-)  A      NH2
 446 SER   ( 477-)  A      N
 447 PHE   ( 478-)  A      N
 448 GLU   ( 479-)  A      N
 473 TYR   ( 504-)  A      OH
 490 THR   ( 521-)  A      N
 547 THR   ( 578-)  A      N
 574 GLN   (  54-)  B      N
 603 LYS   (  83-)  B      N
 652 ASN   ( 131-)  B      ND2
 657 TYR   ( 136-)  B      N
 657 TYR   ( 136-)  B      OH
 659 SER   ( 138-)  B      OG
 669 TYR   ( 148-)  B      OH
 707 GLU   ( 186-)  B      N
 729 GLN   ( 208-)  B      NE2
 769 LYS   ( 248-)  B      N
 776 GLN   ( 255-)  B      NE2
 799 HIS   ( 278-)  B      N
 818 GLY   ( 297-)  B      N
 869 TYR   ( 348-)  B      OH
 878 PHE   ( 357-)  B      N
 909 HIS   ( 388-)  B    A ND1
 935 LEU   ( 414-)  B      N
 998 SER   ( 477-)  B      N
1025 TYR   ( 504-)  B      OH
1058 ASN   ( 537-)  B      N
Only metal coordination for  909 HIS  ( 388-) B    A NE2

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.

  58 HIS   (  90-)  A      ND1
 109 GLU   ( 140-)  A      OE2
 172 GLN   ( 203-)  A      OE1
 308 GLU   ( 339-)  A      OE1
 308 GLU   ( 339-)  A      OE2
 357 HIS   ( 388-)  A    A NE2
 724 GLN   ( 203-)  B      OE1
 860 GLU   ( 339-)  B      OE1
 860 GLU   ( 339-)  B      OE2

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.

1144 HOH   ( 706 )  A      O  0.96  K  5
1144 HOH   ( 788 )  A      O  0.86  K  4 Ion-B
1144 HOH   ( 821 )  A      O  1.14  K  5
1145 HOH   ( 670 )  B      O  1.05  K  5
1145 HOH   ( 766 )  B      O  0.98  K  5
1145 HOH   ( 814 )  B      O  0.98  K  4
1145 HOH   ( 872 )  B      O  1.04  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.

 205 GLU   ( 236-)  A   H-bonding suggests Gln
 291 GLU   ( 322-)  A   H-bonding suggests Gln
 757 GLU   ( 236-)  B   H-bonding suggests Gln
 843 GLU   ( 322-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.473
  2nd generation packing quality :  -1.595
  Ramachandran plot appearance   :  -0.203
  chi-1/chi-2 rotamer normality  :  -0.783
  Backbone conformation          :  -0.831

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.514 (tight)
  Bond angles                    :   0.649 (tight)
  Omega angle restraints         :   1.027
  Side chain planarity           :   0.457 (tight)
  Improper dihedral distribution :   0.690
  B-factor distribution          :   0.399
  Inside/Outside distribution    :   1.106

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 :  -1.1
  2nd generation packing quality :  -1.1
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :   0.2
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.514 (tight)
  Bond angles                    :   0.649 (tight)
  Omega angle restraints         :   1.027
  Side chain planarity           :   0.457 (tight)
  Improper dihedral distribution :   0.690
  B-factor distribution          :   0.399
  Inside/Outside distribution    :   1.106
==============

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.