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 pdb2dgk.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 : 0.503
CA-only RMS fit for the two chains : 0.255

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: A and C

All-atom RMS fit for the two chains : 0.472
CA-only RMS fit for the two chains : 0.242

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 C

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 D

All-atom RMS fit for the two chains : 0.359
CA-only RMS fit for the two chains : 0.114

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 D

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 E

All-atom RMS fit for the two chains : 0.463
CA-only RMS fit for the two chains : 0.246

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 E

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 F

All-atom RMS fit for the two chains : 0.537
CA-only RMS fit for the two chains : 0.248

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 F

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.

2634 PLP   (1500-)  A  -
2637 PLP   (1501-)  B  -
2641 PLP   (1502-)  C  -
2645 PLP   (1503-)  D  -
2648 PLP   (1504-)  E  -
2653 PLP   (1505-)  F  -

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.

 437 HIS   ( 465-)  A  -   NE2 bound to 2634 PLP   (1500-)  A  -   C4A
 875 HIS   ( 465-)  B  -   NE2 bound to 2637 PLP   (1501-)  B  -   C4A
1312 HIS   ( 465-)  C  -   NE2 bound to 2641 PLP   (1502-)  C  -   C4A
1750 HIS   ( 465-)  D  -   NE2 bound to 2645 PLP   (1503-)  D  -   C4A
2188 HIS   ( 465-)  E  -   NE2 bound to 2648 PLP   (1504-)  E  -   C4A
2626 HIS   ( 465-)  F  -   NE2 bound to 2653 PLP   (1505-)  F  -   C4A

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

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) : 90.000

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

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.261
RMS-deviation in bond distances: 0.006

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

 |  0.998417 -0.000093  0.000012|
 | -0.000093  0.998352  0.000158|
 |  0.000012  0.000158  0.998905|
Proposed new scale matrix

 |  0.010796  0.000001  0.000000|
 |  0.000000  0.006317 -0.000001|
 |  0.000000  0.000000  0.004970|
With corresponding cell

    A    =  92.626  B   = 158.293  C    = 201.189
    Alpha=  89.992  Beta=  90.002  Gamma=  90.006

The CRYST1 cell dimensions

    A    =  92.770  B   = 158.560  C    = 201.420
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 185.512
(Under-)estimated Z-score: 10.038

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.

 190 GLU   ( 218-)  A      N    CA   C    96.91   -5.1
 213 HIS   ( 241-)  A      N    CA   C    99.60   -4.1
 628 GLU   ( 218-)  B      N    CA   C    96.54   -5.2
1065 GLU   ( 218-)  C      N    CA   C    97.12   -5.0
1088 HIS   ( 241-)  C      N    CA   C    99.95   -4.0
1503 GLU   ( 218-)  D      N    CA   C    96.57   -5.2
1526 HIS   ( 241-)  D      N    CA   C    99.88   -4.0
1941 GLU   ( 218-)  E      N    CA   C    98.27   -4.6
2379 GLU   ( 218-)  F      N    CA   C    96.57   -5.2

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.594
RMS-deviation in bond angles: 1.310

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 628 GLU   ( 218-)  B    5.09
1503 GLU   ( 218-)  D    5.08
2379 GLU   ( 218-)  F    5.07
 190 GLU   ( 218-)  A    4.96
1065 GLU   ( 218-)  C    4.89
1941 GLU   ( 218-)  E    4.49
 213 HIS   ( 241-)  A    4.33
1526 HIS   ( 241-)  D    4.21
1088 HIS   ( 241-)  C    4.18
 136 ILE   ( 164-)  A    4.05
1011 ILE   ( 164-)  C    4.01

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.

 574 ILE   ( 164-)  B    -2.5
1370 ILE   (  85-)  D    -2.5
 932 ILE   (  85-)  C    -2.5
1808 ILE   (  85-)  E    -2.5
2246 ILE   (  85-)  F    -2.5
  57 ILE   (  85-)  A    -2.4
 495 ILE   (  85-)  B    -2.4
2478 PHE   ( 317-)  F    -2.4
2139 THR   ( 416-)  E    -2.4
2345 PRO   ( 184-)  F    -2.3
1056 PHE   ( 209-)  C    -2.3
 360 PRO   ( 388-)  A    -2.3
2370 PHE   ( 209-)  F    -2.3
1932 PHE   ( 209-)  E    -2.2
1209 PRO   ( 362-)  C    -2.2
2040 PHE   ( 317-)  E    -2.2
2098 ILE   ( 375-)  E    -2.2
2109 GLU   ( 386-)  E    -2.2
1057 GLY   ( 210-)  C    -2.2
1495 GLY   ( 210-)  D    -2.2
1933 GLY   ( 210-)  E    -2.1
 620 GLY   ( 210-)  B    -2.1
 385 GLY   ( 413-)  A    -2.1
1031 PRO   ( 184-)  C    -2.1
 619 PHE   ( 209-)  B    -2.1
2371 GLY   ( 210-)  F    -2.1
 727 PHE   ( 317-)  B    -2.1
 182 GLY   ( 210-)  A    -2.1
1844 THR   ( 121-)  E    -2.1
1494 PHE   ( 209-)  D    -2.1
 772 PRO   ( 362-)  B    -2.1
1872 GLY   ( 149-)  E    -2.1
 181 PHE   ( 209-)  A    -2.1
 968 THR   ( 121-)  C    -2.1
2352 PRO   ( 191-)  F    -2.1
  93 THR   ( 121-)  A    -2.1
2282 THR   ( 121-)  F    -2.0
1434 GLY   ( 149-)  D    -2.0
 531 THR   ( 121-)  B    -2.0
1406 THR   ( 121-)  D    -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.

  28 ALA   (  56-)  A  Poor phi/psi
  81 HIS   ( 109-)  A  Poor phi/psi
 133 PRO   ( 161-)  A  Poor phi/psi
 233 ASP   ( 261-)  A  Poor phi/psi
 248 LYS   ( 276-)  A  Poor phi/psi
 251 LEU   ( 279-)  A  Poor phi/psi
 255 GLY   ( 283-)  A  Poor phi/psi
 289 PHE   ( 317-)  A  Poor phi/psi
 348 PRO   ( 376-)  A  Poor phi/psi
 385 GLY   ( 413-)  A  Poor phi/psi
 388 THR   ( 416-)  A  Poor phi/psi
 437 HIS   ( 465-)  A  Poor phi/psi
 466 ALA   (  56-)  B  Poor phi/psi
 519 HIS   ( 109-)  B  Poor phi/psi
 571 PRO   ( 161-)  B  Poor phi/psi
 671 ASP   ( 261-)  B  Poor phi/psi
 686 LYS   ( 276-)  B  Poor phi/psi
 689 LEU   ( 279-)  B  Poor phi/psi
 727 PHE   ( 317-)  B  Poor phi/psi
 729 ARG   ( 319-)  B  Poor phi/psi
 786 PRO   ( 376-)  B  Poor phi/psi
 875 HIS   ( 465-)  B  Poor phi/psi
 903 ALA   (  56-)  C  Poor phi/psi
 956 HIS   ( 109-)  C  Poor phi/psi
1008 PRO   ( 161-)  C  Poor phi/psi
And so on for a total of 66 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.

1378 SER   (  93-)  D    0.36
 421 SER   ( 449-)  A    0.36
2069 SER   ( 346-)  E    0.36

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 ARG   (  31-)  A      0
   4 PHE   (  32-)  A      0
   5 PRO   (  33-)  A      0
   6 LEU   (  34-)  A      0
   7 HIS   (  35-)  A      0
   9 MET   (  37-)  A      0
  23 TYR   (  51-)  A      0
  25 ASP   (  53-)  A      0
  27 ASN   (  55-)  A      0
  28 ALA   (  56-)  A      0
  30 GLN   (  58-)  A      0
  32 LEU   (  60-)  A      0
  35 PHE   (  63-)  A      0
  38 THR   (  66-)  A      0
  56 TRP   (  84-)  A      0
  57 ILE   (  85-)  A      0
  59 LYS   (  87-)  A      0
  62 TYR   (  90-)  A      0
  80 TRP   ( 108-)  A      0
  91 VAL   ( 119-)  A      0
  94 ASN   ( 122-)  A      0
  96 ILE   ( 124-)  A      0
 123 PRO   ( 151-)  A      0
 124 THR   ( 152-)  A      0
 125 ASP   ( 153-)  A      0
And so on for a total of 988 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.295

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!

2352 PRO   ( 191-)  F   1.96   13
 601 PRO   ( 191-)  B   1.78   12
1914 PRO   ( 191-)  E   1.76   12
1038 PRO   ( 191-)  C   1.75   13
1476 PRO   ( 191-)  D   1.60   15
 163 PRO   ( 191-)  A   1.53   16

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].

1673 PRO   ( 388-)  D    45.2 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.

1561 LYS   ( 276-)  D      NZ  <-> 2645 PLP   (1503-)  D      C4A    1.62    1.48  INTRA BL
 248 LYS   ( 276-)  A      NZ  <-> 2634 PLP   (1500-)  A      C4A    1.62    1.48  INTRA BL
1123 LYS   ( 276-)  C      NZ  <-> 2641 PLP   (1502-)  C      C4A    1.62    1.48  INTRA BL
 686 LYS   ( 276-)  B      NZ  <-> 2637 PLP   (1501-)  B      C4A    1.62    1.48  INTRA BL
1999 LYS   ( 276-)  E      NZ  <-> 2648 PLP   (1504-)  E      C4A    1.62    1.48  INTRA BL
2437 LYS   ( 276-)  F      NZ  <-> 2653 PLP   (1505-)  F      C4A    1.62    1.48  INTRA BL
2626 HIS   ( 465-)  F      NE2 <-> 2653 PLP   (1505-)  F      C4A    1.25    1.45  INTRA BL
1561 LYS   ( 276-)  D      CE  <-> 2645 PLP   (1503-)  D      C4A    0.78    2.42  INTRA BL
1999 LYS   ( 276-)  E      CE  <-> 2648 PLP   (1504-)  E      C4A    0.78    2.42  INTRA BL
2437 LYS   ( 276-)  F      CE  <-> 2653 PLP   (1505-)  F      C4A    0.77    2.43  INTRA BL
 248 LYS   ( 276-)  A      CE  <-> 2634 PLP   (1500-)  A      C4A    0.77    2.43  INTRA BL
 686 LYS   ( 276-)  B      CE  <-> 2637 PLP   (1501-)  B      C4A    0.77    2.43  INTRA BL
1123 LYS   ( 276-)  C      CE  <-> 2641 PLP   (1502-)  C      C4A    0.77    2.43  INTRA BL
2626 HIS   ( 465-)  F      CE1 <-> 2653 PLP   (1505-)  F      C4A    0.76    2.44  INTRA BL
2626 HIS   ( 465-)  F      CD2 <-> 2653 PLP   (1505-)  F      C4A    0.68    2.52  INTRA BL
 686 LYS   ( 276-)  B      NZ  <-> 2637 PLP   (1501-)  B      C4     0.66    2.44  INTRA BL
1123 LYS   ( 276-)  C      NZ  <-> 2641 PLP   (1502-)  C      C4     0.65    2.45  INTRA BL
1561 LYS   ( 276-)  D      NZ  <-> 2645 PLP   (1503-)  D      C4     0.65    2.45  INTRA BL
 248 LYS   ( 276-)  A      NZ  <-> 2634 PLP   (1500-)  A      C4     0.64    2.46  INTRA BL
1999 LYS   ( 276-)  E      NZ  <-> 2648 PLP   (1504-)  E      C4     0.63    2.47  INTRA BL
2437 LYS   ( 276-)  F      NZ  <-> 2653 PLP   (1505-)  F      C4     0.63    2.47  INTRA BL
1999 LYS   ( 276-)  E      NZ  <-> 2188 HIS   ( 465-)  E      NE2    0.59    2.41  INTRA BL
2437 LYS   ( 276-)  F      NZ  <-> 2626 HIS   ( 465-)  F      NE2    0.57    2.43  INTRA BL
1561 LYS   ( 276-)  D      NZ  <-> 1750 HIS   ( 465-)  D      NE2    0.54    2.46  INTRA BL
 248 LYS   ( 276-)  A      NZ  <->  437 HIS   ( 465-)  A      NE2    0.54    2.46  INTRA BL
And so on for a total of 312 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

2275 LYS   ( 114-)  F      -6.56
 524 LYS   ( 114-)  B      -6.47
1399 LYS   ( 114-)  D      -6.46
1837 LYS   ( 114-)  E      -6.38
  86 LYS   ( 114-)  A      -6.28
 961 LYS   ( 114-)  C      -6.26
 878 ARG   (  31-)  C      -6.07
2150 ARG   ( 427-)  E      -5.90
2374 TYR   ( 213-)  F      -5.81
   3 ARG   (  31-)  A      -5.79
 837 ARG   ( 427-)  B      -5.78
1712 ARG   ( 427-)  D      -5.75
2588 ARG   ( 427-)  F      -5.72
1274 ARG   ( 427-)  C      -5.67
2192 ARG   (  31-)  F      -5.64
1754 ARG   (  31-)  E      -5.63
 399 ARG   ( 427-)  A      -5.61
 623 TYR   ( 213-)  B      -5.53
1936 TYR   ( 213-)  E      -5.50
 185 TYR   ( 213-)  A      -5.49
 155 ARG   ( 183-)  A      -5.46
1498 TYR   ( 213-)  D      -5.41
 441 ARG   (  31-)  B      -5.41
1137 ARG   ( 290-)  C      -5.32
1316 ARG   (  31-)  D      -5.19
1468 ARG   ( 183-)  D      -5.12
1060 TYR   ( 213-)  C      -5.11
 262 ARG   ( 290-)  A      -5.01

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

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: D

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: E

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: F

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.

 927 ILE   (  80-)  C   -2.90
2241 ILE   (  80-)  F   -2.88
1365 ILE   (  80-)  D   -2.83
  24 LEU   (  52-)  A   -2.81
1803 ILE   (  80-)  E   -2.81
 490 ILE   (  80-)  B   -2.80
  52 ILE   (  80-)  A   -2.75
1713 GLY   ( 428-)  D   -2.72
2213 LEU   (  52-)  F   -2.68
 590 ILE   ( 180-)  B   -2.67
1775 LEU   (  52-)  E   -2.67
 152 ILE   ( 180-)  A   -2.67
2151 GLY   ( 428-)  E   -2.66
1337 LEU   (  52-)  D   -2.61
 462 LEU   (  52-)  B   -2.61
 400 GLY   ( 428-)  A   -2.60
1275 GLY   ( 428-)  C   -2.60
2589 GLY   ( 428-)  F   -2.59
 838 GLY   ( 428-)  B   -2.59
 899 LEU   (  52-)  C   -2.56
1465 ILE   ( 180-)  D   -2.54
1903 ILE   ( 180-)  E   -2.53
2180 ILE   ( 457-)  E   -2.51
 429 ILE   ( 457-)  A   -2.51

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

1137 ARG   ( 290-)  C     - 1141 ALA   ( 294-)  C        -1.71

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

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

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.

2654 HOH   (4894 )  A      O    -21.77   53.39   75.52
2656 HOH   (5025 )  C      O     64.09   18.24   76.85
2658 HOH   (4957 )  E      O      6.72   80.33   76.94

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.

 956 HIS   ( 109-)  C
1394 HIS   ( 109-)  D
Atom is not a donor  437 HIS  ( 465-) A      NE2
Atom is not a donor  875 HIS  ( 465-) B      NE2
Atom is not a donor 1312 HIS  ( 465-) C      NE2
Atom is not a donor 1750 HIS  ( 465-) D      NE2
Atom is not a donor 2188 HIS  ( 465-) E      NE2
Atom is not a donor 2626 HIS  ( 465-) F      NE2

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.

   2 LYS   (  30-)  A      N
   3 ARG   (  31-)  A      N
  53 ASN   (  81-)  A      ND2
  55 ASN   (  83-)  A      N
  99 SER   ( 127-)  A      N
 135 GLN   ( 163-)  A      NE2
 154 MET   ( 182-)  A      N
 176 GLY   ( 204-)  A      N
 184 THR   ( 212-)  A      OG1
 185 TYR   ( 213-)  A      N
 186 THR   ( 214-)  A      OG1
 195 LEU   ( 223-)  A      N
 218 SER   ( 246-)  A      OG
 233 ASP   ( 261-)  A      N
 247 HIS   ( 275-)  A      NE2
 248 LYS   ( 276-)  A      NZ
 250 GLY   ( 278-)  A      N
 263 ASP   ( 291-)  A      N
 270 GLU   ( 298-)  A      N
 277 TYR   ( 305-)  A      N
 290 SER   ( 318-)  A      N
 290 SER   ( 318-)  A      OG
 359 ASP   ( 387-)  A      N
 362 TYR   ( 390-)  A      N
 384 GLY   ( 412-)  A      N
And so on for a total of 165 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.

  69 ASP   (  97-)  A      OD1
 507 ASP   (  97-)  B      OD1
 944 ASP   (  97-)  C      OD1
1382 ASP   (  97-)  D      OD1
1820 ASP   (  97-)  E      OD1
2095 ASP   ( 372-)  E      OD1
2258 ASP   (  97-)  F      OD1

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.

 404 ASP   ( 432-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 635 ASP   ( 225-)  B   H-bonding suggests Asn
1072 ASP   ( 225-)  C   H-bonding suggests Asn
1279 ASP   ( 432-)  C   H-bonding suggests Asn; Ligand-contact
1287 ASP   ( 440-)  C   H-bonding suggests Asn; but Alt-Rotamer
1297 ASP   ( 450-)  C   H-bonding suggests Asn
1333 ASP   (  48-)  D   H-bonding suggests Asn; but Alt-Rotamer
1717 ASP   ( 432-)  D   H-bonding suggests Asn; Ligand-contact
1956 ASP   ( 233-)  E   H-bonding suggests Asn
2155 ASP   ( 432-)  E   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
2575 GLU   ( 414-)  F   H-bonding suggests Gln; but Alt-Rotamer
2611 ASP   ( 450-)  F   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 :  -0.101
  2nd generation packing quality :  -0.909
  Ramachandran plot appearance   :  -0.692
  chi-1/chi-2 rotamer normality  :  -0.576
  Backbone conformation          :  -0.300

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.261 (tight)
  Bond angles                    :   0.594 (tight)
  Omega angle restraints         :   0.235 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.569
  B-factor distribution          :   0.334
  Inside/Outside distribution    :   0.988

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -0.0
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.261 (tight)
  Bond angles                    :   0.594 (tight)
  Omega angle restraints         :   0.235 (tight)
  Side chain planarity           :   0.258 (tight)
  Improper dihedral distribution :   0.569
  B-factor distribution          :   0.334
  Inside/Outside distribution    :   0.988
==============

WHAT IF
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    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.