WHAT IF Check report

This file was created 2013-12-10 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 pdb4idx.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 159.200  B   = 159.200  C    = 157.800
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 137.468  B   = 137.468  C    = 137.468
    Alpha= 109.948  Beta= 109.234  Gamma= 109.234

Dimensions of the conventional cell

    A    = 157.800  B   = 159.200  C    = 159.200
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  0.000000  1.000000|
 | -1.000000  0.000000  0.000000|
 |  0.000000 -1.000000  0.000000|

Crystal class of the cell: TETRAGONAL

Crystal class of the conventional CELL: CUBIC

Space group name: I 4 2 2

Bravais type of conventional cell is: I

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 A

All-atom RMS fit for the two chains : 2.643
CA-only RMS fit for the two chains : 2.234

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 A

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 : 2.812
CA-only RMS fit for the two chains : 2.392

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

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 : 2.112
CA-only RMS fit for the two chains : 1.372

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

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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: B

Note: Ramachandran plot

Chain identifier: A

Note: Ramachandran plot

Chain identifier: C

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

 171 THR   ( 187-)  B    High
 172 MET   ( 188-)  B    High
 173 THR   ( 189-)  B    High
 174 ALA   ( 190-)  B    High
 175 GLU   ( 191-)  B    High
 176 GLU   ( 192-)  B    High
 177 TRP   ( 193-)  B    High
 178 MET   ( 194-)  B    High
 179 THR   ( 195-)  B    High
 180 GLN   ( 196-)  B    High
 209 PHE   ( 225-)  B    High
 210 PRO   (  11-)  A    High
 211 GLN   (  12-)  A    High
 212 ARG   (  13-)  A    High
 213 ASN   (  14-)  A    High
 214 ALA   (  15-)  A    High
 215 ALA   (  16-)  A    High
 216 THR   (  17-)  A    High
 232 GLN   (  33-)  A    High
 240 ARG   (  41-)  A    High
 248 LYS   (  49-)  A    High
 254 HIS   (  55-)  A    High
 275 ASN   (  76-)  A    High
 277 PHE   (  78-)  A    High
 278 PRO   (  79-)  A    High
And so on for a total of 245 lines.

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: 7

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: B

Note: B-factor plot

Chain identifier: A

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

  15 TYR   (  31-)  B

Warning: Phenylalanine convention problem

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

 202 PHE   ( 218-)  B
 270 PHE   (  71-)  A

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.

 101 GLU   ( 117-)  B
 316 GLU   ( 117-)  A
 391 GLU   ( 192-)  A
 399 GLU   ( 200-)  A
 603 GLU   ( 191-)  C
 612 GLU   ( 200-)  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.

 582 ASP   ( 170-)  C      CA   CB    1.62    4.3

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

 |  0.997067 -0.000258 -0.000341|
 | -0.000258  0.998628 -0.000419|
 | -0.000341 -0.000419  0.997529|
Proposed new scale matrix

 |  0.006299  0.000002  0.000002|
 |  0.000002  0.006290  0.000003|
 |  0.000002  0.000003  0.006353|
With corresponding cell

    A    = 158.743  B   = 158.992  C    = 157.414
    Alpha=  90.048  Beta=  90.039  Gamma=  90.030

The CRYST1 cell dimensions

    A    = 159.200  B   = 159.200  C    = 157.800
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 111.136
(Under-)estimated Z-score: 7.769

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.

  94 ALA   ( 110-)  B      N    CA   C   131.69    7.3
  94 ALA   ( 110-)  B      C    CA   CB  101.32   -6.1
  95 SER   ( 111-)  B      N    CA   C    96.63   -5.2
 161 MET   ( 177-)  B      N    CA   C    73.28  -13.5
 161 MET   ( 177-)  B      C    CA   CB  119.10    4.7
 162 LYS   ( 178-)  B     -C    N    CA  128.94    4.0
 162 LYS   ( 178-)  B      N    CA   C    96.29   -5.3
 162 LYS   ( 178-)  B      N    CA   CB  129.37   11.1
 165 LEU   ( 181-)  B      C    CA   CB  118.93    4.6
 196 ALA   ( 212-)  B      C    CA   CB  122.48    8.0
 208 THR   ( 224-)  B      C    CA   CB  121.18    5.8
 313 LYS   ( 114-)  A      N    CA   CB  127.74   10.1
 391 GLU   ( 192-)  A      C    CA   CB  126.78    8.8
 392 TRP   ( 193-)  A      N    CA   C    75.12  -12.9
 392 TRP   ( 193-)  A      C    CA   CB  118.07    4.2
 393 MET   ( 194-)  A      N    CA   C   140.56   10.5
 393 MET   ( 194-)  A      C    CA   CB   77.58  -17.1
 482 LYS   (  70-)  C      N    CA   C   124.56    4.8
 523 SER   ( 111-)  C      N    CA   C   135.50    8.7
 524 VAL   ( 112-)  C      N    CA   CB  124.15    8.0
 581 LYS   ( 169-)  C      N    CA   C    95.96   -5.4
 582 ASP   ( 170-)  C      N    CA   C    91.33   -7.1
 582 ASP   ( 170-)  C      C    CA   CB  129.21   10.1
 598 GLY   ( 186-)  C      N    CA   C    82.36  -10.4
 599 THR   ( 187-)  C      N    CA   CB   96.48   -8.2
 611 THR   ( 199-)  C      N    CA   C   129.34    6.5
 633 ALA   ( 221-)  C      C    CA   CB  117.54    4.7
 636 THR   ( 224-)  C      C    CA   CB  128.71    9.8
 637 PHE   ( 225-)  C      N    CA   C   122.48    4.0
 637 PHE   ( 225-)  C      N    CA   CB  101.17   -5.5

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

 101 GLU   ( 117-)  B
 316 GLU   ( 117-)  A
 391 GLU   ( 192-)  A
 399 GLU   ( 200-)  A
 603 GLU   ( 191-)  C
 612 GLU   ( 200-)  C

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.

 391 GLU   ( 192-)  A      CA    -9.4    18.63    33.96
 393 MET   ( 194-)  A      CA    11.5    54.79    34.17
 482 LYS   (  70-)  C      CA    -7.0    22.35    33.92
 523 SER   ( 111-)  C      CA    -9.6    16.44    34.32
 603 GLU   ( 191-)  C      C     -7.8   -11.41    -0.03
 609 LYS   ( 197-)  C      C      7.6    11.56     0.11
 636 THR   ( 224-)  C      CA    -9.5    17.97    33.84
The average deviation= 0.730

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.

  94 ALA   ( 110-)  B   14.05
 392 TRP   ( 193-)  A   13.83
 161 MET   ( 177-)  B   11.37
 598 GLY   ( 186-)  C   11.20
 523 SER   ( 111-)  C    9.11
 393 MET   ( 194-)  A    8.66
 582 ASP   ( 170-)  C    6.75
 611 THR   ( 199-)  C    6.17
 581 LYS   ( 169-)  C    5.91
 162 LYS   ( 178-)  B    5.78
  95 SER   ( 111-)  B    5.71
 270 PHE   (  71-)  A    5.34
 482 LYS   (  70-)  C    5.09
 637 PHE   ( 225-)  C    4.33
 633 ALA   ( 221-)  C    4.22

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.627

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -4.686

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.

 611 THR   ( 199-)  C    -3.7
 607 THR   ( 195-)  C    -3.6
 601 THR   ( 189-)  C    -3.6
 179 THR   ( 195-)  B    -3.5
 636 THR   ( 224-)  C    -3.3
 609 LYS   ( 197-)  C    -2.9
 400 ILE   ( 201-)  A    -2.9
 419 PRO   ( 220-)  A    -2.8
 216 THR   (  17-)  A    -2.7
 171 THR   ( 187-)  B    -2.6
 545 THR   ( 133-)  C    -2.5
 332 THR   ( 133-)  A    -2.5
 312 LEU   ( 113-)  A    -2.5
 161 MET   ( 177-)  B    -2.5
 423 THR   ( 224-)  A    -2.5
 638 LEU   ( 226-)  C    -2.5
 392 TRP   ( 193-)  A    -2.5
 117 THR   ( 133-)  B    -2.5
 181 LYS   ( 197-)  B    -2.4
  54 LYS   (  70-)  B    -2.4
 606 MET   ( 194-)  C    -2.4
 204 PRO   ( 220-)  B    -2.4
 311 VAL   ( 112-)  A    -2.4
 394 THR   ( 195-)  A    -2.4
 356 PHE   ( 157-)  A    -2.4
And so on for a total of 51 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.

  16 GLY   (  32-)  B  Poor phi/psi, omega poor
  17 GLN   (  33-)  B  Poor phi/psi
  53 VAL   (  69-)  B  omega poor
  54 LYS   (  70-)  B  Poor phi/psi
 114 LYS   ( 130-)  B  Poor phi/psi
 117 THR   ( 133-)  B  Poor phi/psi
 141 PHE   ( 157-)  B  Poor phi/psi
 160 PHE   ( 176-)  B  Poor phi/psi
 161 MET   ( 177-)  B  Poor phi/psi
 162 LYS   ( 178-)  B  Poor phi/psi
 168 ARG   ( 184-)  B  Poor phi/psi
 171 THR   ( 187-)  B  Poor phi/psi
 175 GLU   ( 191-)  B  Poor phi/psi
 176 GLU   ( 192-)  B  Poor phi/psi
 177 TRP   ( 193-)  B  Poor phi/psi
 181 LYS   ( 197-)  B  Poor phi/psi
 196 ALA   ( 212-)  B  Poor phi/psi
 199 LYS   ( 215-)  B  Poor phi/psi
 200 SER   ( 216-)  B  Poor phi/psi, omega poor
 202 PHE   ( 218-)  B  Poor phi/psi
 208 THR   ( 224-)  B  Poor phi/psi
 211 GLN   (  12-)  A  Poor phi/psi
 212 ARG   (  13-)  A  omega poor
 215 ALA   (  16-)  A  Poor phi/psi
 216 THR   (  17-)  A  Poor phi/psi, omega poor
And so on for a total of 85 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -5.452

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!

  14 LYS   (  30-)  B      0
  15 TYR   (  31-)  B      0
  17 GLN   (  33-)  B      0
  30 ASN   (  46-)  B      0
  42 ALA   (  58-)  B      0
  45 SER   (  61-)  B      0
  50 PHE   (  66-)  B      0
  54 LYS   (  70-)  B      0
  60 ASN   (  76-)  B      0
  61 HIS   (  77-)  B      0
  65 TYR   (  81-)  B      0
  67 SER   (  83-)  B      0
  68 ASN   (  84-)  B      0
  73 ASN   (  89-)  B      0
 105 GLN   ( 121-)  B      0
 106 ILE   ( 122-)  B      0
 114 LYS   ( 130-)  B      0
 116 CYS   ( 132-)  B      0
 117 THR   ( 133-)  B      0
 118 TRP   ( 134-)  B      0
 120 ASP   ( 136-)  B      0
 130 PRO   ( 146-)  B      0
 132 ALA   ( 148-)  B      0
 140 ASP   ( 156-)  B      0
 141 PHE   ( 157-)  B      0
And so on for a total of 286 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!

 479 GLY   (  67-)  C   3.40   24
  16 GLY   (  32-)  B   2.43   14
 267 GLY   (  68-)  A   1.62   80
 115 GLY   ( 131-)  B   1.53   80

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].

  63 PRO   (  79-)  B   103.4 envelop C-beta (108 degrees)
 130 PRO   ( 146-)  B    48.8 half-chair C-delta/C-gamma (54 degrees)
 472 PRO   (  60-)  C  -112.9 envelop C-gamma (-108 degrees)
 497 PRO   (  85-)  C   -64.5 envelop C-beta (-72 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.

 601 THR   ( 189-)  C      CG2 <->  602 ALA   ( 190-)  C      N      0.76    2.24  INTRA BF
 268 VAL   (  69-)  A      CA  <->  269 LYS   (  70-)  A      CB     0.69    2.31  INTRA BL
 569 PHE   ( 157-)  C      CZ  <->  597 TYR   ( 185-)  C      CD2    0.69    2.51  INTRA BL
 268 VAL   (  69-)  A      CG1 <->  269 LYS   (  70-)  A      CB     0.63    2.47  INTRA BL
 404 PHE   ( 205-)  A      CG  <->  405 ASN   ( 206-)  A      N      0.62    2.38  INTRA BF
 611 THR   ( 199-)  C      O   <->  613 ILE   ( 201-)  C      N      0.60    2.10  INTRA BL
 216 THR   (  17-)  A      CA  <->  217 PHE   (  18-)  A      CB     0.57    2.43  INTRA BF
 400 ILE   ( 201-)  A      CG2 <->  401 LYS   ( 202-)  A      N      0.56    2.44  INTRA BF
 632 PRO   ( 220-)  C      CA  <->  633 ALA   ( 221-)  C      CB     0.56    2.44  INTRA BF
 569 PHE   ( 157-)  C      CE2 <->  597 TYR   ( 185-)  C      CE2    0.55    2.65  INTRA BL
 603 GLU   ( 191-)  C      CB  <->  605 TRP   ( 193-)  C      CB     0.55    2.65  INTRA BF
  18 GLN   (  34-)  B      NE2 <->   54 LYS   (  70-)  B      NZ     0.52    2.33  INTRA BL
  53 VAL   (  69-)  B      CA  <->   54 LYS   (  70-)  B      CB     0.48    2.52  INTRA BL
 552 MET   ( 140-)  C      SD  <->  623 LEU   ( 211-)  C      CD2    0.47    2.93  INTRA BF
 606 MET   ( 194-)  C      O   <->  610 ILE   ( 198-)  C      CA     0.47    2.33  INTRA BF
 218 ASN   (  19-)  A      CB  <->  219 PRO   (  20-)  A      CD     0.46    2.64  INTRA BL
  50 PHE   (  66-)  B      N   <->   53 VAL   (  69-)  B      O      0.42    2.28  INTRA BL
 606 MET   ( 194-)  C      CA  <->  610 ILE   ( 198-)  C      CB     0.40    2.80  INTRA BF
 603 GLU   ( 191-)  C      CA  <->  604 GLU   ( 192-)  C      CB     0.40    2.60  INTRA BF
 569 PHE   ( 157-)  C      CE2 <->  597 TYR   ( 185-)  C      CD2    0.40    2.80  INTRA BL
 613 ILE   ( 201-)  C      CG2 <->  614 LYS   ( 202-)  C      N      0.40    2.60  INTRA BL
 207 ARG   ( 223-)  B      O   <->  208 THR   ( 224-)  B      OG1    0.40    1.90  INTRA BL
 214 ALA   (  15-)  A      O   <->  216 THR   (  17-)  A      N      0.38    2.32  INTRA BF
 603 GLU   ( 191-)  C      CB  <->  605 TRP   ( 193-)  C      N      0.36    2.74  INTRA BF
 599 THR   ( 187-)  C      C   <->  601 THR   ( 189-)  C      CA     0.36    2.84  INTRA BF
And so on for a total of 190 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: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: A

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.

 212 ARG   (  13-)  A      -8.27
 202 PHE   ( 218-)  B      -7.57
 207 ARG   ( 223-)  B      -7.27
 637 PHE   ( 225-)  C      -7.00
 383 ARG   ( 184-)  A      -6.90
 630 PHE   ( 218-)  C      -6.86
 639 GLN   ( 227-)  C      -6.85
 600 MET   ( 188-)  C      -6.84
 199 LYS   ( 215-)  B      -6.77
 635 ARG   ( 223-)  C      -6.76
 172 MET   ( 188-)  B      -6.75
 638 LEU   ( 226-)  C      -6.65
 211 GLN   (  12-)  A      -6.51
 425 LEU   ( 226-)  A      -6.50
 217 PHE   (  18-)  A      -6.42
 596 ARG   ( 184-)  C      -6.41
 417 PHE   ( 218-)  A      -6.33
 430 PHE   (  18-)  C      -6.28
 393 MET   ( 194-)  A      -6.08
   2 PHE   (  18-)  B      -5.84
 426 GLN   ( 227-)  A      -5.84
 168 ARG   ( 184-)  B      -5.83
 312 LEU   ( 113-)  A      -5.73
 597 TYR   ( 185-)  C      -5.65
 581 LYS   ( 169-)  C      -5.61
 105 GLN   ( 121-)  B      -5.53
 533 GLN   ( 121-)  C      -5.37
 627 LYS   ( 215-)  C      -5.10
 233 GLN   (  34-)  A      -5.09
 409 GLN   ( 210-)  A      -5.06

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

 199 LYS   ( 215-)  B       202 - PHE    218- ( B)         -5.78
 210 PRO   (  11-)  A       213 - ASN     14- ( A)         -5.85
 391 GLU   ( 192-)  A       393 - MET    194- ( A)         -5.01
 421 ALA   ( 222-)  A       423 - THR    224- ( A)         -4.34
 637 PHE   ( 225-)  C       639 - GLN    227- ( C)         -6.83

Warning: Structural average packing environment a bit worrysome

The structural average packing score is a bit low.

The protein is probably threaded correctly, but either poorly refined, or it is just a protein with an unusual (but correct) structure. The average packing score of 200 highly refined X-ray structures was -0.5+/-0.4 [REF].

Average for range 1 - 640 : -1.735

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: 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: 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.

 281 VAL   (  82-)  A   -3.02

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.

 346 GLY   ( 147-)  A     -  349 MET   ( 150-)  A        -1.90

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: B

Note: Second generation quality Z-score plot

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: C

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 641 HOH   ( 302 )  B      O
 643 HOH   ( 304 )  C      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

  18 GLN   (  34-)  B
  39 HIS   (  55-)  B
 246 GLN   (  47-)  A
 467 HIS   (  55-)  C
 506 HIS   (  94-)  C
 595 GLN   ( 183-)  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   (  36-)  B      N
  43 GLN   (  59-)  B      N
  64 GLN   (  80-)  B      N
  79 ARG   (  95-)  B      N
  86 ARG   ( 102-)  B      NH1
  97 LEU   ( 113-)  B      N
 107 VAL   ( 123-)  B      N
 110 LEU   ( 126-)  B      N
 117 THR   ( 133-)  B      N
 118 TRP   ( 134-)  B      NE1
 140 ASP   ( 156-)  B      N
 154 ASP   ( 170-)  B      N
 162 LYS   ( 178-)  B      N
 163 LYS   ( 179-)  B      N
 164 VAL   ( 180-)  B      N
 165 LEU   ( 181-)  B      N
 173 THR   ( 189-)  B      N
 173 THR   ( 189-)  B      OG1
 177 TRP   ( 193-)  B      NE1
 178 MET   ( 194-)  B      N
 182 ILE   ( 198-)  B      N
 197 TRP   ( 213-)  B      NE1
 207 ARG   ( 223-)  B      N
 207 ARG   ( 223-)  B      NH1
 207 ARG   ( 223-)  B      NH2
And so on for a total of 106 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.

 147 GLU   ( 163-)  B      OE2
 149 HIS   ( 165-)  B      ND1
 175 GLU   ( 191-)  B      OE1
 275 ASN   (  76-)  A      OD1
 390 GLU   ( 191-)  A      OE2
 604 GLU   ( 192-)  C      OE1
 604 GLU   ( 192-)  C      OE2

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.

  90 ASP   ( 106-)  B   H-bonding suggests Asn; but Alt-Rotamer
 120 ASP   ( 136-)  B   H-bonding suggests Asn; but Alt-Rotamer
 147 GLU   ( 163-)  B   H-bonding suggests Gln
 287 ASP   (  88-)  A   H-bonding suggests Asn; but Alt-Rotamer
 335 ASP   ( 136-)  A   H-bonding suggests Asn; but Alt-Rotamer
 390 GLU   ( 191-)  A   H-bonding suggests Gln; but Alt-Rotamer
 548 ASP   ( 136-)  C   H-bonding suggests Asn
 565 ASP   ( 153-)  C   H-bonding suggests Asn
 604 GLU   ( 192-)  C   H-bonding suggests Gln
 612 GLU   ( 200-)  C   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 :  -3.087
  2nd generation packing quality :  -3.607 (poor)
  Ramachandran plot appearance   :  -4.686 (bad)
  chi-1/chi-2 rotamer normality  :  -5.452 (bad)
  Backbone conformation          :  -1.487

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.494 (tight)
  Bond angles                    :   0.697
  Omega angle restraints         :   0.916
  Side chain planarity           :   0.249 (tight)
  Improper dihedral distribution :   0.946
  B-factor distribution          :   0.357
  Inside/Outside distribution    :   1.012

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 : 3.21


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.7
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -1.7
  chi-1/chi-2 rotamer normality  :  -3.0
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.494 (tight)
  Bond angles                    :   0.697
  Omega angle restraints         :   0.916
  Side chain planarity           :   0.249 (tight)
  Improper dihedral distribution :   0.946
  B-factor distribution          :   0.357
  Inside/Outside distribution    :   1.012
==============

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.